title: E. coli K-12 MG1655, 1-day exposure of fluoxetine induced chloramphenicol resistant mutant biological replicate-1

description:
Flu1d-Chlr-1
antibiotics resistant mutants

source_name: Escherichia coli K-12 MG1655, 1-day exposure of fluoxetine induced chloramphenicol resistant mutant


title: E. coli, wild-type K-12 MG1655 Biological replicate-1

status: Public on Dec 18 2020

type: SRA

city: Brisbane

first: Min

last: Jin

address: st lucia,QLD

country: Australia

institute: The University of Queensland

description:
control-1
control

library_source: transcriptomic

data_processing:
base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

molecule: total RNA

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

source_name: Escherichia coli, wild-type K-12 MG1655

growth_protocol: liquid LB culture at 37 °C

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted from the mutants using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: resistant strains as well as the original strain E. coli K-12 MG1655 were cultured in  triplicate in 10 mL liquid LB with 100 mg/L fluoxetine at 37 °C for 8 h, shaken at 150 rpm.

tag: strain

tag: resistance

value: wild-type

tag: agent

value: control


title: E. coli K-12 MG1655, 1-day exposure of fluoxetine induced chloramphenicol resistant mutant biological replicate-2

description:
Flu1d-Chlr-2
antibiotics resistant mutants

value: chloramphenicol resistant mutant

value: fluoxetine


title: Hoxd4-Liver_WT-Batch3-ZT16-WT-S227 [4C-Seq]

city: Lausanne

first: Felix

last: Naef

address: AAB 040 Station 15

department: Bioengineering

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

description:
4CSeq of Liver_WT of mice
processed_4Cseq_log10_counts_around_the_clock.txt.gz;processed_4Cseq_log10_counts_around_the_clock_FourierTransformed.txt.gz;processed_4Cseq_log10_counts_around_the_clock_AvgOverTime.txt.gz

library_source: genomic

data_processing:
Library strategy: 4C-Seq
mm9
Mapping was done using HTS station (http://htsstation.epfl.ch). See Supplemental methods of paper for detailed processing methods. In brief, read counts were normalized by total counts on the cis chromosome. For each fragment, we fit a weighted linear model with a Gaussian window of 2.5kb in order to incorporate signal from neighboring fragments.
Log10 4CSeq signal (value A with variance Avar). Processed formats show fragments within +/- 2MB of the bait. Zscore and p-value represent differential contacts between liver and kidney

molecule: genomic DNA

organism: Mus musculus

source_name: Crosslinked genomic DNA

extract_protocol: Liver and kidney nuclei were prepared as previously described (Ripperger and Schibler 2006) with some minor changes.         In brief, liver and kidneys from individual animals were homogenized and fixed in 4ml of PBS including 1.5percent formaldehyde for 10 minutes at room temperature.         Cross-linking reaction was stopped by adding 25 ml of ice-cold stop reaction buffer (2.2 M sucrose; 150 mM glycine; 10 mM HEPES pH 7.6; 15 mM KCl; 2 mM EDTA; 0.15 mM spermine; 0.5 mM spermidine; 0.5 mM DTT; 0.5 mM PMSF)         to the homogenates and kept 5 minutes on ice. Homogenates were then loaded on top of 10 ml cushion buffer (2.05 M sucrose; 10 % glycerol; 125 mM glycine; 10 mM HEPES pH 7.6; 15 mM KCl; 2 mM EDTA; 0.15 mM spermine; 0.5 mM spermidine; 0.5 mM DTT; 0.5 mM PMSF)         and centrifuged for 45 minutes at 105g at  4degC. Nuclei were washed twice in PBS and immediately frozen.

tag: tissue

tag: feeding

value: Ad libitum

tag: age

value: post-natal 8-12 weeks

tag: genotype

value: WT

tag: bait

tag: batch

tag: zeitgeber time


title: E. coli, wild-type K-12 MG1655 Biological replicate-2

description:
control-2
control


title: Hoxd4-Liver_WT-Batch3-ZT12-WT-S237 [4C-Seq]


title: E. coli K-12 MG1655, 30-day exposure of fluoxetine induced tetracycline resistant mutant biological replicate-2

description:
Flu30d-Tetr-2
antibiotics resistant mutants

source_name: Escherichia coli K-12 MG1655, 30-day exposure of fluoxetine induced tetracycline resistant mutant

value: tetracycline resistant mutant


title: Hoxd4-Liver_WT-Batch3-ZT0-WT-S231 [4C-Seq]


title: Hoxd4-Liver_WT-Batch3-ZT16-WT-S215 [4C-Seq]


title: Hoxd4-Liver_WT-Batch3-ZT0-WT-S219 [4C-Seq]


title: E. coli K-12 MG1655, 30-day exposure of fluoxetine induced chloramphenicol resistant mutant biological replicate-3

description:
Flu30d-Chlr-3
antibiotics resistant mutants

source_name: Escherichia coli K-12 MG1655, 30-day exposure of fluoxetine induced chloramphenicol resistant mutant


title: Hoxd4-Liver_WT-Batch3-ZT0-WT-S210 [4C-Seq]


title: U2OS_GR_EtOH

city: San Francisco

first: Delsy

last: Martinez

state: California

country: USA

institute: UCSF

data_processing:
50 bp reads mapped using Bowtie v1.1.2  to an index containing hg38 genome.
Parameters allowed for up to two mismatches with one alignment reported per read.
PCR duplicates were removed with samtools v1.3.1 rmdup.
Peaks were called with MAC2 v2.1.1, using the vehicle as the control file.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

organism: Homo sapiens

source_name: U2OS cells

growth_protocol: Cells were maintained in DMEM supplemented with FBS until ~90% confluent.

extract_protocol:
ChIPs were performed as previously described in Keck et al., 2017, using 20mg N499 GR antibody.
Deep sequencing libraries were prepared by adaptor-mediated amplification using Ovation Ultralow Library System V2 (NuGEN).

treatment_protocol: Media was supplemented with ethanol or the appropriate concetration of dexamethasone for 90 minutes and kept in a 37° C incubator with 5% CO2 during the incubation.

tag: cell line

tag: treatment

value: vehicle (EtOH)

tag: chip antibody

value: GR antibody


title: U2OS_GR_Dex

value: 100 nM Dex


title: A549_GR_EtOH

source_name: A549 cells


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT8-Cry1intronKO-S236 [4C-Seq]

description:
4CSeq of Liver_Cry1intronKO of mice
processed_4Cseq_log10_counts_around_the_clock.txt.gz;processed_4Cseq_log10_counts_around_the_clock_FourierTransformed.txt.gz;processed_4Cseq_log10_counts_around_the_clock_AvgOverTime.txt.gz


title: A549_GR_Dex


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT8-Cry1intronKO-S224 [4C-Seq]


title: E. coli K-12 MG1655, 30-day exposure of fluoxetine induced amoxicillin resistant mutant biological replicate-1

description:
Flu30d-Amor-1
antibiotics resistant mutants

source_name: Escherichia coli K-12 MG1655, 30-day exposure of fluoxetine induced amoxicillin resistant mutant

value: amoxicillin resistant mutant


title: siZMAT3 Nutlin-3a rep 2

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

institute: NIAMS/NIH

data_processing:
RTA 1.18.64 software used for basecalling.
Sequenced reads were trimmed for low-quality bases using Cutadapt, then mapped to hg19 genome using STAR 2.6.1.
Gene expression was quantified using RSEM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including output from RSEM for genes (expected counts, TPM and FPKM)

molecule: polyA RNA

source_name: Colorectal cancer cell line

extract_protocol:
Samples had their RNA extracted with RNeasy Plus Mini Kit.
RNA libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep

value: Colorectal cancer cell line

value: 48 hours siZMAT3 + 6 hours Nutlin-3a


title: siZMAT3 Nutlin-3a rep 3


title: siCTRL Nutlin-3a rep 3

value: 48 hours siCTRL + 6 hours Nutlin-3a


title: siZMAT3 Nutlin-3a rep 1


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT4-Cry1intronKO-S222 [4C-Seq]


title: E. coli K-12 MG1655, 30-day exposure of fluoxetine induced amoxicillin resistant mutant biological replicate-2

description:
Flu30d-Amor-2
antibiotics resistant mutants


title: siCTRL Nutlin-3a rep 1


title: siCTRL Nutlin-3a rep 2


title: Hoxd4-Liver_WT-Batch3-ZT12-WT-S225 [4C-Seq]


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT4-Cry1intronKO-S212 [4C-Seq]


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT20-Cry1intronKO-S230 [4C-Seq]


title: siZMAT3 DMSO rep 2

value: 48 hours siZMAT3 + 6 hours DMSO


title: siZMAT3 DMSO rep 3


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT20-Cry1intronKO-S242 [4C-Seq]


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT20-Cry1intronKO-S218 [4C-Seq]


title: siZMAT3 DMSO rep 1


title: siCTRL DMSO rep 3

value: 48 hours siCTRL + 6 hours DMSO


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT16-Cry1intronKO-S240 [4C-Seq]


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT16-Cry1intronKO-S228 [4C-Seq]


title: siCTRL DMSO rep 1


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT8-Cry1intronKO-S214 [4C-Seq]


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT4-Cry1intronKO-S234 [4C-Seq]


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT12-Cry1intronKO-S226 [4C-Seq]


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT0-Cry1intronKO-S232 [4C-Seq]


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT16-Cry1intronKO-S216 [4C-Seq]


title: Patient 367

type: RNA

city: Buffalo

first: Song

last: Yao

state: NY

address: Elm and Carlton Streets

department: Cancer Prevention and Control

institute: Roswell Park Comprehensive Cancer Center

hyb_protocol: Manufacturer protocol

scan_protocol: Manufacturer protocol

data_processing: NanoString nSolver with Advanced Analysis 2.0

source_name: primary breast cancer

label_protocol: Manufacturer protocol

extract_protocol: Roche High Pure FFPET RNA Isolation Kit

tag: race

value: EA

value: breast cancer

tag: age at diagnosis, years

tag: er

value: positive

tag: pr

value: negative

tag: subtype

value: Luminal A


title: Gys2_TSS-Liver_WT-Batch3-ZT8-WT-S507 [4C-Seq]

tag: strain

value: Ad libitum

value: post-natal 8-12 weeks


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT0-Cry1intronKO-S211 [4C-Seq]


title: Gys2_TSS-Liver_WT-Batch3-ZT8-WT-S513 [4C-Seq]

value: WT


title: siCTRL DMSO rep 2


title: Gys2_TSS-Liver_WT-Batch3-ZT8-WT-S502 [4C-Seq]


title: Patient 364


title: Patient 365

value: AA


title: Patient 363

value: Triple Negative


title: Gys2_TSS-Liver_WT-Batch3-ZT4-WT-S512 [4C-Seq]


title: Gys2_TSS-Liver_WT-Batch3-ZT20-WT-S516 [4C-Seq]


title: Patient 359

value: Luminal B


title: Gys2_TSS-Liver_WT-Batch3-ZT4-WT-S506 [4C-Seq]


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT12-Cry1intronKO-S238 [4C-Seq]


title: Patient 366


title: Patient 362


title: Patient 360


title: Hoxd4-Liver_Cry1intronKO-Batch3-ZT0-Cry1intronKO-S220 [4C-Seq]


title: Patient 361


title: Gys2_TSS-Liver_WT-Batch3-ZT20-WT-S510 [4C-Seq]


title: Patient 356


title: Patient 357


title: Gys2_TSS-Liver_WT-Batch3-ZT20-WT-S504 [4C-Seq]


title: Gys2_TSS-Liver_WT-Batch3-ZT16-WT-S515 [4C-Seq]


title: Patient 355


title: Gys2_TSS-Liver_WT-Batch3-ZT16-WT-S509 [4C-Seq]


title: Patient 353


title: Patient 354


title: Patient 350


title: Gys2_TSS-Liver_WT-Batch3-ZT12-WT-S508 [4C-Seq]


title: Patient 351


title: Gys2_TSS-Liver_WT-Batch3-ZT16-WT-S503 [4C-Seq]


title: Gys2_TSS-Liver_WT-Batch3-ZT0-WT-S511 [4C-Seq]


title: Patient 349


title: Patient 358


title: Patient 348


title: Gys2_Exon8-Liver_WT-Batch3-ZT8-WT-S529 [4C-Seq]


title: Gys2_TSS-Liver_WT-Batch3-ZT0-WT-S501 [4C-Seq]


title: Gys2_Exon8-Liver_WT-Batch3-ZT4-WT-S522 [4C-Seq]


title: Gys2_Exon8-Liver_WT-Batch3-ZT8-WT-S518 [4C-Seq]


title: Patient 346


title: Patient 345


title: Gys2_Exon8-Liver_WT-Batch3-ZT20-WT-S532 [4C-Seq]


title: Gys2_Exon8-Liver_WT-Batch3-ZT20-WT-S526 [4C-Seq]


title: Patient 344


title: Gys2_TSS-Liver_WT-Batch3-ZT0-WT-S505 [4C-Seq]


title: Gys2_TSS-Liver_WT-Batch3-ZT12-WT-S514 [4C-Seq]


title: Patient 352


title: Gys2_Exon8-Liver_WT-Batch3-ZT20-WT-S520 [4C-Seq]


title: Patient 343


title: Patient 341


title: Patient 342


title: Patient 340


title: Patient 339


title: Gys2_Exon8-Liver_WT-Batch3-ZT16-WT-S525 [4C-Seq]


title: Gys2_Exon8-Liver_WT-Batch3-ZT16-WT-S519 [4C-Seq]


title: Gys2_Exon8-Liver_WT-Batch3-ZT16-WT-S531 [4C-Seq]


title: Gys2_Exon8-Liver_WT-Batch3-ZT12-WT-S530 [4C-Seq]


title: Gys2_Exon8-Liver_WT-Batch3-ZT12-WT-S524 [4C-Seq]


title: Patient 336


title: Patient 335


title: Patient 337


title: Patient 334


title: Patient 338


title: Patient 347


title: Gys2_Exon8-Liver_WT-Batch3-ZT8-WT-S523 [4C-Seq]


title: Gys2_Exon8-Liver_WT-Batch3-ZT0-WT-S527 [4C-Seq]


title: Patient 332


title: Gys2_Exon8-Liver_WT-Batch3-ZT0-WT-S517 [4C-Seq]


title: Patient 331


title: Cry1_UP-Liver_WT-Batch3-ZT8-WT-S414 [4C-Seq]


title: Cry1_UP-Liver_WT-Batch3-ZT8-WT-S404 [4C-Seq]


title: Cry1_UP-Liver_WT-Batch3-ZT4-WT-S412 [4C-Seq]


title: Cry1_UP-Liver_WT-Batch3-ZT4-WT-S424 [4C-Seq]


title: Patient 328


title: Patient 330


title: Patient 329


title: Cry1_UP-Liver_WT-Batch3-ZT20-WT-S432 [4C-Seq]


title: Patient 327


title: Patient 333


title: Gys2_Exon8-Liver_WT-Batch3-ZT4-WT-S528 [4C-Seq]


title: Cry1_UP-Liver_WT-Batch3-ZT20-WT-S420 [4C-Seq]


title: Patient 326


title: Cry1_UP-Liver_WT-Batch3-ZT16-WT-S430 [4C-Seq]


title: Patient 325


title: Patient 323


title: Cry1_UP-Liver_WT-Batch3-ZT16-WT-S418 [4C-Seq]


title: Cry1_UP-Liver_WT-Batch3-ZT12-WT-S416 [4C-Seq]


title: Cry1_UP-Liver_WT-Batch3-ZT20-WT-S408 [4C-Seq]


title: Gys2_Exon8-Liver_WT-Batch3-ZT0-WT-S521 [4C-Seq]


title: Cry1_UP-Liver_WT-Batch3-ZT8-WT-S426 [4C-Seq]


title: Patient 322


title: Patient 321


title: Patient 319


title: Cry1_UP-Liver_WT-Batch3-ZT0-WT-S410 [4C-Seq]


title: Patient 320


title: Patient 317


title: Patient 318


title: Patient 316


title: Patient 324


title: Cry1_UP-Liver_WT-Batch3-ZT0-WT-S401 [4C-Seq]


