title: Treatment, high mutation load kidney, replicate 1, RNA-seq

data_processing:
Raw sequencing data were processed using fastp (v0.23.2) to remove low-quality reads and sequencing adapters. High-quality reads were aligned to the mm10 genome using Hisat2 (v2.2.1). SAM files were converted to BAM files using SAMtools (v1.11). Read counts for each gene were calculated using featureCounts (v2.0.1). Differentially expressed genes were identified using edgeR.
Assembly: mm10
Supplementary files format and content: Tab-separated text file includes raw counts for each sample

extract_protocol:
Total RNA was isolated using the TRIzol method, and its concentration was quantified with the Qubit RNA XR Assay Kit (Thermo Fisher Scientific). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).
Sequencing libraries were prepared with the Illumina TruSeq RNA Preparation Kit. High-throughput sequencing was performed on a DNBSEQ platform, producing 150 bp paired-end reads, following the manufacturer’s recommendations

value: Kidney

value: 75% mutation load mouse


title: THP-1 Cells-Infected-Untreated, Control, 12hrs, Rep 1

status: Public on Jun 16 2025

type: SRA

city: Cape Town

first: Bienyameen

last: Baker

state: Western

address: Francie Van Zijl Drive, Tygerberg

department: Department of Biomedical Sciences

country: South Africa

institute: Stellenbosch University Tygerberg Medical Campus, SAMRC Centre for TB Research

description:
Library name: IonCode_0103
IU – 1 (12hrs TP) (Exp 1)

library_source: transcriptomic

data_processing:
Reads were quality trimmed during the base calling step using a moving window of 30pb and a cutoff of quality value (QV) 15. Reads were mapped to the hg19_AmpliSeq_Transcriptome_v1.1 reference genome and only reads with an alignment length of 17 and more were retained.
Assembly: hg19 Ampliseq transcriptome V1.1
Supplementary files format and content: CSV file, matrix counts

molecule: total RNA

organism: Homo sapiens

source_name: THP-1 cells

extract_protocol:
RNeasy ®Plus Mini Kit (Qiagen) was used to extract the total RNA.
Ion AmpliSeq™ Transcriptome Human Gene Expression Panel Chef-Ready Kit was used to prepare the RNA libraries according to manufacturer's protocol.

tag: cell line

value: THP-1 cells

tag: cell type

value: monocytes

tag: genotype

value: WT

tag: treatment

value: macrophage differentiation


title: J-1476

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

description: Library name: J-1476

data_processing:
adapters and low-quality reads have been filtered by BGI
alignment to reference with STARv2.7.0f
Read count extraction via STRINGTIE v1.3.6 and prepDE.py (following Protocol stringtie webpage)
Assembly: GRCh38/hg38
Supplementary files format and content: tsv file including raw counts for all samples

source_name: quadriceps

extract_protocol:
RNA was extracted using the miRNA micro kit (Qiagen, Hilden, Germany)
done by BGI (Yantian District Shenzhen China)

tag: tissue

value: quadriceps

tag: age


title: THP-1 Cells-Uninfected, IFIT2-induced, 12hrs, Rep 1

description:
Library name: IonCode_0102
UT – 1 (Exp 1)