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT8-Cry1intronKO-S415 [4C-Seq]


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT8-Cry1intronKO-S427 [4C-Seq]


title: Patient 315


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT4-Cry1intronKO-S425 [4C-Seq]


title: Cry1_UP-Liver_WT-Batch3-ZT16-WT-S406 [4C-Seq]


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT8-Cry1intronKO-S405 [4C-Seq]


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT4-Cry1intronKO-S413 [4C-Seq]


title: Patient 312


title: Patient 314


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT4-Cry1intronKO-S403 [4C-Seq]


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT20-Cry1intronKO-S421 [4C-Seq]


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT20-Cry1intronKO-S433 [4C-Seq]


title: Cry1_UP-Liver_WT-Batch3-ZT0-WT-S422 [4C-Seq]


title: Patient 310


title: Patient 311


title: Patient 309


title: Patient 308


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT20-Cry1intronKO-S409 [4C-Seq]


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT16-Cry1intronKO-S431 [4C-Seq]


title: Patient 307


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT16-Cry1intronKO-S407 [4C-Seq]


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT16-Cry1intronKO-S419 [4C-Seq]


title: Patient 305


title: Patient 303


title: Patient 304


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT12-Cry1intronKO-S417 [4C-Seq]


title: Patient 313


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT0-Cry1intronKO-S423 [4C-Seq]


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT12-Cry1intronKO-S429 [4C-Seq]


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT0-Cry1intronKO-S411 [4C-Seq]


title: Patient 302


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT0-Cry1intronKO-S402 [4C-Seq]


title: Patient 300


title: Cry1_TSS-Liver_WT-Batch3-ZT8-WT-S314 [4C-Seq]


title: Cry1_TSS-Liver_WT-Batch3-ZT8-WT-S326 [4C-Seq]


title: Patient 301


title: Cry1_TSS-Liver_WT-Batch3-ZT8-WT-S304 [4C-Seq]


title: Patient 306


title: Cry1_TSS-Liver_WT-Batch3-ZT4-WT-S312 [4C-Seq]


title: Patient 299


title: Patient 297


title: Patient 295


title: Patient 296


title: Cry1_TSS-Liver_WT-Batch3-ZT20-WT-S332 [4C-Seq]


title: Patient 294


title: Cry1_TSS-Liver_WT-Batch3-ZT4-WT-S324 [4C-Seq]


title: Patient 293


title: Cry1_TSS-Liver_WT-Batch3-ZT20-WT-S308 [4C-Seq]


title: Patient 292


title: Patient 291


title: Cry1_TSS-Liver_WT-Batch3-ZT16-WT-S330 [4C-Seq]


title: Cry1_TSS-Liver_WT-Batch3-ZT16-WT-S318 [4C-Seq]


title: Cry1_TSS-Liver_WT-Batch3-ZT16-WT-S306 [4C-Seq]


title: Patient 290


title: Cry1_TSS-Liver_WT-Batch3-ZT0-WT-S322 [4C-Seq]


title: Patient 289


title: Cry1_TSS-Liver_WT-Batch3-ZT12-WT-S316 [4C-Seq]


title: Cry1_TSS-Liver_WT-Batch3-ZT0-WT-S310 [4C-Seq]


title: Patient 287


title: Patient 286


title: Patient 288


title: Patient 284


title: Cry1_TSS-Liver_WT-Batch3-ZT0-WT-S301 [4C-Seq]


title: Patient 285


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT8-Cry1intronKO-S327 [4C-Seq]


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT8-Cry1intronKO-S315 [4C-Seq]


title: Cry1_TSS-Liver_WT-Batch3-ZT20-WT-S320 [4C-Seq]


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT8-Cry1intronKO-S305 [4C-Seq]


title: Patient 281


title: Patient 280


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT4-Cry1intronKO-S313 [4C-Seq]


title: Cry1_TSS-Liver_WT-Batch3-ZT12-WT-S328 [4C-Seq]


title: Patient 278


title: Patient 279


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT20-Cry1intronKO-S333 [4C-Seq]


title: Patient 277


title: Patient 276


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT20-Cry1intronKO-S309 [4C-Seq]


title: Patient 283


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT16-Cry1intronKO-S319 [4C-Seq]


title: Patient 282


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT12-Cry1intronKO-S329 [4C-Seq]


title: Patient 273


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT16-Cry1intronKO-S307 [4C-Seq]


title: Patient 274


title: Patient 272


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT12-Cry1intronKO-S317 [4C-Seq]


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT16-Cry1intronKO-S331 [4C-Seq]


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT0-Cry1intronKO-S323 [4C-Seq]


title: Patient 270


title: Patient 271


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT0-Cry1intronKO-S311 [4C-Seq]


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT0-Cry1intronKO-S302 [4C-Seq]


title: Patient 268


title: Cry1-Liver_WT-Batch3-ZT8-WT-S204 [4C-Seq]


title: Patient 269


title: Patient 267


title: Cry1-Liver_WT-Batch3-ZT0-WT-S201 [4C-Seq]


title: Patient 266


title: Patient 263


title: Patient 265


title: Patient 264


title: Cry1-Liver_Cry1intronKO-Batch3-ZT8-Cry1intronKO-S205 [4C-Seq]


title: Cry1-Liver_Cry1intronKO-Batch3-ZT4-Cry1intronKO-S203 [4C-Seq]


title: Cry1-Liver_Cry1intronKO-Batch3-ZT20-Cry1intronKO-S209 [4C-Seq]


title: Cry1-Liver_Cry1intronKO-Batch3-ZT16-Cry1intronKO-S207 [4C-Seq]


title: Bmal1_TSS-Liver_WT-Batch3-ZT8-WT-S633 [4C-Seq]


title: Bmal1_TSS-Liver_WT-Batch3-ZT8-WT-S627 [4C-Seq]


title: Patient 261


title: Bmal1_TSS-Liver_WT-Batch3-ZT4-WT-S632 [4C-Seq]


title: Patient 262


title: Patient 259


title: Patient 257


title: Patient 258


title: Cry1-Liver_WT-Batch3-ZT20-WT-S208 [4C-Seq]


title: Bmal1_TSS-Liver_WT-Batch3-ZT4-WT-S626 [4C-Seq]


title: Bmal1_TSS-Liver_WT-Batch3-ZT20-WT-S636 [4C-Seq]


title: Patient 256


title: Patient 255


title: Bmal1_TSS-Liver_WT-Batch3-ZT20-WT-S630 [4C-Seq]


title: Bmal1_TSS-Liver_WT-Batch3-ZT16-WT-S629 [4C-Seq]


title: Bmal1_TSS-Liver_WT-Batch3-ZT16-WT-S635 [4C-Seq]


title: Bmal1_TSS-Liver_WT-Batch3-ZT12-WT-S634 [4C-Seq]


title: Patient 260


title: Patient 252


title: Bmal1_TSS-Liver_WT-Batch3-ZT0-WT-S631 [4C-Seq]


title: Patient 250


title: Patient 253


title: Slc45a3short-Liver-GH-ZT20-WT-lane4 [4C-Seq]

description:
4CSeq of Liver of mice
processed_4Cseq_log10_counts_ZT20_ZT08.txt.gz;processed_4Cseq_log10_counts_differential_analysis_ZT20_ZT08.txt.gz

value: Liver


title: Slc45a3short-Liver-EF-ZT20-WT-lane3 [4C-Seq]


title: Patient 254


title: Slc45a3short-Liver-CD-ZT08-WT-lane2 [4C-Seq]


title: Patient 245


title: Patient 247


title: Patient 244


title: Patient 248


title: Slc45a3short-Liver-AB-ZT08-WT-lane1 [4C-Seq]


title: Patient 246


title: Patient 243


title: Slc45a3short-Kidney-GH-ZT20-WT-lane8 [4C-Seq]

description:
4CSeq of Kidney of mice
processed_4Cseq_log10_counts_ZT20_ZT08.txt.gz;processed_4Cseq_log10_counts_differential_analysis_ZT20_ZT08.txt.gz

value: Kidney


title: Patient 242


title: Patient 249


title: Patient 251


title: Slc45a3short-Kidney-EF-ZT20-WT-lane7 [4C-Seq]


title: Patient 241


title: Slc45a3short-Kidney-CD-ZT08-WT-lane6 [4C-Seq]


title: Patient 298


title: Bmal1_TSS-Liver_WT-Batch3-ZT0-WT-S625 [4C-Seq]


title: Slc45a3short-Kidney-AB-ZT08-WT-lane5 [4C-Seq]


title: Slc45a3long-Liver-GH-ZT20-WT-lane4 [4C-Seq]


title: Slc45a3long-Liver-EF-ZT20-WT-lane3 [4C-Seq]


title: Patient 239


title: Slc45a3long-Liver-CD-ZT08-WT-lane2 [4C-Seq]


title: Patient 238


title: Slc45a3long-Kidney-GH-ZT20-WT-lane8 [4C-Seq]


title: Patient 236


title: Slc45a3long-Kidney-EF-ZT20-WT-lane7 [4C-Seq]


title: Patient 234


title: Slc45a3long-Kidney-AB-ZT08-WT-lane5 [4C-Seq]


title: Patient 235


title: Slc45a3long-Kidney-CD-ZT08-WT-lane6 [4C-Seq]


title: Slc44a1-Liver-EF-ZT20-WT-lane3 [4C-Seq]


title: Patient 232


title: Patient 233


title: Patient 240


title: Slc44a1-Liver-CD-ZT08-WT-lane2 [4C-Seq]


title: Patient 228


title: Patient 230


title: Patient 237


title: Slc44a1-Kidney-GH-ZT20-WT-lane8 [4C-Seq]


title: Patient 227


title: Patient 231


title: Slc44a1-Kidney-EF-ZT20-WT-lane7 [4C-Seq]


title: Slc44a1-Kidney-CD-ZT08-WT-lane6 [4C-Seq]


title: Slc44a1-Kidney-AB-ZT08-WT-lane5 [4C-Seq]


title: Slc45a3long-Liver-AB-ZT08-WT-lane1 [4C-Seq]


title: Slc44a1-Liver-GH-ZT20-WT-lane4 [4C-Seq]


title: Pi3kap1-Liver-GH-ZT20-WT-lane4 [4C-Seq]


title: Patient 229


title: Pi3kap1-Liver-CD-ZT08-WT-lane2 [4C-Seq]


title: Pi3kap1-Liver-EF-ZT20-WT-lane3 [4C-Seq]


title: Patient 222


title: Patient 224


title: Patient 226


title: Pi3kap1-Liver-AB-ZT08-WT-lane1 [4C-Seq]


title: Patient 223


title: Patient 225


title: Slc44a1-Liver-AB-ZT08-WT-lane1 [4C-Seq]


title: Patient 219


title: Patient 220


title: Pi3kap1-Kidney-GH-ZT20-WT-lane8 [4C-Seq]


title: Pi3kap1-Kidney-EF-ZT20-WT-lane7 [4C-Seq]


title: Pi3kap1-Kidney-CD-ZT08-WT-lane6 [4C-Seq]


title: Patient 218


title: Patient 217


title: Patient 216


title: Mreg-Liver-GH-ZT20-WT-lane4 [4C-Seq]

value: Mreg


title: Pi3kap1-Kidney-AB-ZT08-WT-lane5 [4C-Seq]


title: Mreg-Liver-EF-ZT20-WT-lane3 [4C-Seq]


title: Patient 221


title: Mreg-Liver-CD-ZT08-WT-lane2 [4C-Seq]


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT4-Cry1intronKO-S303 [4C-Seq]