value: IFIT2 -Knockup


title: cnr.wt.ctrl.igg.rep3

city: Research Triangle Park

first: Paul

middle: A

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

country: USA

institute: NIEHS

library_source: genomic

data_processing:
Adapters were clipped from raw read pairs with TrimGalore v0.6.6.
Read pairs were mapped to the hg38 reference assembly with bowtie2 v2.4.5 using parameters "--local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700", then filtered with samtools v1.19.2 for minimum MAPQ of 30.
Duplicate mapped fragments were then removed by MarkDuplicate from the Picard tool suite v.2.27.1 with parameter REMOVE_DUPLICATES=TRUE.
Biological triplicate samples were combined with samtools merge function.
Peaks calls were made with MACS2 v2.2.9.1 on the merged replicates using IgG per condition (WT Control, WT DOX, TA1del Control, TA1del DOX) with -q 0.00001;  peak sets per antibody and experimental subset were then concatenated, merged with bedtools v2.30.0 (-d 10), and filtered to remove exclusion list regions (ENCODE) and non-canonical chromosomes.
Fragments at peaks were counted by the featureCounts function of subread v2.0.3 with parameters "-p -countReadPairs".
Genomic coverage tracks were generated by deeptools bamCoverage v3.5.3 with parameters "--normalizeUsing None --binSize 10 --ignoreDuplicates --effectiveGenomeSize 2913022398 --scaleFactor", where the scale factors were calculated by 1/[(E.Coli fragment count/Sample fragment count)*100.  For lenti-empty and lenti-AFOS treated samples, only the 2nd and 3rd replicates contributed to the coverage tracks to avoid bias resulting from the separate pAG-MNase batch used for the 1st replicate.
Assembly: hg38
Supplementary files format and content: Fragment counts per peak in tab-delimited text format.
Supplementary files format and content: Normalized genomic coverage tracks in bigWig format.
Library strategy: CUT&Run

molecule: genomic DNA

growth_protocol: Doxycycline (dox) inducible wildtype (wt) and TA1del (ta1) GATA3 cell lines were generated in SUM159PT basal breast cancer cell line.

extract_protocol:
CUT&RUN was performed following standard CUT&RUN conditions outlined in protocol provided by Henikoff lab on protocols.io (Skene and Henikoff 2017, Janssens 2019, Meers et al. 2019) with minor modification of increasing wash steps to 4 times. Purified pAG-MNase was provided by the NIEHS Protein Expression Core and purified using Meers et al. 2019 protocol. For each reaction, 5e5 cells were harvested. Antibody dilutions (overnight incubation) were as follows: IgG Rabbit (Antibodies online ABIN101961; 1:100), Mouse IgG (Abcam ab46540; 1:100), FLAG M2 (Sigma F1804; 1:50), FRA1 (Abcam ab252421; 1:50), p300 (CST 86377S; 1:50), H3K4me1 (Epicypher 13-0057; 1:50), H3K27ac (Millipore MABE647; 1:50), BRG1 (Abcam ab110641; 1:50), SNF5/SMARCB1 (CST 91735S; 1:50).
Library preparations were performed with NEBNext Ultra II (NEB #E7645) described for transcription factors(Liu et al. 2018, Liu 2021) at half volume reactions. Additional modifications were made using NEBNext unique Dual Index Primers (NEB #E6440, #E6442), 15 ng of input DNA, and 0.5 µM diluted adapter.

treatment_protocol: To investigate changes in histone modifications, transcirption factor/chromatin remodeler binding in WT and TA1del-GATA3 expression, cells were induced with +/- DOX (1 ug/mL) for 24 hr.To determine the effect of AP-1 binding, cells were transduced with lentivirus containing empty vector or AFOS (dominant negative AP-1 that inhibits binding) for 48 hrs prior to DOX induction for 24 hrs. To determine the effect of ATPase function by SWI/SNF, cells were treated concurrently +/- DOX (1 ug/ml) and either DMSO (8 uL) or BRM014 (8 uM) for 24 hrs.

value: basal breast cancer line

value: WT GATA3 (1-444aa)

tag: induced

value: Control/Uninduced

tag: antibody

value: IgG Rabbit (Guinea pig anti-rabbit) [Antibodies Online, ABIN101961]


title: Control, low mutation load kidney, replicate 2, RNA-seq

city: Hangzhou

first: Guo-shi

last: Chai

state: --- Select One ---

address: No. 600 Dunyu Road, Sandun Town, Xihu District, Hangzhou, Zhejiang PR China

country: China

institute: Westlake University

organism: Mus musculus

source_name: Kidney

value: 5% mutation load mouse


title: Treatment, high mutation load kidney, replicate 3, RNA-seq

value: 80% mutation load mouse


title: J-1474

description: Library name: J-1474


title: cnr.wt.ctrl.p300.rep1


title: Zebrafish_Normal_PNP_18hpf_2

city: Birmingham

first: John

middle: M

last: Parant

state: AL

address: 1670 University Blvd

institute: University of Alabama at Birmingham

description: Library name: Sample 4

data_processing:
Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR (version 2.7.3a, GCC 6.4.0-2.28) with default setting.
Following alignment, raw read counts were generated using HTSeq (version 0.12.3, foss-2018b, Python-3.6.6). The corresponding gene annotation files used in HTSeq were Danio_rerio.GRCz11.102.chr.gtf for zebrafish samples.
Differentially expressed genes (DEGs) were identified using DESeq2 (version 1.42.1) in R (version 4.3.3).
Normalized counts were obtained using RSEM (version 1.3.3)
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes TPM values for each samples

organism: Danio rerio

source_name: 30-hpf embryos

growth_protocol: The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hours after fertilization, with approximately 30 embryos pooled in each Petri dish.