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT20-Cry1intronKO-S321 [4C-Seq]


title: Mreg-Liver-AB-ZT08-WT-lane1 [4C-Seq]


title: DU 145-KR, RNA-seq

city: Shenzhen

first: Jin-Tang

last: Dong

state: Guangdong

address: 1088 Xueyuan Blvd

department: Human Cell Biology and Genetics

country: China

institute: Southern University of Science and Technology

data_processing:
DU 145 libraries were sequenced using single-end 50 bp reads on a BGISEQ-500 at BGI (Shenzhen, Guangzhou, China) and PC-3 libraries were sequenced at Novogene (Sacramento, CA) using paired-end 150 bp reads on a NovaSeq.
FASTQ files from sequencing were quality controlled and adapter trimmed using FASTQC (v0.11.5) and mapped to HG19 reference genome using the STAR aligner (v2.5.0a)
Putative PCR duplicates were marked and removed with SAMtools (v1.7) for downstream analysis
Genome_build: UCSC HG19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

source_name: Prostate cancer

extract_protocol:
DU 145 and PC-3 cells expressing different forms of KLF5 were collected freshly in Trizol reagent for RNA isolation
RNA libraries were prepared for sequencing using standard Illumina protocols

value: acetylation deficient mutant KLF5K369R (KR)


title: DU 145-KLF5, RNA-seq

value: wildtype KLF5


title: DU 145-EV, RNA-seq

value: KLF5 null


title: Mreg-Kidney-GH-ZT20-WT-lane8 [4C-Seq]


title: DU 145-KQ, RNA-seq

value: acetylation mimicking mutant KLF5K369Q (KQ)


title: DU 145-KR, ChIP-seq

data_processing:
The DNA samples were sequenced with the BGISEQ-500 sequencer
FASTQ files of sequencing were quality controlled and adapter trimmed using FASTQC (v0.11.5) prior to mapping them to the HG19 reference genome using bowtie (v2.2.6)
Enriched regions were determined using MACS2 (v2.1.0.20151222) relative to input files with a q value (FDR adjusted p value) of 0.05
The union of all enriched regions was determined and coverage in these regions were determined using the ‘summarizeOverlaps’ function in R/Bioconductor (v3.6.1) prior to differential analysis using edgeR (v3.26.5) where regions with an FDR ≤0.05 were considered significant
Genome_build: UCSC HG19
Supplementary_files_format_and_content: BigWig for peaks.  Peak comparison among samples are summrized in "KLF5-ChIP-Seq-Summary-DU 145.xlsx".

extract_protocol:
The KLF5 antibody from R&D (#AF3758) was used to pull down KLF5 bound DNA sequences
The DNA samples were sent to BGI for quality control and library construction (SE50) following standard procedures


title: DU 145-KLF5, ChIP-seq


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT4-Cry1intronKO-S325 [4C-Seq]


title: DU 145-KQ, ChIP-seq


title: DU 145-EV, ChIP-seq


title: Patient 209

value: EA

value: breast cancer


title: Patient 210

value: positive


title: Patient 214

value: negative

value: Luminal A


title: Patient 212


title: Patient 213


title: Patient 211


title: Patient 215


title: DU 145-KQ, input


title: Patient 275


title: Mreg-Kidney-CD-ZT08-WT-lane6 [4C-Seq]

value: Ad libitum

value: post-natal 8-12 weeks


title: DU 145-KR, input


title: Mreg-Kidney-AB-ZT08-WT-lane5 [4C-Seq]

value: WT


title: DU 145-KLF5, input


title: DU 145-EV, input


title: Patient 208


title: Gys2intron-Liver-G-ZT20-WT-lane7 [4C-Seq]


title: Gys2intron-Liver-H-ZT20-WT-lane8 [4C-Seq]


title: Mreg-Kidney-EF-ZT20-WT-lane7 [4C-Seq]


title: Sample23_Con_BL_11

city: Toronto

first: Stephen

last: Matthews

state: Ontario

address: 1 King's College Circle

country: Canada

institute: University of Toronto

data_processing:
Adaptor sequences were trimmed using Trim Galore.
Additional filtering was performed to remove reads that did not contain an MspI site signature at the 5’ end using a script provided by NuGEN (https://github.com/nugentechnologies/NuMetRRBS/blob/master/  trimRRBSdiversityAdaptCustomers.py).
The reads were then aligned using Bismark (version 0.16.0) and sorted by Samtools (version 1.7).
We then used MethPipe (version 3.4.2) to identify significant differentially methylated CpG sites (DMCs) with at least 10X reads with FDR < 0.05.
CompEpitool was used to annotate the differentially methylated CpG sites to the guinea pig genome (cavPor3).
Genome_build: Broad/cavPor3
Supplementary_files_format_and_content: Tab-delimited text files with at least 10X reads (formatted as "chr", "loc", "strand", "fdr", )

organism: Cavia porcellus

source_name: whole blood

extract_protocol:
DNA from the hippocampus and whole blood of each animal was extracted using AllPrep Mini Kit (Qiagen: Cat#80204) and QIAamp DNA Mini Kit (Qiagen: Cat#51304) respectively.
RRBS libraries were generated from 100ng of high-quality dsDNA using the RRBS Methyl_seq System 1-16 (Ovation: Part #0353) and EpiTect Fast DNA Bisulfite kit (Qiagen: Cat. #59824) following the manufacturer’s protocols.

tag: maternal treatment

value: Saline

tag: subject id


title: Patient 205

value: AA

tag: tissue

value: Triple Negative


title: Sample20_Con_BL_8


title: Sample21_Con_BL_9


title: Patient 207


title: Patient 206


title: Gys2intron-Liver-D-ZT08-WT-lane4 [4C-Seq]

value: Liver

tag: feeding

tag: age


title: Gys2intron-Liver-E-ZT20-WT-lane5 [4C-Seq]

tag: genotype

tag: bait


title: Sample17_sGC_BL_5

value: sGC


title: Sample18_sGC_BL_6


title: Sample19_Con_BL_7


title: Gys2intron-Liver-C-ZT08-WT-lane3 [4C-Seq]

tag: batch

tag: zeitgeber time


title: Sample16_sGC_BL_4


title: Patient 202


title: Sample15_sGC_BL_3


title: Sample24_Con_BL_12


title: Patient 203


title: Patient 204

value: Luminal B


title: Sample13_sGC_BL_1


title: Gys2intron-Liver-B-ZT08-WT-lane2 [4C-Seq]


title: Sample22_Con_BL_10


title: Patient 200


title: Sample12_Con_HPC_12

source_name: hippocampus


title: Gys2intron-Liver-A-ZT08-WT-lane1 [4C-Seq]


title: Sample10_Con_HPC_10


title: Bmal1_TSS-Liver_WT-Batch3-ZT12-WT-S628 [4C-Seq]


title: Sample11_Con_HPC_11


title: Patient 198


title: Sample9_Con_HPC_9


title: Sample8_Con_HPC_8


title: Gys2-Kidney-H-ZT20-WT-lane8 [4C-Seq]

value: Kidney


title: Sample14_sGC_BL_2


title: Sample6_sGC_HPC_6


title: Sample5_sGC_HPC_5


title: Gys2-Kidney-F-ZT20-WT-lane6 [4C-Seq]


title: Patient 197


title: Gys2-Kidney-G-ZT20-WT-lane7 [4C-Seq]


title: Patient 196


title: Sample4_sGC_HPC_4


title: Sample2_sGC_HPC_2


title: Sample1_sGC_HPC_1


title: Patient 201


title: Sample3_sGC_HPC_3


title: Gys2-Kidney-D-ZT08-WT-lane4 [4C-Seq]


title: Gys2-Kidney-E-ZT20-WT-lane5 [4C-Seq]


title: Patient 195


title: Dis_Ecoli_DCTN1_Rep1

city: Heidelberg

first: Kai

last: Fenzl

address: Meyerhofstraße 1

country: Germany

institute: EMBL

description: Additionally containing gene name: SF_DCTN1_TS

data_processing:
library strategy: Ribosome Profiling
Raw NextSeq550 sequencing files were converted with bcl2fastq2 conversion software (v2.20) to obtain single fastq files per indexed sample using following command: bcl2fastq -p16 -r4 -w4 --no-lane-splitting -R <path_to_input_folder> -o <path_to_output_folder>. Only samples 5-8 were sequenced by the DKFZ Sequencing Facility on a HighSeq2000 machine and converted to fastq files.
3' adaptor sequences were trimmed with Cutadapt (v1.13) with the following command:  cutadapt --cores=4 -q20 -m23 --discard-untrimmed -O6 -a ATCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -o <path_to_output>.fastq.gz <path_to_input>.fastq.gz For samples sequenced on HiSeq2000 following command was used:  cutadapt --cores=4 -q20 -m23 --discard-untrimmed -O6 -a CTGTAGGCACCATCAATTCGTATGCCGTCTTCTGCTTG -o <path_to_output>.fastq.gz <path_to_input>.fastq.gz
Unique molecular identifiers (UMIs) were extracted from each read for the downstream analysis using a custom Julia script (available as supplement information of this study) with the following command: julia <path_to_script>/Script1.jl <path_to_input>.fastq.gz <path_to_output>.fastq.gz --umi3 5 --umi5 2. Only samples 5-8 did not contain UMI sequences in the adaptors, therefore this step was not included for U2OS samples.
For removal of human rRNA contaminants, sequenced libraries were aligned to rRNA sequences including: RNA45SN1 - RNA45SN5 (human 28S, 18S, 5.8S), RNA5S1 (human 5S), MTRNR2L10 (Mito 16S), MT-RNR1 (Mito 12S), MT-RNR2U1 (Mito 16S), 22 mito tRNAs, 631 nuclear human tRNAs. The E. coli rRNA file included: 5S rRNA (rrfA -  rrfH), 16S rRNA (rrsA, rrsB, rrsC, rrsD, rrsE, rrsG, and rrsH), 23S rRNA (rrlA, rrlB, rrlC, rrlD, rrlE, rrlG, and rrlH). All rRNA contaminations were removed by Bowtie2 (v.2.3.5.1) with the following command: bowtie2 -p4 -t -x <path_to_folder_with_Bowtie-indexed_rRNA_contamination> -q <path_to_input_file>.fastq.gz' --un <path_to_output_file>.fastq -S /dev/null
Reads that did not align to rRNA were aligned to the human genome (GRCh38p10) or E.coli genome (GCA_000022665.2, E. coli BL21(DE3), including additional chromosome files containing custom plasmid sequences, see the corresponding sample description field) using STAR (v2.7.1a) with the following command: STAR --runThreadN 24 --genomeDir <path_to_indexed_genome> --readFilesIn <path_to_input>.fastq --outFilterMultimapNmax 1 --outFilterType BySJout --alignIntronMin 5 --outFileNamePrefix <path_to_output> --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All XS --quantMode GeneCounts --twopassMode Basic
All reads aligning to the coding sequence (CDS) were assigned (a-, p-, e-site) via a custom Julia script (available as supplement information of this study). p-site assigned reads were used for all downstream analysis.This script accounts for soft-clipping via the '-c 1' option: the integer indicates the bases at the 5' end that often arise from untemplated addition by the reverse transcriptase during library preparation by using the following command: julia <path_to_script>/Script2.jl -c 1 -g <path_to_genome_annotation>.gff' -u -o <path_to_output> <path_to_input>.bam
Genome_build: Human genome (GRCh38p10), E.coli genome (GCF_000009565.1, E. coli BL21(DE3))
Supplementary_files_format_and_content: Processed data are stored in HDF5 files. Each HDF5 file contains one data set per gene. Each data set consists of a 2-row matrix, with the first row containing the 1-based position within the CDS, and the second row the number of detected P-site reads at this position. Additional information is stored in the data set attributes, including: gene and protein names, transcript isoform used for position assignment, length of the coding sequence, chromosome and strand location of the gene. In this study the p-side assignments stored in such HDF5 files were further analyzed using RiboSeqTools (available at: https://github.com/ilia-kats/RiboSeqTools).

organism: Escherichia coli

growth_protocol: Human cells were cultivated in the indicated temperature and growth medium (as indicated in the corresponding sample "characteristics: growth conditions" field). Cells were passaged regularly through trypsinization. For all experiments cells were seeded 18-24 hours before lysis in 15 cm2 dishes (3.5 million U2OS and 6 million HEK293-T cells) to reach 70-90% confluency at the time of harvesting. E. coli cells were cultivated in the indicated temperature and growth medium (as indicated in the corresponding sample "characteristics: growth conditions") with shaking at 120 rpm. For all experiments 200 ml of EZ-RDM were inoculated with an overnight culture to an initial OD600 of 0.05 and grown untill a cell density of OD600 = 0.4 - 0.6 was reached for harvest.

extract_protocol:
RNA from frozen ribosome fractions was extracted using the hot acid phenol method as described in Galmozzi and Merker et al. 2019
Libraries from isolated ribosome footprints were prepared following the previously published protocol (Galmozzi and Merker et al. 2019)

treatment_protocol: General information on treatments is indicated in the corresponding sample characteristics field. For detailed information, please refer to the Material and Methods of the original publication.