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit (QIAGEN, #74134) according to the manufacturer’s instructions. ~500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform, generating 2x150 bp paired-end reads, and was conducted by Genewiz from Azenta Life Sciences.

value: 30-hpf embryos


title: Control, low mutation load kidney, replicate 1, RNA-seq

value: 10% mutation load mouse


title: Control, low mutation load kidney, replicate 3, RNA-seq

value: 15% mutation load mouse


title: cnr.wt.ctrl.h3k4me1.rep3

value: H3K4me1 [Epicypher, 13-0057]


title: J-1475

description: Library name: J-1475


title: cnr.wt.ctrl.igg.rep2


title: 4LT-dSTR-M-R10

city: Baltimore

first: Jean Lud

last: Cadet

state: Maryland

address: 251 Bayview BLVD

department: Molecular Neuropsychiatry Research Branch

institute: National Institute On Drug Abuse

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Rattus norvegicus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts were added to the table
Assembly: Rattus norvegicus Rnor6.0
Supplementary files format and content: Txt file and counts

organism: Rattus norvegicus

source_name: Dorsal striatum

extract_protocol:
RNA was extracted using the protocol from RNeasy Mini Handbook (Qiagen)
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on two flowcell lanes. After clustering, the flowcells were loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

treatment_protocol: Female (n= 24, 350-500 g) and male (n= 24, 450-600 g) Long Evans rats were group-housed with free access to water and food. The rats were anaesthetized using ketamine and xylazine (50 and 5 mg/kg, i.p., respectively). We then implanted a silastic catheter (SAI Infusion Technologies, USA) into the right jugular vein as reported previously (Blackwood et al., 2019; Daiwile et al., 2019). Post-surgery, rats were injected with buprenorphine (0.1 mg/kg, s.c.) to relieve the pain. The animals used in the present study had not been exposed to any substance before surgery. They were also not food-trained prior to METH SA. Post-recovery, rats were randomly allocated to saline (n= 6) and METH (n=18) groups. We performed METH SA training as previously reported (Daiwile et al., 2021; Daiwile et al., 2019). Active lever press delivered METH (0.1 mg/kg/infusion) to METH group rats. METH SA phase consisted of two 3-hour per day sessions separated by a 30 min timeout where the light was turned off and the active levers were retracted. This phase was carried out for 5 days a week. During weekends, rats were disconnected from i.v. SA lines and remained in the chamber. Control rats self-administered saline under similar conditions. After 20 days of self-administration, rats were housed individually in the vivarium and had no access to METH.

value: Dorsal striatum

value: Neural tissue

tag: strain

value: Long Evans

value: wild type

tag: Sex

value: male

value: Methamphetamine Self-Administration


title: THP-1 Cells-Infected, IFIT2-induced,12hrs, Rep 1

description:
Library name: IonCode_0101
IFIT2 – 1 (Exp 1)

value: THP-1 cells

value: monocytes

value: IFIT2 -Knockup

value: macrophage differentiation


title: J-1473

description: Library name: J-1473

value: quadriceps


title: cnr.wt.ctrl.igg.rep1

value: basal breast cancer line

value: WT GATA3 (1-444aa)

value: Control/Uninduced

value: IgG Rabbit (Guinea pig anti-rabbit) [Antibodies Online, ABIN101961]


title: J-1477

description: Library name: J-1477


title: J-1472

description: Library name: J-1472


title: Zebrafish_Normal_PNP_18hpf_1

description: Library name: Sample 3

value: 30-hpf embryos


title: Treatment, high mutation load kidney, replicate 2, RNA-seq

value: Kidney

value: 75% mutation load mouse


title: cnr.wt.ctrl.h3k4me1.rep2

value: H3K4me1 [Epicypher, 13-0057]