tag: cell line/strain

value: Rosetta

value: wild-type with plasmid expression of:pET3d-splitFlAsH-DCTN1-TwinStrep

tag: sample type

value: Footprints from disome fraction

tag: growth condition

value: EZ-rich defined medium, 37°C

tag: treatment

value: Plasmid gene expression induced for 16 min with 1mM IPTG


title: Mono_Ecoli_DCTN1_Rep1

value: Footprints from monosome fraction


title: Gys2-Kidney-C-ZT08-WT-lane3 [4C-Seq]


title: Patient 194

tag: race

value: breast cancer

tag: age at diagnosis, years

tag: er

value: negative


title: Sample7_Con_HPC_7


title: Gys2-Kidney-B-ZT08-WT-lane2 [4C-Seq]

tag: strain

value: Ad libitum

value: post-natal 8-12 weeks


title: Mono_Ecoli_1B*-Cherry_Rep1

description: Additionally containing gene name: SF_Coil1B_Mut_mCherry_TS

value: wild-type with plasmid expression of:pET3a-splitFlAsH-1B*-mCherry-TwinStrep


title: Dis_Ecoli_1B*-Cherry_Rep1


title: Patient 192

value: AA

value: positive

tag: pr

tag: subtype


title: Dis_Ecoli_1B-Cherry_Rep2

description: Additionally containing gene name: SF_Coil1B_WT_mCherry_TS

value: wild-type with plasmid expression of:pET3a-splitFlAsH-1B-mCherry-TwinStrep


title: Cry1intron-Liver-H-ZT20-WT-lane8 [4C-Seq]

tag: tissue

value: Liver

value: WT


title: Cry1intron-Liver-G-ZT20-WT-lane7 [4C-Seq]

tag: feeding


title: Patient 193

value: Luminal A


title: Cry1intron-Liver-F-ZT20-WT-lane6 [4C-Seq]

tag: age


title: Gys2-Kidney-A-ZT08-WT-lane1 [4C-Seq]

value: Kidney

tag: genotype


title: Mono_Ecoli_LMNC_Rep2

description: Additionally containing gene name: SFLMNCTS

value: Rosetta

value: wild-type with plasmid expression of:pET3a-splitFlAsH-LMNC-TwinStrep


title: Patient 188

value: EA


title: Patient 189


title: Dis_Ecoli_1B*-Cherry_Rep2

value: Footprints from disome fraction

value: EZ-rich defined medium, 37°C

value: Plasmid gene expression induced for 16 min with 1mM IPTG


title: Cry1intron-Liver-E-ZT20-WT-lane5 [4C-Seq]

tag: bait


title: Mono_Ecoli_1B*-Cherry_Rep2

value: Footprints from monosome fraction


title: Patient 187

value: breast cancer

value: negative

value: Triple Negative


title: Mono_Ecoli_LMNC_Rep1

value: Plasmid gene expression induced for 4 min with 1mM IPTG


title: Dis_Ecoli_1B-Cherry_Rep1


title: Mono_Ecoli_1B-Cherry_Rep2


title: Cry1intron-Liver-D-ZT08-WT-lane4 [4C-Seq]

value: Ad libitum

value: post-natal 8-12 weeks

tag: batch


title: Patient 186


title: Dis_Ecoli_LMNC_Rep2


title: Cry1intron-Liver-C-ZT08-WT-lane3 [4C-Seq]

value: Liver

tag: zeitgeber time


title: Patient 185

value: positive

value: Luminal B


title: Patient 190

value: AA

value: Luminal A


title: Mono_Ecoli_1B-Cherry_Rep1

tag: cell line/strain

value: Rosetta

value: wild-type with plasmid expression of:pET3a-splitFlAsH-1B-mCherry-TwinStrep


title: siUPF1 DMSO rep3

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for low-quality bases using Cutadapt, then mapped to hg19 genome using TopHat.
Gene expression was quantified using RSEM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including output from RSEM for genes (expected counts, TPM and FPKM)

extract_protocol:
Samples had their RNA extracted with TRIzol™ Reagent
We used the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Catalog No. E7760) with NEBNext rRNA Depletion Kit (NEB, Catalog No. E6318) for library preparation

tag: cell line

value: Colorectal cancer cell line

value: 48 hours siUPF1


title: stage10.5_scATACseq_part4

city: Nijmegen

first: Ann

middle: Rose

last: Bright

address: Geert Grooteplein Zuid 30

department: Department of Molecular Biology

country: Netherlands

institute: RIMLS

description:
snATAC-seq
fragments_v2_CoVar1.0.tsv.gz
fragments_v2_CoVar1.0.tsv.gz.tbi

data_processing:
BCL to fastq using cellranger-atac mkfastq.
Fastq to count matrix using cellranger-atac count.
Genome_build: xt10
Supplementary_files_format_and_content: fragments_v2_CoVar1.0.tsv.gz : Barcoded and aligned fragment file used for downstream analysis.
Supplementary_files_format_and_content: fragments_v2_CoVar1.0.tsv.gz.tbi : Fragment file index

organism: Xenopus tropicalis

source_name: Whole embryo

extract_protocol:
Nuclei were isolated with method adapted from Mariano (Mariano, 1964).
Libraries were generated using Chromium Single Cell ATAC (v1.1 Chemistry; 10X Genomics).

value: Whole embryo

tag: Stage

value: stage10.5 (Gastrula)


title: stage10.5_scATACseq_part1


title: stage10.5_scATACseq_part3


title: Cry1intron-Liver-B-ZT08-WT-lane2 [4C-Seq]

value: WT


title: siUPF1 DMSO rep2

tag: treatment


title: stage10.5_scATACseq_part2


title: siCTRL DMSO rep3

value: 48 hours siCTRL


title: Patient 184

tag: race

value: breast cancer

value: negative


title: siCTRL DMSO rep2


title: siUPF1 DMSO rep1


title: siCTRL DMSO rep1


title: Patient 183

tag: age at diagnosis, years

value: Triple Negative


title: Cry1intron-Liver-A-ZT08-WT-lane1 [4C-Seq]

value: Ad libitum

value: post-natal 8-12 weeks


title: Nutlin-3a rep4

description: RNA bound to ZMAT3

data_processing:
Library strategy: PAR-CLIP
Illumina software used for basecalling.
The analyis was performed as described previously using PARalyzer (Corcoran et al., 2011a) built into the PARpipe (Corcoran et al., 2011b) pipeline
Genome_build: hg19
Supplementary_files_format_and_content: csv files including binding sites positions

extract_protocol:
After 16 hours, cells were crosslinked at 312 nm UV light using a Spectrolinker XL-1500 (Spectronics Corporation) at 0.15 J/cm2, they were scraped on ice and recovered.
PAR-CLIP method was performed in four biological replicates as previously described in (Benhalevy et al., 2016; Hafner et al., 2010) but using a modified approach to track the RBP-bound RNAs. Briefly, after immunoprecipitation using magnetic beads Pierce™ Protein A/G Magnetic Beads (Thermo Scientific, Catalog no. 88803) coupled with anti-FLAG or anti-IgG antibodies; RNA digestion and dephosphorylation, bound RNAs were ligated to fluorescent 3’ adapter (5'-rAppNNTGACTGTGGAATTCTCGGGTGCCAAGG-F) on beads. Subsequently, ligated RNAs were dissociated from beads and loaded into SDS-Polyacrylamide gel NuPAGE™ 4 to 12%, Bis-Tris, 1.0 mm, Midi Protein Gel, 12+2-well (Thermo Fisher, Catalog no. WG1401BOX) and the band correspondent to the size of ZMAT3 plus ~20 kDa (since the ligation of the adapter increases bound RNAs size), was cut and purified. Then, the recovered RNA was phosphorylated, ligated to the 5’ adapter (5' [aminolinker] GTTCAGAGTTCTACAGTCCGACGATCrNrNrNrN), converted to cDNA, PCR amplified with barcoded primers and purified.

treatment_protocol: HCT116 ZMAT3-FLAG cells were seeded in ten 15 mm cell culture dishes at 6 x 106 cells per plate. 48 hours later, Nutlin-3a (Sigma, Catalog no. SML0580) dissolved in DMSO enough for 10 uM or the same volume of DMSO was added to the medium. After 2 hours, it was added 4-Thiouridine (Sigma, Catalog no. T4509) enough for 100 M to the same cells.

value: 18 hours Nutlin-3a


title: HMGCR-Liver-Batch1-ZT08-WT-LibraryH [4C-Seq]

value: Liver

value: HMGCR


title: Patient 182

value: AA

tag: er


title: Nutlin-3a rep2

description: RNA bound to ZMAT3


title: POR-Liver-Batch1-ZT08-WT-LibraryH [4C-Seq]

tag: strain

value: POR


title: Nutlin-3a rep3

description: RNA bound to ZMAT3


title: Patient 181

value: positive

tag: pr

value: Luminal A


title: Nutlin-3a rep1

description: RNA bound to ZMAT3

value: Colorectal cancer cell line


title: DMSO rep2

description: RNA bound to ZMAT3

value: 18 hours DMSO


title: NR1D1-Liver-Batch1-ZT08-WT-LibraryH [4C-Seq]


title: DMSO rep4

description: RNA bound to ZMAT3


title: Patient 180

tag: subtype


title: Patient 179

value: EA

tag: tissue


title: NAMPT-Liver-Batch1-ZT08-WT-LibraryH [4C-Seq]

tag: feeding

value: WT

value: NAMPT


title: MFSD2A-Liver-Batch1-ZT08-WT-LibraryH [4C-Seq]

tag: age


title: DMSO rep1

description: RNA bound to ZMAT3


title: Gys2intron-Liver-F-ZT20-WT-lane6 [4C-Seq]

tag: genotype


title: PFKFB3-Liver-Batch1-ZT08-WT-LibraryH [4C-Seq]

tag: bait


title: sc_BL2_266_sample_0023

data_processing:
samplename_reads.tab file is generated with STAR 2.5.0 with the option of  --quantMode GeneCounts
Genome_build: xt9

source_name: Tissue

extract_protocol:
Dissected embryo explants were dissociated into single cells using  Ca2+ and Mg2+ free media (Sive, Grainger, & Harland, 2007). 200 cells were picked for performing single-cell RNA-seq using the modified version of Tang et al protocol (Tang et al., 2008).
Amplified cDNA was purified with XP beads and the Zymo purification kit respectively and its concentration measured with Qubit® 2.0 Fluorometer (Q32866, Life Technologies). The quality of the amplified cDNA and distribution of DNA fragment size were assessed by Agilent 2100 Bioanalyzer (Agilent Technologies) with the High Sensitivity DNA Kit (5067-4626, Agilent). The sequencing libraries were prepared using the KAPA Hyper Pre Kit (KR0961 – v6.17, Kapa Biosystems). The concentrations of the fragments with the approximate indexed adapters were quantified by KAPA library quantification.

value: stage10 .5 (Gastrula)

tag: antibody


title: sc_BL2_266_sample_0024


title: sc_BL2_266_sample_0022


title: Patient 178

value: breast cancer

value: negative


title: LIPG-Liver-Batch1-ZT08-WT-LibraryH [4C-Seq]

value: Ad libitum

value: LIPG

tag: batch

tag: zeitgeber time


title: Patient 177


title: Patient 176


title: sc_BL2_266_sample_0021

tag: cell line


title: sc_BL2_266_sample_0020

tag: Stage


title: Patient 175

value: Luminal B


title: DMSO rep3

description: RNA bound to ZMAT3

tag: treatment


title: sc_BL2_266_sample_0025


title: Patient 191

tag: race

value: Triple Negative


title: CRY1-Liver-Batch1-ZT08-WT-LibraryH [4C-Seq]

value: Liver

value: post-natal 8-12 weeks


title: sc_BL2_266_sample_0019


title: sc_BL2_266_sample_0018


title: SLC2A2-Liver-Batch1-ZT08-WT-LibraryH [4C-Seq]


title: Patient 174

tag: age at diagnosis, years


title: sc_BL2_266_sample_0017


title: sc_BL2_266_sample_0015


title: sc_BL2_266_sample_0016


title: GYS2-Liver-Batch1-ZT08-WT-LibraryH [4C-Seq]


title: sc_BL2_266_sample_0013


title: Patient 173

value: AA

tag: er


title: sc_BL2_266_sample_0014


title: sc_BL2_266_sample_0012


title: Patient 172

value: positive


title: POR-Liver-Batch1-ZT08-WT-LibraryG [4C-Seq]

tag: strain

value: POR


title: Patient 171

tag: pr


title: NR1D1-Liver-Batch1-ZT08-WT-LibraryG [4C-Seq]


title: sc_BL2_266_sample_0009


title: sc_BL2_266_sample_0008


title: sc_BL2_266_sample_0010


title: sc_BL2_266_sample_0007


title: Patient 170

tag: subtype

value: Luminal A


title: Patient 169

tag: tissue


title: sc_BL2_266_sample_0006


title: MFSD2A-Liver-Batch1-ZT08-WT-LibraryG [4C-Seq]

tag: feeding


title: sc_BL2_266_sample_0005


title: NAMPT-Liver-Batch1-ZT08-WT-LibraryG [4C-Seq]

tag: age


title: sc_BL2_266_sample_0004


title: HMGCR-Liver-Batch1-ZT08-WT-LibraryG [4C-Seq]

tag: genotype

value: HMGCR


title: PFKFB3-Liver-Batch1-ZT08-WT-LibraryG [4C-Seq]

tag: bait


title: sc_BL2_266_sample_0003

tag: antibody


title: LIPG-Liver-Batch1-ZT08-WT-LibraryG [4C-Seq]

tag: batch


title: Patient 168


title: sc_BL2_266_sample_0011


title: sc_BL1_266_sample_0025


title: CRY1-Liver-Batch1-ZT08-WT-LibraryG [4C-Seq]

tag: zeitgeber time


title: sc_BL1_266_sample_0024

tag: cell line


title: Patient 166


title: sc_BL2_266_sample_0002

tag: Stage


title: sc_BL1_266_sample_0023


title: SLC2A2-Liver-Batch1-ZT08-WT-LibraryG [4C-Seq]


title: amIL12p40_DSS (956071)

city: Tarrytown

first: Ruoyu

last: Zhang

address: 777 Old Saw Mill River Road

institute: Regeneron

description: gut.counts.txt

data_processing:
Array Studio software (OmicSoft) used for reads mapping.
Sense strand exon reads were used to quantify the gene expression level by RSEM algorithm implemented in ArrayStudio to generate the skin.counts.txt and gut.counts.txt files.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include read count for each sample

source_name: colon

extract_protocol:
mRNA was extracted with MagMAX kit (Life Tech) and purified with Dynabeads mRNA Purification  Kit
Strand-specific RNA-seq libraries were  constructed using ScriptSeq mRNA-Seq Library Preparation Kit

value: 75% C57BL/6NTac 25% 129S6/SvEvTac

tag: disease state

value: DITRA model

value: colon

tag: treatment

value: DSS + anti mouse IL12p40 antibody


title: GYS2-Liver-Batch1-ZT08-WT-LibraryG [4C-Seq]

value: WT


title: PBS_DSS (956070)

description: gut.counts.txt


title: HMGCR-Liver-Batch1-ZT08-KO-LibraryG [4C-Seq]

value: KO


title: Patient 164

tag: race

value: EA

value: breast cancer

tag: age at diagnosis, years

value: negative


title: Patient 165

tag: er

value: Triple Negative


title: Patient 163

tag: pr

value: Luminal B


title: Patient 167

tag: subtype


title: sc_BL1_266_sample_0021

value: stage10 .5 (Gastrula)


title: POR-Liver-Batch1-ZT08-KO-LibraryG [4C-Seq]

tag: strain

tag: tissue

value: Liver

value: Ad libitum

value: post-natal 8-12 weeks


title: PBS_DSS (956068)

description: gut.counts.txt


title: sc_BL2_266_sample_0001


title: sc_BL1_266_sample_0019


title: Patient 199


title: sc_BL1_266_sample_0020


title: NAMPT-Liver-Batch1-ZT08-KO-LibraryG [4C-Seq]

tag: feeding

tag: age

value: NAMPT


title: Patient 160

value: positive

value: Luminal A


title: Patient 161


title: aIL36R_DSS (956067)