title: Zebrafish_Abnormal_MPNP_18hpf_1

description: Library name: Sample 1


title: Zebrafish_Abnormal_MPNP_18hpf_2

description: Library name: Sample 2


title: 4LT-dSTR-M-R09

value: Dorsal striatum

value: Neural tissue

value: Long Evans


title: 4LT-dSTR-M-R07

value: wild type

value: male

value: Methamphetamine Self-Administration


title: J-1470

description: Library name: J-1470


title: 4LT-dSTR-M-L04


title: J-1471

description: Library name: J-1471


title: cnr.wt.ctrl.h3k27ac.rep3

value: H3K27Ac [Millipore, MABE647]


title: cnr.wt.ctrl.h3k4me1.rep1


title: Zebrafish_PNP_16hpf_1

description: Library name: Sample 19

source_name: 16-hpf embryos

value: 16-hpf embryos


title: J-1468

description: Library name: J-1468

value: quadriceps


title: 4HT-dSTR-M-R08


title: Zebrafish_PNP_16hpf_2

description: Library name: Sample 20


title: Zebrafish_MPNP_16hpf_2

description: Library name: Sample 18


title: cnr.wt.ctrl.h3k27ac.rep2

value: basal breast cancer line


title: 4HT-dSTR-M-R01


title: J-1467

description: Library name: J-1467


title: J-1466

description: Library name: J-1466


title: Zebrafish_MPNP_16hpf_1

description: Library name: Sample 17


title: cnr.wt.ctrl.h3k27ac.rep1

value: WT GATA3 (1-444aa)


title: cnr.wt.ctrl.fra1.rep3

value: Control/Uninduced

value: FRA1 [Abcam, ab252421]


title: Zebrafish_PNP_14hpf_2

description: Library name: Sample 16

source_name: 14-hpf embryos

value: 14-hpf embryos


title: 4HT-dSTR-M-L09


title: J-1465

description: Library name: J-1465


title: cnr.wt.ctrl.fra1.rep2


title: Zebrafish_PNP_14hpf_1

description: Library name: Sample 15


title: J-1464

description: Library name: J-1464


title: 4HT-dSTR-M-L07


title: cnr.wt.ctrl.fra1.rep1


title: Zebrafish_MPNP_14hpf_2

description: Library name: Sample 14


title: J-1469

description: Library name: J-1469


title: 4HT-dSTR-M-L05


title: J-1463

description: Library name: J-1463


title: cnr.wt.ctrl.flag.rep3

value: FLAG M2 SIGMA [SIGMA, F1804]


title: J-1462

description: Library name: J-1462


title: 4CT-dSTR-M-R12

value: Saline Control


title: cnr.wt.ctrl.flag.rep2


title: 4CT-dSTR-M-R11


title: cnr.wt.ctrl.flag.rep1


title: Zebrafish_PNP_12hpf_2

description: Library name: Sample 12

source_name: 12-hpf embryos

value: 12-hpf embryos


title: Zebrafish_PNP_12hpf_1

description: Library name: Sample 11


title: J-1461

description: Library name: J-1461


title: 4HT-dSTR-M-L10

value: Dorsal striatum


title: 4CT-dSTR-M-R06

value: Neural tissue


title: J-1460

description: Library name: J-1460


title: J-1459

description: Library name: J-1459


title: Zebrafish_MPNP_12hpf_2

description: Library name: Sample 10


title: 4CT-dSTR-M-R05

value: Long Evans


title: cnr.ta1.dox.p300.rep3

value: TA1del GATA3 (126-444aa)

value: DOX


title: Zebrafish_MPNP_12hpf_1

description: Library name: Sample 9


title: J-1458

description: Library name: J-1458


title: cnr.ta1.dox.p300.rep2


title: cnr.ta1.dox.p300.rep1


title: Zebrafish_PNP_10hpf_2

description: Library name: Sample 8

source_name: 10-hpf embryos

value: 10-hpf embryos


title: 4CT-dSTR-M-L11

value: wild type

value: male


title: J-1457

description: Library name: J-1457

value: quadriceps


title: Zebrafish_PNP_10hpf_1

description: Library name: Sample 7


title: cnr.ta1.dox.igg.rep3

value: basal breast cancer line

value: IgG Rabbit (Guinea pig anti-rabbit) [Antibodies Online, ABIN101961]


title: 3LT-dSTR-F-R09

value: Female

value: Methamphetamine Self-Administration


title: Zebrafish_MPNP_14hpf_1

description: Library name: Sample 13

value: 14-hpf embryos


title: J-1456

description: Library name: J-1456


title: cnr.ta1.dox.igg.rep2


title: 3LT-dSTR-F-R03


title: Zebrafish_MPNP_10hpf_2

description: Library name: Sample 6


title: J-1455

description: Library name: J-1455


title: J-1454

description: Library name: J-1454


title: Zebrafish_MPNP_10hpf_1

description: Library name: Sample 5


title: cnr.ta1.dox.h3k4me1.rep3

value: H3K4me1 [Epicypher, 13-0057]


title: 3LT-dSTR-F-L08


title: Zebrafish_PNP_8hpf_2

description: Library name: Sample 4

source_name: 8-hpf embryos

value: 8-hpf embryos


title: J-1453

description: Library name: J-1453


title: 3LT-dSTR-F-L06


title: 4CT-dSTR-M-L12

value: Saline Control


title: cnr.ta1.dox.h3k4me1.rep2


title: Zebrafish_PNP_8hpf_1

description: Library name: Sample 3


title: J-1452

description: Library name: J-1452


title: Zebrafish_MPNP_8hpf_2

description: Library name: Sample 2


title: cnr.ta1.dox.h3k4me1.rep1


title: cnr.ta1.dox.h3k27ac.rep3

value: H3K27Ac [Millipore, MABE647]


title: Zebrafish_MPNP_8hpf_1

description: Library name: Sample 1


title: J-1451

description: Library name: J-1451


title: 3HT-dSTR-F-R08

value: Dorsal striatum

value: Neural tissue


title: J-1450

description: Library name: J-1450


title: Zebrafish_WT_untreated_2

description: Library name: Sample 18

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit (QIAGEN, #74134) according to the manufacturer’s instructions. ~500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using the Illumina RNA kit with PolyA selection, and sequencing was performed on Illumina HiSeq platform, either with 2x150 bp paired-end reads (sequenced by Genewiz from Azenta Life Sciences or 2x75 bp pair-end reads (sequenced by UAB Heflin Center for Genomic Core).

treatment_protocol: Zebrafish embryos were placed at the closest position to the ionizing radiation source in an X-RAD 320 X-ray irradiator, exposing the embryos to 5 Gy/min of radiation for a total dose of 30 Gy.

value: 30-hpf embryos

value: w/o ionizing radiation-irradiation


title: cnr.ta1.dox.h3k27ac.rep2

value: TA1del GATA3 (126-444aa)

value: DOX


title: 3HT-dSTR-F-R04

value: Long Evans

value: wild type


title: J-1449

description: Library name: J-1449

value: quadriceps


title: cnr.ta1.dox.igg.rep1

value: basal breast cancer line

value: IgG Rabbit (Guinea pig anti-rabbit) [Antibodies Online, ABIN101961]


title: cnr.ta1.dox.h3k27ac.rep1


title: Zebrafish_WT_untreated_1

description: Library name: Sample 17


title: 3HT-dSTR-F-R01

value: Female

value: Methamphetamine Self-Administration


title: J-1448

description: Library name: J-1448


title: 3HT-dSTR-F-L10


title: Zebrafish_WT_3hpi_2

description: Library name: Sample 16

value: ionizing radiation-irradiation


title: cnr.ta1.dox.fra1.rep3

value: FRA1 [Abcam, ab252421]


title: 3LT-dSTR-F-L03


title: Zebrafish_WT_3hpi_1

description: Library name: Sample 15


title: cnr.ta1.dox.fra1.rep2


title: 3LT-dSTR-F-L01


title: J-1446

description: Library name: J-1446


title: Zebrafish_PNP_untreated_2

description: Library name: Sample 14


title: 3HT-dSTR-F-L09


title: S-1094

description: Library name: S-1094


title: 3HT-dSTR-F-L05


title: Zebrafish_PNP_untreated_1

description: Library name: Sample 13


title: cnr.ta1.dox.flag.rep3

value: FLAG M2 SIGMA [SIGMA, F1804]