description: gut.counts.txt

value: 75% C57BL/6NTac 25% 129S6/SvEvTac

value: DITRA model

value: DSS + anti human IL36R antibody


title: sc_BL1_266_sample_0018


title: MFSD2A-Liver-Batch1-ZT08-KO-LibraryG [4C-Seq]

tag: genotype

tag: bait


title: amIL12p40_DSS (956066)

description: gut.counts.txt

value: colon

value: DSS + anti mouse IL12p40 antibody


title: sc_BL1_266_sample_0017

tag: antibody


title: Patient 159

value: AA


title: sc_BL1_266_sample_0022


title: Patient 158

value: breast cancer


title: PFKFB3-Liver-Batch1-ZT08-KO-LibraryG [4C-Seq]

value: KO

tag: batch

tag: zeitgeber time


title: aIL36R_DSS (956069)

description: gut.counts.txt


title: aIL36R_DSS (956065)

description: gut.counts.txt


title: sc_BL1_266_sample_0016

tag: cell line

tag: Stage


title: Patient 162

value: EA

value: negative


title: amIL12p40_DSS (956064)

description: gut.counts.txt

tag: disease state

tag: treatment


title: Patient 157

tag: race

tag: age at diagnosis, years


title: sc_BL1_266_sample_0014

value: stage10 .5 (Gastrula)


title: SLC2A2-Liver-Batch1-ZT08-KO-LibraryG [4C-Seq]

value: Liver


title: Patient 156

tag: er

tag: pr

value: Luminal B


title: PBS_DSS (956061)

description: gut.counts.txt

tag: strain


title: amIL12p40_DSS (956060)

description: gut.counts.txt

tag: tissue


title: GYS2-Liver-Batch1-ZT08-KO-LibraryG [4C-Seq]

tag: feeding

value: Ad libitum

value: post-natal 8-12 weeks


title: sc_BL1_266_sample_0013


title: Patient 155

tag: subtype

value: Triple Negative


title: PBS_DSS (956059)

description: gut.counts.txt


title: HMGCR-Liver-Batch1-ZT08-WT-LibraryF [4C-Seq]

tag: age

tag: genotype

value: WT

value: HMGCR


title: sc_BL1_266_sample_0012

tag: antibody


title: Patient 154

value: positive


title: amIL12p40_DSS (956056)

description: gut.counts.txt

value: 75% C57BL/6NTac 25% 129S6/SvEvTac

value: DITRA model


title: POR-Liver-Batch1-ZT08-WT-LibraryF [4C-Seq]

tag: bait

value: POR

tag: batch


title: Dis_Ecoli_LMNC_Rep1

tag: cell line/strain

value: Rosetta

value: wild-type with plasmid expression of:pET3a-splitFlAsH-LMNC-TwinStrep

tag: sample type

value: Footprints from disome fraction

tag: growth condition

value: EZ-rich defined medium, 37°C

value: Plasmid gene expression induced for 4 min with 1mM IPTG


title: Patient 153

value: EA

value: breast cancer

value: negative


title: sc_BL1_266_sample_0011

tag: cell line

tag: Stage

value: stage10 .5 (Gastrula)


title: NR1D1-Liver-Batch1-ZT08-WT-LibraryF [4C-Seq]

value: Liver

value: Ad libitum

value: post-natal 8-12 weeks

tag: zeitgeber time


title: amIL12p40_DSS (956054)

description: gut.counts.txt

tag: disease state

value: colon

tag: treatment

value: DSS + anti mouse IL12p40 antibody


title: Patient 152

tag: race

value: AA

tag: age at diagnosis, years

tag: er

tag: pr

value: positive


title: sc_BL1_266_sample_0010


title: LIPG-Liver-Batch1-ZT08-KO-LibraryG [4C-Seq]

tag: strain

tag: tissue

tag: feeding

tag: age

value: KO

value: LIPG


title: aIL36R_DSS (956052)

description: gut.counts.txt

value: 75% C57BL/6NTac 25% 129S6/SvEvTac

value: DITRA model

value: DSS + anti human IL36R antibody


title: NAMPT-Liver-Batch1-ZT08-WT-LibraryF [4C-Seq]

tag: genotype

value: WT

tag: bait

value: NAMPT

tag: batch


title: sc_BL1_266_sample_0015

tag: antibody


title: sc_BL1_266_sample_0009

tag: cell line


title: Patient 151

value: EA

value: breast cancer

tag: subtype

value: Triple Negative


title: aIL36R_DSS (956051)

description: gut.counts.txt


title: sc_BL1_266_sample_0008

tag: Stage

value: stage10 .5 (Gastrula)


title: Patient 150

value: Luminal B


title: sc_BL1_266_sample_0007


title: PBS_DSS (956050)

description: gut.counts.txt

tag: disease state


title: Patient 149

value: negative


title: CRY1-Liver-Batch1-ZT08-WT-LibraryF [4C-Seq]

value: Liver

value: Ad libitum

value: post-natal 8-12 weeks

tag: zeitgeber time


title: sc_BL1_266_sample_0006


title: Patient 148

tag: race

value: AA

value: positive

value: Luminal A


title: sc_BL1_266_sample_0005


title: amIL12p40_DSS (956049)

description: gut.counts.txt

value: 75% C57BL/6NTac 25% 129S6/SvEvTac

value: colon

tag: treatment

value: DSS + anti mouse IL12p40 antibody


title: Patient 147

tag: age at diagnosis, years

tag: er


title: aIL36R_DSS (956048)

description: gut.counts.txt

tag: strain

value: DITRA model

value: DSS + anti human IL36R antibody


title: SLC2A2-Liver-Batch1-ZT08-WT-LibraryF [4C-Seq]

tag: tissue

value: WT


title: aIL36R_DSS (956047)

description: gut.counts.txt


title: sc_BL1_266_sample_0004


title: Patient 146

value: breast cancer

tag: pr


title: PBS_DSS (956046)

description: gut.counts.txt


title: Patient 145

value: EA


title: HMGCR-Liver-Batch1-ZT08-KO-LibraryF [4C-Seq]

tag: feeding

tag: age

value: KO

value: HMGCR


title: sc_BL1_266_sample_0003

value: stage10 .5 (Gastrula)


title: aIL36R_DSS (956044)

description: gut.counts.txt


title: MFSD2A-Liver-Batch1-ZT08-WT-LibraryF [4C-Seq]

value: Liver

tag: genotype

tag: bait


title: GYS2-Liver-Batch1-ZT08-WT-LibraryF [4C-Seq]

value: Ad libitum

tag: batch


title: POR-Liver-Batch1-ZT08-KO-LibraryF [4C-Seq]

value: post-natal 8-12 weeks

value: POR


title: PFKFB3-Liver-Batch1-ZT08-WT-LibraryF [4C-Seq]


title: Patient 144

value: negative

value: positive


title: sc_BL1_266_sample_0002

tag: cell line

tag: antibody


title: PBS_water (956043)

description: gut.counts.txt

value: 75% C57BL/6NTac 25% 129S6/SvEvTac


title: LIPG-Liver-Batch1-ZT08-WT-LibraryF [4C-Seq]

value: LIPG


title: NAMPT-Liver-Batch1-ZT08-KO-LibraryF [4C-Seq]

value: NAMPT


title: sc_BL1_266_sample_0001

tag: Stage


title: Patient 143

value: AA

tag: subtype

value: Luminal A


title: sc_AC2_266_sample_0025


title: Patient 142

value: Triple Negative


title: MFSD2A-Liver-Batch1-ZT08-KO-LibraryF [4C-Seq]

tag: zeitgeber time


title: PBS_water (956041)

description: gut.counts.txt

tag: disease state

value: DITRA model

value: colon


title: Patient 141

tag: race

value: EA

value: breast cancer


title: PFKFB3-Liver-Batch1-ZT08-KO-LibraryF [4C-Seq]

value: KO


title: PBS_water (956040)

description: gut.counts.txt

tag: treatment


title: Patient 140

tag: age at diagnosis, years

tag: er


title: sc_AC2_266_sample_0024

value: stage10 .5 (Gastrula)


title: PBS_water (956039)

description: gut.counts.txt

tag: strain

tag: tissue


title: PBS-IMQ (884312)

description: skin.counts.txt

source_name: skin

value: skin

value: PBS-IMQ


title: SLC2A2-Liver-Batch1-ZT08-KO-LibraryF [4C-Seq]

value: Liver

tag: feeding

value: Ad libitum

value: post-natal 8-12 weeks


title: sc_AC2_266_sample_0021


title: Patient 139

value: positive

tag: pr

value: Luminal B


title: sc_AC2_266_sample_0022


title: aIL-36R-IMQ (884311)

description: skin.counts.txt

value: 75% C57BL/6NTac 25% 129S6/SvEvTac

value: IMQ + anti human IL36R antibody


title: GYS2-Liver-Batch1-ZT08-KO-LibraryF [4C-Seq]

tag: age

tag: genotype


title: Patient 138

value: AA

value: negative

value: Luminal A


title: sc_AC2_266_sample_0020


title: PBS_water (956042)

description: gut.counts.txt

value: DITRA model

value: colon


title: Patient 137

value: breast cancer


title: HMGCR-Liver-Batch1-ZT08-WT-LibraryE [4C-Seq]

value: WT

tag: bait

value: HMGCR

tag: batch


title: Patient 136


title: PBS-IMQ (884309)

description: skin.counts.txt

value: skin


title: Patient 135

value: Triple Negative


title: POR-Liver-Batch1-ZT08-WT-LibraryE [4C-Seq]

value: Liver

value: POR


title: sc_AC2_266_sample_0018

tag: cell line

value: stage10 .5 (Gastrula)

tag: antibody


title: PBS-IMQ (884310)

description: skin.counts.txt

value: PBS-IMQ


title: sc_AC2_266_sample_0019

tag: Stage


title: aIL-36R-IMQ (884308)

description: skin.counts.txt


title: sc_AC2_266_sample_0017


title: NR1D1-Liver-Batch1-ZT08-WT-LibraryE [4C-Seq]

value: Ad libitum

value: post-natal 8-12 weeks

tag: zeitgeber time


title: sc_AC2_266_sample_0023


title: LIPG-Liver-Batch1-ZT08-KO-LibraryF [4C-Seq]

value: KO

value: LIPG


title: NAMPT-Liver-Batch1-ZT08-WT-LibraryE [4C-Seq]

value: NAMPT


title: Patient 134

value: AA

value: positive

value: negative

tag: subtype

value: Luminal A


title: aIL-36R-IMQ (884307)

description: skin.counts.txt

value: 75% C57BL/6NTac 25% 129S6/SvEvTac

tag: disease state

value: DITRA model

value: IMQ + anti human IL36R antibody


title: Patient 133

tag: race

value: breast cancer

value: Luminal B


title: MFSD2A-Liver-Batch1-ZT08-WT-LibraryE [4C-Seq]

value: Liver

value: WT


title: Patient 132

value: EA

tag: age at diagnosis, years


title: aIL-36R-IMQ (884306)

description: skin.counts.txt

value: skin

tag: treatment


title: sc_AC2_266_sample_0015

value: stage10 .5 (Gastrula)


title: PFKFB3-Liver-Batch1-ZT08-WT-LibraryE [4C-Seq]

tag: strain

value: Ad libitum

value: post-natal 8-12 weeks


title: sc_AC2_266_sample_0014


title: LIPG-Liver-Batch1-ZT08-WT-LibraryE [4C-Seq]

tag: tissue

value: LIPG


title: aIL-36R-IMQ (884305)

description: skin.counts.txt


title: Patient 131

tag: er


title: sc_AC2_266_sample_0013


title: aIL-36R-IMQ (884304)

description: skin.counts.txt


title: Patient 130

tag: pr


title: CRY1-Liver-Batch1-ZT08-WT-LibraryE [4C-Seq]

tag: feeding

tag: age


title: aIL-36R-IMQ (884303)

description: skin.counts.txt


title: sc_AC2_266_sample_0016


title: SLC2A2-Liver-Batch1-ZT08-WT-LibraryE [4C-Seq]

tag: genotype

tag: bait


title: amIL-12p40-IMQ (884281)

description: skin.counts.txt

value: IMQ + anti mouse IL12p40 antibody


title: sc_AC2_266_sample_0012

tag: cell line


title: sc_AC2_266_sample_0011

tag: antibody


title: Patient 129

value: Triple Negative


title: amIL-12p40-IMQ (884279)

description: skin.counts.txt


title: Patient 127

value: AA

value: negative

value: positive


title: sc_AC2_266_sample_0010

tag: Stage


title: sc_AC2_266_sample_0009


title: POR-Liver-Batch1-ZT20-KO-LibraryE [4C-Seq]

value: KO

value: POR

tag: batch

tag: zeitgeber time


title: amIL-12p40-IMQ (884280)

description: skin.counts.txt

value: 75% C57BL/6NTac 25% 129S6/SvEvTac

tag: disease state

value: DITRA model


title: Patient 128

tag: race

value: breast cancer

tag: subtype


title: NAMPT-Liver-Batch1-ZT20-KO-LibraryE [4C-Seq]

value: Liver

value: NAMPT


title: Patient 126

tag: age at diagnosis, years


title: amIL-12p40-IMQ (884278)

description: skin.counts.txt

tag: strain

value: skin

tag: treatment


title: MFSD2A-Liver-Batch1-ZT20-KO-LibraryE [4C-Seq]

tag: tissue


title: sc_AC2_266_sample_0008

value: stage10 .5 (Gastrula)


title: amIL-12p40-IMQ (884277)

description: skin.counts.txt


title: Patient 124

tag: er

tag: pr


title: sc_AC2_266_sample_0007


title: GYS2-Liver-Batch1-ZT08-WT-LibraryE [4C-Seq]

tag: feeding

value: Ad libitum

tag: age

value: WT


title: PFKFB3-Liver-Batch1-ZT20-KO-LibraryE [4C-Seq]

value: post-natal 8-12 weeks

tag: genotype

tag: bait


title: amIL-12p40-IMQ (884276)

description: skin.counts.txt

value: IMQ + anti mouse IL12p40 antibody


title: sc_AC2_266_sample_0006

tag: cell line

tag: antibody


title: HMGCR-Liver-Batch1-ZT08-KO-LibraryE [4C-Seq]