title: S-1093

description: Library name: S-1093


title: Zebrafish_PNP_3hpi_2

description: Library name: Sample 12


title: 3CT-dSTR-F-R5

value: Saline Control


title: S-1091

description: Library name: S-1091


title: cnr.ta1.dox.flag.rep1


title: Zebrafish_PNP_3hpi_1

description: Library name: Sample 11


title: 3CT-dSTR-F-R12

value: Dorsal striatum


title: D-1111

description: Library name: D-1111


title: cnr.ta1.ctrl.p300.rep3

value: Control/Uninduced


title: Zebrafish_PNP_2hpi_2

description: Library name: Sample 10

value: 30-hpf embryos


title: J-1447

description: Library name: J-1447


title: 3CT-dSTR-F-R11

value: Neural tissue


title: cnr.ta1.ctrl.p300.rep2

value: TA1del GATA3 (126-444aa)


title: cnr.ta1.dox.fra1.rep1

value: DOX


title: D-1109

description: Library name: D-1109


title: 3CT-dSTR-F-L12

value: Long Evans


title: cnr.ta1.ctrl.p300.rep1


title: Zebrafish_PNP_1hpi_2

description: Library name: Sample 8


title: 3CT-dSTR-F-L11

value: wild type


title: D-1108

description: Library name: D-1108

value: quadriceps


title: cnr.ta1.ctrl.igg.rep3

value: basal breast cancer line


title: 3CT-dSTR-F-R6


title: Zebrafish_PNP_1hpi_1

description: Library name: Sample 7


title: cnr.ta1.ctrl.igg.rep2

value: IgG Rabbit (Guinea pig anti-rabbit) [Antibodies Online, ABIN101961]


title: prospective, acute leukemia, RTC_005

city: Boston

first: Salvatore

last: Benfatto

state: Massachusetts

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Library name: RTC_005

data_processing:
Pod5 raw data files were processed using dorado (v. 0.3.2)
The methylation calls were extracted from the bam files using the modkit tool (v. 0.1.13)
Assembly: hg19
Supplementary files format and content: txt files restricted to the CpGs positions of our reference cohort and containing the methylation status of the covered CpGs.
Supplementary files format and content: txt files containing the methylation status of all the covered CpGs.

source_name: Bone Marrow

extract_protocol:
Collected samples were processed to obtain DNA. DNA was extracted using the Qiagen DNeasy Blood and Tissue DNA extraction kit (Qiagen, Cat. no 69506), following manufacturer’s instructions for non-nucleated blood specimens. For every patient sample retrieved, 150-200 μL of specimen was mixed with 20 μL of proteinase K, adjusting the volume to 220 μL with PBS. Then 200 μL of ALT lysis buffer was added and samples were gently vortexed. To complete the cell lysis step, samples were incubated for 10 minutes at 56° C. For DNA precipitation, 200 μL of 100% ethanol was added to the samples. This mixture was then placed into a mini column and centrifuged for 1 minute at 8000 rpm. The mini column was placed into a new collection tube and a first washing step was performed adding 500 μL of buffer AW1 and centrifuging for 1 minute at 8000 rpm. The collection tube was discarded and a second washing step was done using 500 μL of AW2 buffer, centrifuging for 3 minutes at 14000 rpm. Finally, the DNA was eluted from the column by adding 200 μL of elution buffer and centrifuging for 1 minute at 8000 rpm. The elution step was repeated several times to increase DNA recovery and DNA quantification was done using the Qubit fluorometer (ThermoFisher Scientific, Cat. no. Q33238).
Retrospective samples: samples were processed using the Rapid Barcoding Kit 24 V14 (Oxford Nanopore Technologies, Cat. no. SQK-RBK114.24), according to the manufacturer's instructions. Prospective samples: DNA was extracted as described above. DNA was then prepared using the Rapid Sequencing Kit V14 (Oxford Nanopore Technologies, Cat. no. LSK-RAD114).