value: HMGCR

tag: batch


title: Patient 125

value: AA

value: Luminal A


title: LIPG-Liver-Batch1-ZT20-KO-LibraryE [4C-Seq]

value: LIPG

tag: zeitgeber time


title: amIL-12p40-IMQ (884275)

description: skin.counts.txt

tag: disease state


title: sc_AC2_266_sample_0004

tag: Stage


title: Patient 122

tag: race

value: negative

tag: subtype

value: Triple Negative


title: GYS2-Liver-Batch1-ZT08-KO-LibraryE [4C-Seq]

tag: strain

value: KO


title: sc_AC2_266_sample_0003


title: sc_AC2_266_sample_0005


title: HMGCR-Liver-Batch1-ZT08-WT-LibraryD [4C-Seq]


title: SLC2A2-Liver-Batch1-ZT08-KO-LibraryE [4C-Seq]


title: sc_AC2_266_sample_0002


title: PBS-IMQ (884265)

description: skin.counts.txt

value: 75% C57BL/6NTac 25% 129S6/SvEvTac

value: DITRA model

tag: treatment

value: PBS-IMQ


title: Patient 121

tag: tissue

value: breast cancer

tag: age at diagnosis, years


title: PBS-water (884245)

description: skin.counts.txt

value: skin

value: PBS-water


title: PBS-water (884267)

description: skin.counts.txt


title: Patient 120

value: EA

tag: er

value: positive

tag: pr


title: PBS-water (884246)

description: skin.counts.txt


title: sc_AC2_266_sample_0001

value: stage10 .5 (Gastrula)


title: POR-Liver-Batch1-ZT08-WT-LibraryD [4C-Seq]

value: Liver

tag: feeding

value: Ad libitum

tag: age

value: post-natal 8-12 weeks

value: WT

value: POR


title: Patient 123

value: negative

value: Luminal A


title: Patient 118

value: AA

value: Luminal B


title: sc_AC1_266_sample_0025


title: Patient 119


title: NR1D1-Liver-Batch1-ZT08-WT-LibraryD [4C-Seq]

tag: genotype

tag: bait


title: Patient 116

value: Triple Negative


title: PBS-IMQ (884243)

description: skin.counts.txt

value: 75% C57BL/6NTac 25% 129S6/SvEvTac

value: DITRA model

value: PBS-IMQ


title: NAMPT-Liver-Batch1-ZT08-WT-LibraryD [4C-Seq]

value: NAMPT


title: sc_AC1_266_sample_0024

tag: cell line

tag: antibody


title: sc_AC1_266_sample_0023


title: Patient 115

value: EA

value: breast cancer


title: LIPG-Liver-Batch1-ZT08-WT-LibraryD [4C-Seq]

value: LIPG

tag: batch

tag: zeitgeber time


title: sc_AC1_266_sample_0022

tag: Stage

value: stage10 .5 (Gastrula)


title: MFSD2A-Liver-Batch1-ZT08-WT-LibraryD [4C-Seq]

value: Liver

value: Ad libitum


title: WT3-OP9

city: Montréal

first: Eric

last: Milot

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

institute: HMR research center/Université de Montréal

description: co-cultured on OP9 cells

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the mm10 genome with TopHat 2.0.9
Raw alignment counts were calculated with htseq-count 0.5.3
Differential expression measurements were performed with DESeq2 v1.0.19
Genome_build: mm10
Supplementary_files_format_and_content: Diff files with differential expression
Supplementary_files_format_and_content: NORMALIZED COUNT

source_name: erythroid cells

growth_protocol: For the OP9/OP9-DL1 co-culture system, E14.5 fetal liver EryC were placed on stromal OP9 or OP9-DL1 cells and co-cultured in α-MEM, 20% FBS, 1% penicillin-streptomycin and 2U/mL Erythropoietin. Co-cultures were maintained for 48 hours and then fetal liver EryC were isolated through a 40µm filter for the following experiments.

extract_protocol:
Total RNA from E14.5 fetal liver EryC was extracted with Trizol (Invitrogen). RNA was further purified with the RNeasy column kit (Qiagen) according to manufacturer instructions. mRNA was enriched with oligodT beads. The library was performed with the TruSeq RNA Sample Preparation Kit (fragmentation- cDNA – dsDNA – ER – ATL – Ligation with adaptators – PCR Enrichment) (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: e14.5 fetal liver

tag: genotype/variation

value: wild type for Ikaros (IKZF1)


title: sc_AC1_266_sample_0021


title: CRY1-Liver-Batch1-ZT08-WT-LibraryD [4C-Seq]

tag: strain

value: post-natal 8-12 weeks

value: WT


title: Patient 114

tag: race

value: AA

value: negative

value: positive

tag: subtype


title: Patient 112

tag: tissue

tag: age at diagnosis, years

value: Luminal A


title: PBS-IMQ (884244)

description: skin.counts.txt

value: 75% C57BL/6NTac 25% 129S6/SvEvTac

tag: disease state

value: DITRA model

value: skin

tag: treatment


title: IK3-OP9

description: co-cultured on OP9 cells

value: homozygote Ikaros null mutation


title: IK3-dL1

description: co-cultured on OP9-DL1 cells


title: PFKFB3-Liver-Batch1-ZT08-WT-LibraryD [4C-Seq]

tag: feeding

tag: age


title: IK2-dL1

description: co-cultured on OP9-DL1 cells


title: Patient 117

value: EA

value: breast cancer

tag: er

tag: pr

value: Luminal B


title: WT3-dL1

description: co-cultured on OP9-DL1 cells


title: sc_AC1_266_sample_0019

tag: cell line

value: stage10 .5 (Gastrula)

tag: antibody


title: SLC2A2-Liver-Batch1-ZT08-WT-LibraryD [4C-Seq]

value: Liver

value: Ad libitum

tag: genotype

tag: bait

tag: batch

tag: zeitgeber time


title: sc_AC1_266_sample_0018

tag: Stage


title: IK2-OP9

description: co-cultured on OP9 cells

tag: strain

tag: cell type

value: e14.5 fetal liver

tag: genotype/variation


title: WT4-OP9

description: co-cultured on OP9 cells

tag: tissue

value: wild type for Ikaros (IKZF1)


title: sc_AC1_266_sample_0017


title: Patient 108

tag: race

tag: age at diagnosis, years

tag: subtype


title: Patient 109

value: Triple Negative


title: Patient 113


title: Patient 111


title: HMGCR-Liver-Batch1-ZT08-WT-LibraryC [4C-Seq]

tag: feeding

tag: age

value: post-natal 8-12 weeks

value: WT

value: HMGCR


title: sc_AC1_266_sample_0016


title: POR-Liver-Batch1-ZT08-WT-LibraryC [4C-Seq]

value: POR


title: NR1D1-Liver-Batch1-ZT08-WT-LibraryC [4C-Seq]


title: Patient 107

value: AA

tag: er

value: positive

tag: pr

value: negative

value: Luminal A


title: sc_AC1_266_sample_0014

tag: cell line

tag: antibody


title: WT4-dL1

description: co-cultured on OP9-DL1 cells


title: Patient 110


title: IK1-dL1

description: co-cultured on OP9-DL1 cells

value: homozygote Ikaros null mutation


title: Patient 106

value: breast cancer


title: WT1-dL1

description: co-cultured on OP9-DL1 cells


title: sc_AC1_266_sample_0013


title: WT1-OP9

description: co-cultured on OP9 cells


title: sc_AC1_266_sample_0015


title: GYS2-Liver-Batch1-ZT08-WT-LibraryD [4C-Seq]

tag: genotype

tag: bait


title: Patient 105

value: EA


title: Patient 104


title: MFSD2A-Liver-Batch1-ZT08-WT-LibraryC [4C-Seq]

tag: batch

tag: zeitgeber time


title: PFKFB3-Liver-Batch1-ZT08-WT-LibraryC [4C-Seq]

tag: strain


title: Patient 103

value: Luminal B


title: LIPG-Liver-Batch1-ZT08-WT-LibraryC [4C-Seq]

value: Liver

value: LIPG


title: sc_AC1_266_sample_0012

tag: Stage

value: stage10 .5 (Gastrula)


title: CRY1-Liver-Batch1-ZT08-WT-LibraryC [4C-Seq]

value: Ad libitum


title: NAMPT-Liver-Batch1-ZT08-WT-LibraryC [4C-Seq]

value: NAMPT


title: sc_AC1_266_sample_0010


title: GYS2-Liver-Batch1-ZT08-WT-LibraryC [4C-Seq]

value: post-natal 8-12 weeks


title: sc_AC1_266_sample_0008


title: Patient 100

value: Triple Negative


title: Patient 099


title: sc_AC1_266_sample_0009


title: SLC2A2-Liver-Batch1-ZT08-WT-LibraryC [4C-Seq]

value: WT


title: sc_AC1_266_sample_0007


title: sc_AC1_266_sample_0020


title: POR-Liver-Batch1-ZT08-KO-LibraryC [4C-Seq]

value: KO

value: POR


title: Patient 098

value: AA

value: positive


title: sc_AC1_266_sample_0006


title: C2C12_PARP2_depleted_rep3

city: Debrecen

first: Judit

last: Márton

state: HajdU-Bihar

address: Egyetem tér

country: Hungary

institute: University Of Debrecen

hyb_protocol: Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450. Core software Affymetrix GeneChip Command Console (AGCC).

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix). Core software Affymetrix GeneChip Command Console (AGCC).

data_processing: Microarray data were analyzed by GeneSpring 10 GX software (Agilent BioTechnologies). Affymetrix CEL files were normalized Robust Multichip Analysis (RMA) algorithm and median normalization. Expressed genes were determined by filtering out the lowest 20th percentile of genes based on raw signal intensity. Then genes, which did not show at least 2-fold change difference from the median, were also filtered out, called non-changing genes. Statistical analysis was performed on the list of changing genes using T test, statistically significant difference was considered to p < 0.05 and fold change cut off value was 1.5.

label: biotin

source_name: C2C12 cell

label_protocol: Global expression pattern was analyzed on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. Ambion WT Expression Kit (Life Technologies, Hungary) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 250 ng of total RNA samples. Samples were hybridized at 45 oC for 16 hours and then standard washing protocol was performed using Affymetrix GeneChip Fluidics Station 450, the arrays were scanned on GeneChip Scanner 7G (Affymetrix). RNA labeling and hybridization was processed by UD-GenoMed Medical Genomic Technologies Ltd (Debrecen, Hungary).

growth_protocol: DMEM (4.5 g/L glucose, 10% FCS)

extract_protocol: Total RNA was extracted from C2C12 cells using the RNeasy Mini Kit (Qiagen). RNA integrity was checked on Agilent Bioanalyser 2100 (Agilent Technologies), RNA samples with ď€ľ9.0 RIN value were used in the further experiments. NanoDrop ND-1000 was used to determine RNA concentration.

treatment_protocol: PARP-2 silencing was performed employing shPARP-2 (small hairpin) and scPARP-2 (scrambled) shRNA by lentiviral delivery (Sigma) using 40 MOI lentiviruses coding shRNA sequence against PARP-2.

tag: transfection

value: shPARP-2 transfected


title: Patient 097

tag: tissue

value: negative

value: Luminal A


title: Patient 096

tag: race

value: breast cancer


title: Patient 102

value: EA

tag: age at diagnosis, years


title: sc_AC1_266_sample_0005


title: C2C12_PARP2_depleted_rep1


title: C2C12_control_rep1

value: scrambled transfected


title: C2C12_control_rep3


title: NAMPT-Liver-Batch1-ZT08-KO-LibraryC [4C-Seq]

source_name: Crosslinked genomic DNA

value: Liver


title: sc_AC1_266_sample_0004

value: stage10 .5 (Gastrula)


title: C2C12_control_rep2


title: HMGCR-Liver-Batch1-ZT08-KO-LibraryC [4C-Seq]

value: Ad libitum

value: HMGCR


title: MFSD2A-Liver-Batch1-ZT08-KO-LibraryC [4C-Seq]

value: post-natal 8-12 weeks


title: PFKFB3-Liver-Batch1-ZT08-KO-LibraryC [4C-Seq]


title: Patient 094

tag: subtype

value: Triple Negative


title: Patient 095

value: Luminal B


title: sc_AC1_266_sample_0002


title: sc_AC1_266_sample_0001


title: SLC2A2-Liver-Batch1-ZT08-KO-LibraryC [4C-Seq]

tag: feeding

value: KO


title: Patient 093


title: Anti-miR-128-3p treated mice 4

city: New Delhi

first: Neeru

last: Saini

state: Delhi

address: Mall road

department: FGU

country: India

institute: CSIR-IGIB

description: Gene expression data from liver tissue in mice fed with high fat diet for 13 weeks and then treated with five intra-peritoneal injections of anti-miR-128-3p

hyb_protocol: Hybridization was done for 16 hr at 45°C on MTA 1.0, GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed using RMA normalization and summarization method.

source_name: Mouse liver after high fat diet feeding for 13 weeks followed by treatment with anti-miR-128-3p

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All mice were fed with a high fat diet for 13 weeks

extract_protocol: Total RNA  was extrected using TRIzol reagent as per the manufacturer's instructions.

treatment_protocol: Mice received five intra-peritoneal injections of either miR-128-3p or vehicle control.

tag: gender

value: Male


title: sc_AC1_266_sample_0003


title: Patient 091

tag: er


title: LHX8_Rep2_RNA-Seq

extract_protocol:
Total RNA was extracted from animal caps using our in-house adapted Trizol-Zymo Hybrid protocol.
The concentrations of all the RNA samples were measured using the  DeNovix dsDNA High Sensitivity Assay (Catalog number: KIT-DSDNA-HIGH-1). The cDNA was constructed using KAPA RNA HyperPrep with RiboErase (Catalogue Number: 08278555702, Kapa Biosystems).  We checked the quality of the samples by RT-qPCR using primers spanning coding regions of candidate and housekeeping genes. The prepared libraries were quantified with the KAPA Library Quantification Kit (Kapa Biosystems #KK4844), and then sequenced in a paired-ended manner using the NextSeq 500 (Illumina) according to standard Illumina protocols.


title: GYS2-Liver-Batch1-ZT08-KO-LibraryC [4C-Seq]

extract_protocol: Liver and kidney nuclei were prepared as previously described (Ripperger and Schibler 2006) with some minor changes.         In brief, liver and kidneys from individual animals were homogenized and fixed in 4ml of PBS including 1.5percent formaldehyde for 10 minutes at room temperature.         Cross-linking reaction was stopped by adding 25 ml of ice-cold stop reaction buffer (2.2 M sucrose; 150 mM glycine; 10 mM HEPES pH 7.6; 15 mM KCl; 2 mM EDTA; 0.15 mM spermine; 0.5 mM spermidine; 0.5 mM DTT; 0.5 mM PMSF)         to the homogenates and kept 5 minutes on ice. Homogenates were then loaded on top of 10 ml cushion buffer (2.05 M sucrose; 10 % glycerol; 125 mM glycine; 10 mM HEPES pH 7.6; 15 mM KCl; 2 mM EDTA; 0.15 mM spermine; 0.5 mM spermidine; 0.5 mM DTT; 0.5 mM PMSF)         and centrifuged for 45 minutes at 105g at  4degC. Nuclei were washed twice in PBS and immediately frozen.

tag: age


title: Anti-miR-128-3p treated mice 2


title: Anti-miR-128-3p treated mice 3


title: LHX8_Rep1_RNA-Seq

tag: cell line


title: High fat diet control mice 4

description: Gene expression data from liver tissue in mice fed with high fat diet for 13 weeks

source_name: Mouse liver after high fat diet feeding for 13 weeks


title: Patient 090

tag: pr


title: HMGCR-Liver-Batch1-ZT08-WT-LibraryB [4C-Seq]

tag: genotype

value: WT


title: POR-Liver-Batch1-ZT08-WT-LibraryB [4C-Seq]

tag: bait

value: POR


title: NR1D1-Liver-Batch1-ZT08-WT-LibraryB [4C-Seq]

tag: batch


title: OTX2_Rep1_RNA-Seq

tag: antibody


title: LIPG-Liver-Batch1-ZT08-KO-LibraryC [4C-Seq]

tag: strain

value: LIPG

tag: zeitgeber time


title: Patient 089

value: AA

value: negative


title: C2C12_PARP2_depleted_rep2

tag: transfection

value: shPARP-2 transfected


title: Patient 092

value: EA

tag: tissue

value: breast cancer

value: positive


title: Patient 088

tag: race

value: Luminal A


title: NAMPT-Liver-Batch1-ZT08-WT-LibraryB [4C-Seq]

value: Liver

value: Ad libitum

value: NAMPT


title: Patient 087

tag: age at diagnosis, years

value: Triple Negative


title: 20-2 WL rep2

city: Lincoln

first: Chi

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

description: 20-2 WL rep2

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to wheat genome using tophat2 -p 32 -g 1
Reads counts for each gene with  htseq-count  -q -f sam -t gene -s no -a 15 -i ID
reference genome https://www.nature.com/articles/s41588-019-0381-3#data-availability
http://doi.org/10.6084/m9.figshare.6984035
Genome_build: the Svevo genome assembly
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is gene IDs and the second column is reads counts

organism: Triticum aestivum

source_name: seedling roots

growth_protocol: Seedling grown in grwoth chamber for 6 days and then primary roots harvested for RNA extraction

extract_protocol:
RNeasy Plant mini kit (Qiagen) was used for RNA isolation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Well watered (WW) and Water limited (WL)

value: roots

tag: treatment

value: WL


title: High fat diet control mice 2

value: Male


title: 20-2  WL rep1

description: 20-2  WL rep1


title: OTX2_Rep2_RNA-Seq

tag: Stage

value: stage10 .5 (Gastrula)


title: High fat diet control mice 3

tag: gender


title: IRX3_OTX2_Rep2_RNA-Seq


title: Anti-miR-128-3p treated mice 1


title: Svevo WL rep2

description: Svevo WL rep2

value: Svevo


title: High fat diet control mice 1


title: MFSD2A-Liver-Batch1-ZT08-WT-LibraryB [4C-Seq]

data_processing:
Library strategy: 4C-Seq
mm9
Mapping was done using HTS station (http://htsstation.epfl.ch). See Supplemental methods of paper for detailed processing methods. In brief, read counts were normalized by total counts on the cis chromosome. For each fragment, we fit a weighted linear model with a Gaussian window of 2.5kb in order to incorporate signal from neighboring fragments.
Log10 4CSeq signal (value A with variance Avar). Processed formats show fragments within +/- 2MB of the bait. Zscore and p-value represent differential contacts between liver and kidney

tag: feeding

value: post-natal 8-12 weeks

value: WT


title: IRX3_Rep2_RNA-Seq


title: PFKFB3-Liver-Batch1-ZT08-WT-LibraryB [4C-Seq]

tag: age


title: IRX3_OTX2_Rep1_RNA-Seq

tag: cell line


title: Patient 085

tag: er

tag: pr

value: negative

tag: subtype


title: LIPG-Liver-Batch1-ZT08-WT-LibraryB [4C-Seq]

tag: genotype

tag: bait

value: LIPG

tag: batch


title: Patient 086

value: AA


title: 20-2  WW rep1

description: 20-2  WW rep1

value: WW


title: Patient 084

value: EA

value: breast cancer


title: Eomes_Rep2_RNA-Seq

tag: antibody


title: Patient 083

value: positive


title: Svevo WW rep2

description: Svevo WW rep2


title: Foxb1_Eomes_Rep2_RNA-Seq


title: Svevo WW rep1

description: Svevo WW rep1


title: Patient 081

value: Luminal B


title: Svevo  WL rep1

description: Svevo  WL rep1


title: Patient 082


title: SLC2A2-Liver-Batch1-ZT08-WT-LibraryB [4C-Seq]

tag: strain

value: Liver

value: Ad libitum

tag: zeitgeber time


title: Patient 080

tag: race

tag: tissue


title: HMGCR-Liver-Batch1-ZT08-KO-LibraryB [4C-Seq]

value: KO

value: HMGCR


title: GYS2-Liver-Batch1-ZT08-WT-LibraryB [4C-Seq]


title: 20-2 WW rep1

description: 20-2 WW rep1

value: roots

tag: treatment


title: Foxb1_Eomes_Rep1_RNA-Seq

tag: Stage

value: stage10 .5 (Gastrula)


title: Patient 079

tag: age at diagnosis, years


title: Foxb1_Rep2_RNA-Seq


title: IRX3_Rep1_RNA-Seq


title: POR-Liver-Batch1-ZT08-KO-LibraryB [4C-Seq]

tag: feeding

value: POR


title: Foxb1_Rep1_RNA-Seq


title: WI_Rep2_RNA-Seq


title: NAMPT-Liver-Batch1-ZT08-KO-LibraryB [4C-Seq]

tag: age

value: post-natal 8-12 weeks

value: NAMPT


title: Patient 078

value: negative

value: Luminal A


title: Patient 077

value: AA


title: Eomes_Rep1_RNA-Seq

tag: cell line


title: MFSD2A-Liver-Batch1-ZT08-KO-LibraryB [4C-Seq]


title: WI_Rep1_RNA-Seq


title: PFKFB3-Liver-Batch1-ZT08-KO-LibraryB [4C-Seq]


title: Patient 076

tag: er


title: Patient 075

tag: pr


title: IK1-OP9

description: co-cultured on OP9 cells

tag: cell type

value: e14.5 fetal liver

tag: genotype/variation

value: homozygote Ikaros null mutation


title: DMZ_Rep2_ATAC-Seq

data_processing:
After demultiplexing,  the reads were aligned to the X. tropicalis genome (xt9) with bowtie2 (Langmead & Salzberg, 2012) using default settings.
All mapped reads were offset by +4 bp for the +strand and −5 bp for the −strand. Peaks were called for each sample using MACS2 (Zhang et al., 2008) with parameters “-q 0.05 --nomodel --shift 37 --extsize 73".
Genome_build: xt9

extract_protocol: ATAC-seq was performed as described (Bright & Veenstra, 2018). Library quality was assessed using the Agilent Bioanalyzer High-Sensitivity DNA kit for checking the fragment size distribution and signal to noise ratio was checked by performing qPCR primers spanning open and closed regions.


title: AC_Rep2_ATAC-Seq


title: GYS2-Liver-Batch1-ZT08-KO-LibraryB [4C-Seq]

tag: genotype

tag: bait


title: SLC2A2-Liver-Batch1-ZT08-KO-LibraryB [4C-Seq]

tag: batch


title: genomic DNA from ATRT case 14 [201194010024_R03C01]

type: genomic

city: Hamburg

first: Dörthe

last: Holdhof

address: Martinistraße 52

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip or the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the iScan System and standard recommended Illumina scanner setting.

data_processing:
Bioconductor (Version 3.10) package minifi (Version 1.32.0) using function 'preprocessNoob'
The Matrix_raw.txt.gz contains Unmethylated and methylated signal intensities

label: Cy3, Cy5

source_name: primary ATRT  sample (FFPE)

label_protocol: Standard Illumina Protocol

extract_protocol: For DNA isolation from FFPE tissue, 10 x 10 µm sections were cut and DNA isolated using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). Afterwards, the DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA. Finally, either the HumanMethylation450 BeadChip array or the Infinium MethylationEPIC BeadChip Kit (both Illumina) were used to quantify the methylation status of 450,000 or 850,000 CpG sites, respectively, on an iScan device (Illumina).

tag: subject/case id

value: ATRT case 14

tag: subject status

value: Atypical teratoid/rhabdoid tumors (ATRTs)

tag: Sex

value: male


title: genomic DNA from SCCOHT case 17 [203952880054_R04C01]

source_name: primary SCCOHT sample (FFPE)

value: SCCOHT case 17

value: small cell carcinoma of the ovary hypercalcemic type (SCCOHT)

value: female


title: LIPG-Liver-Batch1-ZT08-KO-LibraryB [4C-Seq]

tag: strain

tag: tissue

value: Liver

value: Ad libitum

value: KO

value: LIPG

tag: zeitgeber time


title: genomic DNA from ATRT case 13 [204234160028_R05C01]

value: ATRT case 13


title: Patient 072

data_processing: NanoString nSolver with Advanced Analysis 2.0

extract_protocol: Roche High Pure FFPET RNA Isolation Kit

tag: race

value: breast cancer

tag: age at diagnosis, years

tag: subtype

value: Triple Negative


title: Patient 073

value: EA

value: positive

value: negative

value: Luminal A


title: AC_Rep1_ATAC-Seq

tag: cell line

tag: Stage

value: stage10 .5 (Gastrula)

tag: antibody


title: HMGCR-Liver-Batch1-ZT08-WT-LibraryA [4C-Seq]

tag: feeding

tag: age

value: post-natal 8-12 weeks

value: WT

value: HMGCR


title: Patient 074

value: AA

tag: er

tag: pr

value: Luminal B


title: POR-Liver-Batch1-ZT08-WT-LibraryA [4C-Seq]

value: Liver

tag: genotype

tag: bait

value: POR

tag: batch


title: genomic DNA from eMRT case 21 [204081740052_R08C01]

source_name: primary eMRT sample (FFPE)

tag: subject/case id

value: eMRT case 21

tag: subject status

value: extracranial malignant rhabdoid tumors (eMRTs)

tag: Sex

value: female


title: Stage16_Rep2_ATAC-Seq

value: stage16 (Neurula)


title: Stage16_Rep1_ATAC-Seq


title: genomic DNA from ATRT case 10 [203952880078_R05C01]

value: ATRT case 10

value: Atypical teratoid/rhabdoid tumors (ATRTs)


title: Patient 071

source_name: primary breast cancer

value: EA

tag: tissue

value: breast cancer

value: Triple Negative


title: Patient 070

tag: race

value: negative


title: DMZ_Rep1_ATAC-Seq

value: stage10 .5 (Gastrula)


title: Patient 069

tag: age at diagnosis, years

value: positive


title: NR1D1-Liver-Batch1-ZT08-WT-LibraryA [4C-Seq]

tag: strain

value: Ad libitum

value: post-natal 8-12 weeks

value: WT

tag: zeitgeber time


title: genomic DNA from ATRT case 08 [203282450133_R03C01]

value: ATRT case 08

value: male


title: NAMPT-Liver-Batch1-ZT08-WT-LibraryA [4C-Seq]

value: Liver

value: NAMPT


title: Stage12_Rep2_ATAC-Seq

tag: cell line

tag: Stage

value: stage12 (Gastrula)


title: genomic DNA from ATRT case 03 [203824800109_R02C01]

value: ATRT case 03

value: female


title: genomic DNA from ATRT case 12 [204234160028_R04C01]

value: ATRT case 12

value: Atypical teratoid/rhabdoid tumors (ATRTs)


title: MFSD2A-Liver-Batch1-ZT08-WT-LibraryA [4C-Seq]

tag: feeding


title: Patient 068

value: EA

value: breast cancer

tag: subtype

value: Luminal B


title: Stage12_Rep1_ATAC-Seq

tag: antibody


title: CRY1-Liver-Batch1-ZT08-WT-LibraryB [4C-Seq]

tag: age


title: Stage10.5_Rep2_ATAC-Seq

value: stage10 .5 (Gastrula)


title: Patient 067

value: AA

tag: er

value: positive

tag: pr


title: Stage10.5_Rep1_ATAC-Seq


title: LIPG-Liver-Batch1-ZT08-WT-LibraryA [4C-Seq]

value: Ad libitum

value: post-natal 8-12 weeks

tag: genotype

tag: bait

value: LIPG

tag: batch


title: genomic DNA from ATRT case 01 [203784950120_R05C01]

tag: subject/case id

value: ATRT case 01

tag: subject status

tag: Sex


title: Patient 066

tag: race

tag: tissue

tag: age at diagnosis, years

value: negative

value: Triple Negative


title: genomic DNA from ATRT case 02 [202761400064_R06C01]

value: ATRT case 02

value: male


title: IMR575-shMYCN_ctrl

first: Frank

last: Westermann

address: Im Neuenheimer Feld 280

institute: Hopp Children's Cancer Center (KiTZ) and German Cancer Research Center (DKFZ)

data_processing:
Alignment and generation of the transcript count matrix was performed using CellRanger v3.1.0 using the hg19 human reference built.
Cells were filtered to keep cells with (1) genes detected per cell > 5000, <15000, (2) total RNA count per cell > 350000 and (3) percentage of mitochondrial expressed genes < 15%.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated values file with filtered gene counts for every gene and cell

source_name: Neuroblastoma cell line

growth_protocol: Cells were cultured in RPMI1640 medium supplemented with 10% FCS, 5 µg/ml Blasticidin and 50 µg/ml Zeocin at 37°C and 5% CO2 and subcultured every 3-4 days.

extract_protocol:
Cells were harvested using versene.
Libraries were prepared according to the 10x Genomics Chromium Single Cell 3' v3.1 protocol.

treatment_protocol: Cells were treated with 100 ng/ml doxycycline or left untreated for 72 hours.

value: Neuroblastoma cell line

tag: cell line

tag: treatment


title: PFKFB3-Liver-Batch1-ZT08-WT-LibraryA [4C-Seq]

tag: strain

value: Liver

tag: feeding

value: WT

tag: zeitgeber time


title: Stage9_Rep1_ATAC-Seq

tag: Stage

value: stage9 (Blastula)

tag: antibody


title: SLC2A2-Liver-Batch1-ZT08-WT-LibraryA [4C-Seq]

tag: age


title: Stage9_Rep2_ATAC-Seq


title: Patient 065

value: breast cancer

tag: er

tag: pr

tag: subtype


title: CRY1-Liver-Batch1-ZT08-WT-LibraryA [4C-Seq]

tag: genotype

tag: bait

tag: batch


title: IMR575-shMYCN_kd

description: 10x Genomics Chromium Single Cell 3' v3.1

value: 100 ng/ml doxycycline


title: Patient 064

tag: race

value: Luminal A


title: GYS2-Liver-Batch1-ZT08-WT-LibraryA [4C-Seq]

tag: tissue


title: Patient 063

value: AA

tag: age at diagnosis, years


title: FF_OF

city: Taoyuan City

first: Yu-Ju

last: Chen

address: No.259, Wenhua 1st Rd.

country: Taiwan

institute: Chung Gang University

description: female OE+AAV9-CB::Fst

data_processing:
none provided by the submitter
Genome_build: GRCm38
Supplementary_files_format_and_content: coutns

source_name: Dentate gyrus

extract_protocol: none provided by the submitter

value: dentate gyrus


title: MBAL563

first: Aartik

last: Sarma

state: CA

address: 513 Parnassus Ave

institute: University of California, San Francisco

data_processing:
*** Raw data submission disallowed by submitter's IRB ***

Pseudoalignment with kallisto 0.46.1
Genome_build: ENSEMBL v.99

source_name: Tracheal aspirate

extract_protocol:
RNA was extracted with Zymo Pathogen Magbead Kit, treated with DNAse, and ribodeplted with FastSelect
NEBNext Ultra II RNAseq Kit

treatment_protocol: TA was collected and mixed 1:1 with DNA/RNA shield

value: Tracheal aspirate

tag: disease state

value: Mechanically ventilated control

tag: gender

value: F

value: Caucasian

tag: hispanic ethnicity

value: N

tag: 30 day mortality

tag: lrti pathogen

tag: lrti type

tag: reason for intubation

value: Neurosurgical procedure


title: genomic DNA from ATRT case 09 [201516250023_R03C01]

tag: subject/case id

value: ATRT case 09

tag: subject status

value: Atypical teratoid/rhabdoid tumors (ATRTs)

tag: Sex


title: HMGCR-Liver-Batch1-ZT08-KO-LibraryA [4C-Seq]

first: Felix

institute: École Polytechnique Fédérale de Lausanne

tag: strain

tag: feeding

value: Ad libitum

tag: age

value: post-natal 8-12 weeks

value: KO

value: HMGCR

tag: zeitgeber time


title: MBAL555

tag: race


title: POR-Liver-Batch1-ZT08-KO-LibraryA [4C-Seq]

tag: tissue

value: Liver

tag: genotype

tag: bait

value: POR

tag: batch


title: MBAL477

tag: disease state

tag: gender

value: M

tag: hispanic ethnicity

value: Y

value: Retroperitoneal bleed


title: FF_CF

description: female KO+AAV9-CB::GFP

value: dentate gyrus


title: MBAL462

value: Tracheal aspirate

value: Mechanically ventilated control

value: Asian

tag: 30 day mortality

tag: lrti pathogen

tag: lrti type

value: Subdural hematoma


title: Patient 062

value: AA

value: breast cancer

tag: age at diagnosis, years

tag: er

value: positive

tag: pr

tag: subtype

value: Luminal B


title: Patient 060

value: EA

value: negative

value: Triple Negative


title: Patient 061


title: FF_OM2

description: male OE+AAV9-CB::Fst

tag: strain


title: NAMPT-Liver-Batch1-ZT08-KO-LibraryA [4C-Seq]

value: Liver

tag: feeding

value: Ad libitum

tag: age

value: post-natal 8-12 weeks

value: KO

value: NAMPT

tag: zeitgeber time


title: FF_CM1

description: male KO+AAV9-CB::GFP

tag: tissue

value: dentate gyrus


title: FF_OM1

description: male OE+AAV9-CB::Fst


title: PFKFB3-Liver-Batch1-ZT08-KO-LibraryA [4C-Seq]

tag: genotype

tag: bait


title: FF_WM2

description: female WT


title: Patient 058

tag: race


title: MBAL575

value: Tracheal aspirate

tag: disease state

value: ARDS not due to COVID

tag: gender

value: M

value: Caucasian

value: N

value: Y

value: Pseudomonas

value: Bacterial

tag: reason for intubation

value: ARDS


title: Patient 057

value: AA

value: breast cancer

value: positive

value: negative

value: Luminal A


title: MBAL319

value: Mechanically ventilated control

value: F

value: Other

tag: hispanic ethnicity

tag: 30 day mortality

tag: lrti pathogen

value: Hemorrhagic stroke


title: Patient 056

value: EA

tag: age at diagnosis, years

tag: er

value: Luminal B


title: FF_WF1

description: male WT

value: dentate gyrus


title: FF_WM1

description: male WT


title: MBAL543

value: Tracheal aspirate

value: ARDS not due to COVID

value: Caucasian

value: N

value: No pathogen identified

tag: lrti type

value: Unknown


title: SLC2A2-Liver-Batch1-ZT08-KO-LibraryA [4C-Seq]

tag: strain

value: Liver

value: Ad libitum

value: post-natal 8-12 weeks

value: KO

tag: batch


title: MBAL551

tag: age

value: M

value: ARDS


title: MBAL657

value: Y

value: HMPV

value: Viral


title: FF_KM2

description: female KO


title: Patient 059

value: EA

value: breast cancer

value: negative

tag: pr

tag: subtype

value: Triple Negative


title: FF_KF1

description: male KO

tag: tissue

value: dentate gyrus


title: Patient 055

value: AA


title: GYS2-Liver-Batch1-ZT08-KO-LibraryA [4C-Seq]

tag: feeding

tag: genotype

tag: bait

tag: zeitgeber time


title: Patient 054

tag: race

value: positive

value: Luminal A


title: MBAL530

value: Tracheal aspirate

tag: disease state

value: ARDS not due to COVID

tag: gender

value: F

value: African American

tag: hispanic ethnicity

value: N

tag: reason for intubation


title: LIPG-Liver-Batch1-ZT08-KO-LibraryA [4C-Seq]

value: Liver

value: Ad libitum

value: post-natal 8-12 weeks

value: KO

value: LIPG


title: Patient 053

value: breast cancer

tag: age at diagnosis, years

tag: er


title: FF_CM2

description: male KO+AAV9-CB::GFP

tag: strain


title: MBAL541

value: Caucasian

tag: 30 day mortality

tag: lrti pathogen

value: No pathogen identified

tag: lrti type

value: Unknown

value: ARDS


title: FF_KM1

description: male KO

value: dentate gyrus


title: Patient 052

value: AA

value: negative

tag: pr

tag: subtype

value: Triple Negative


title: MBAL539

tag: tissue

value: Tracheal aspirate

value: ARDS not due to COVID

tag: age

value: M

value: Y


title: Patient 051

value: positive

value: Luminal A


title: MBAL524

value: F

value: N

value: Influenza A

value: Viral


title: MFSD2A-Liver-Batch1-ZT08-KO-LibraryA [4C-Seq]

value: Liver

tag: feeding

value: Ad libitum

value: post-natal 8-12 weeks

tag: genotype

value: KO

tag: bait

tag: batch


title: Patient 050

tag: race

value: AA

value: breast cancer


title: 56_GTAGAA: TPCA-1+TNFα  replicate4

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

data_processing:
Sequenced reads were mapped to mm10 whole genome using STAR 2.6.1d with default parameters
STAR 2.6.1d was used to obtain read counts per gene based on ENSEMBL annotation Mus_musculus.GRCm38.95.gtf.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include STAR gene-based read counts for each sample

source_name: bone marrow

growth_protocol: Bone marrow-derived macrophages (BMDM) were generated as established by flushing the bone marrow from femurs and tibiae with ice-cold PBS, resuspending in PBS by repeated pipetting and filtering through a 40 µm cell strainer (BD Biosciences). After centrifugation of the cell suspension at 500 g for 10 min, the pellet was resuspended in culture medium (RPMI 1640 containing 10% FCS, 15% L929-cell-conditioned medium (LCM) and 100 µl/ml gentamycin) and plated on 15 cm untreated culture plates (Greiner). 15 % fresh LCM was added again on day 1 and 2 of culturing. For the stimulation experiments, differentiated macrophages were harvested by gentle scraping, transferred onto untreated 6-well or 12-well plates (Greiner) on Day 7 of culturing and left in LCM-free medium for 24 hours, allowing cells to adhere. Cells were then stimulated in FCS-free medium with either 50 ng/ml mouse recombinant TNF-α at different time intervals or left untreated.

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were pretreated with either TMP195 (5 µM) or TPCA-1 (500 nM) for 1 h prior to stimulation with TNF-α (50 ng/ml) for 24 h.

value: Bone marrow-derived macrophages (BMDM)

tag: treament


title: Patient 049

value: Luminal B


title: Patient 048

value: EA

value: negative

value: Triple Negative


title: WT

city: Göttingen

first: Katherine

last: Bohnsack

address: Humboldtallee 23

institute: University Medical Centre Göttingen

data_processing:
Sequencing reads for each experimental sample were demultiplexed using their 5' barcode sequences and barcodes were then clipped
Reads of identical sequence that contained identical 5-nucleotide random barcodes were collapsed
Reads were trimmed and quality controlled using flexbar and aligned to the S.cerevisiae genome (EF2.59.1.0) by Bowtie2 (version 2.3.4.2).
Supplementary_files_format_and_content: tab-delimited text files showing the numbers of reads mapping to each nucleotide of the RDN37 locus encoding the 35S pre-rRNA (35S)

organism: Saccharomyces cerevisiae

source_name: BY4741 yeast strain

growth_protocol: Wild-type BY4741 yeast cells or yeast cells expressing C-terminally His-Tev-ProtA tagged Get4 from its genomic locus were grown in exponential phase in low uracil media supplemented with 4-thiouracil as previously described (Baejen et al., 2014).

extract_protocol:
Crosslinked RNA-protein complexes were purified under denaturing conditions and RNAs associated with His-ProtA-tagged proteins were trimmed (Bohnsack et al., 2012).
3' and 5' adapters were ligated and a cDNA library was prepared by reverse transcription and amplified by PCR (Bohnsack et al., 2012).

treatment_protocol: Cells were crosslinked in culturo using light at 365 nm

tag: expression

value: no tag


title: MBAL503

value: Tracheal aspirate

tag: disease state

value: ARDS not due to COVID

tag: gender

value: Caucasian

tag: hispanic ethnicity

value: Y

value: Rhinovirus

tag: reason for intubation

value: ARDS


title: MBAL479

value: F

value: Other

tag: 30 day mortality

value: N

tag: lrti pathogen


title: 55_CAGATG: TMP195+TNFα  replicate4

tag: strain


title: MBAL473

tag: lrti type


title: Patient 046

first: Song

institute: Roswell Park Comprehensive Cancer Center

tag: tissue

tag: age at diagnosis, years

tag: er

value: positive

tag: pr

tag: subtype


title: Patient 047

value: breast cancer


title: MBAL488

tag: age

value: No pathogen identified

value: Unknown


title: Get4-HTP_2


title: MBAL463

value: M

tag: race

value: Streptococcus

value: Bacterial


title: Get4-HTP


title: 54_AACCGA: TNFα  replicate4

value: Bone marrow-derived macrophages (BMDM)

tag: treament

value: TNFα

tag: genotype


title: Patient 045

value: EA

value: negative

value: Luminal B


title: control 5

description: FACS-sorted CD4+ T cells

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse Gene ST 2.0 arrays containing about 35,000 probe sets.

scan_protocol: Staining and scanning using a GeneChip Scanner 3000 7G was done according to the Affymetrix expression protocol including minor modifications as suggested in the Encore Biotin protocol.

data_processing: R/Bioconductor, rma normalization, default parameters

source_name: CD73-FR4-CD4+ T cells

label_protocol: Total RNA (0.1-30 ng) was amplified and labeled using the Ovation Pico WTA System V2 in combination with the Encore Biotin Module (Nugen).

extract_protocol: The Trizol samples were thawed on ice, 300 µl chloroforn was added, shaken, incubated for 3 minutes at room temperature and spun at 12,000 x g and 4°C. The aqueous phase was transferred to new tubes, 1 volume of isopropanol and 1 µl of  linear polyachrylamide stock solution (25 µg/µl) was added. The samples were precipitated for 16 hours at -20°C and centrifuged for 10 minutes at 12,000 x g and 4°C. Supernatants were removed and RNA pellets washed with 70% ethanol. RNA pellets were resuspended in 100 µl RNAse-free water and purified with NucleoSpin RNA Clean-up XS columns as per manufacturer's instructions, from which the RNA was eluted with 12 µl water and stored at -80°C. RNAs were quantified with an Agilent 2100 Bioanalyzer. All samples had RNA integrity values > 8 and were use for amplification and microarray hybridizations.

tag: sample type

value: control


title: 52_CCAATT: TPCA-1+TNFα  replicate3


title: control 4

description: FACS-sorted CD4+ T cells