value: Bone Marrow


title: cnr.ta1.dox.flag.rep2


title: prospective, acute leukemia, RTC_004

description: Library name: RTC_004


title: Zebrafish_p53KO_untreated_2

description: Library name: Sample 6

value: w/o ionizing radiation-irradiation


title: D-1106

description: Library name: D-1106


title: cnr.ta1.ctrl.igg.rep1


title: prospective, acute leukemia, RTC_003

description: Library name: RTC_003


title: Zebrafish_p53KO_untreated_1

description: Library name: Sample 5


title: D-1105

description: Library name: D-1105


title: Zebrafish_p53KO_3hpi_2

description: Library name: Sample 4

value: ionizing radiation-irradiation


title: prospective, acute leukemia, RTC_002

source_name: Peripheral Blood

extract_protocol:
Collected samples were processed to obtain DNA. DNA was extracted using the Qiagen DNeasy Blood and Tissue DNA extraction kit (Qiagen, Cat. no 69506), following manufacturer’s instructions for non-nucleated blood specimens. For every patient sample retrieved, 150-200 μL of specimen was mixed with 20 μL of proteinase K, adjusting the volume to 220 μL with PBS. Then 200 μL of ALT lysis buffer was added and samples were gently vortexed. To complete the cell lysis step, samples were incubated for 10 minutes at 56° C. For DNA precipitation, 200 μL of 100% ethanol was added to the samples. This mixture was then placed into a mini column and centrifuged for 1 minute at 8000 rpm. The mini column was placed into a new collection tube and a first washing step was performed adding 500 μL of buffer AW1 and centrifuging for 1 minute at 8000 rpm. The collection tube was discarded and a second washing step was done using 500 μL of AW2 buffer, centrifuging for 3 minutes at 14000 rpm. Finally, the DNA was eluted from the column by adding 200 μL of elution buffer and centrifuging for 1 minute at 8000 rpm. The elution step was repeated several times to increase DNA recovery and DNA quantification was done using the Qubit fluorometer (ThermoFisher Scientific, Cat. no. Q33238).
Retrospective samples: 500 ng to 1 μg of patients’ DNA were prepared using the Ligation Sequencing Kit V14 (Oxford Nanopore Technologies, Cat. no. SQK-LSK114). Overall, all samples were prepared according to the manufacturer’s instructions, following an increased AMPureXP incubation period up to 30 minutes in both end-repair and ligation reactions, and a two-in-a-row elution step for 30 minutes each. After end-repair bead incubation and ethanol washing, beads were allowed to dry for 5 minutes. Once finished the ligation step bead incubation and long-fragment buffer washing, the beads were dried for 15 minutes. DNA was eluted in 16 to 18 ul of nuclease-free water. The abundance of the DNA recovered after the library preparation was quantified using the Qubit fluorometer (ThermoFisher Scientific, Cat. no. Q33238) and DNA size was assessed in some specimens with the TapeStation system (Agilent Technologies, Cat. no. G2992AA) to corroborate the existence of high molecular weight DNA in order to get long reads. Prospective samples: DNA was extracted as described above. DNA was then prepared using the Rapid Sequencing Kit V14 (Oxford Nanopore Technologies, Cat. no. LSK-RAD114).

value: Peripheral Blood

tag: group

value: prospective, acute leukemia


title: D-1103

description: Library name: D-1103


title: D-1110

description: Library name: D-1110


title: cnr.ta1.ctrl.h3k4me1.rep2

value: H3K4me1 [Epicypher, 13-0057]


title: Zebrafish_p53KO_3hpi_1

description: Library name: Sample 3


title: Zebrafish_PNP_2hpi_1

description: Library name: Sample 9


title: retrospective, acute leukemia, AL_024

value: retrospective, acute leukemia


title: D-1102

description: Library name: D-1102


title: prospective, acute leukemia, RTC_001


title: D-1107

description: Library name: D-1107


title: Zebrafish_p53KO_1hpi_2

description: Library name: Sample 2


title: D-1101

description: Library name: D-1101


title: cnr.ta1.ctrl.h3k4me1.rep1

value: Control/Uninduced


title: Zebrafish_p53KO_1hpi_1

description: Library name: Sample 1

value: 30-hpf embryos


title: D-1100

description: Library name: D-1100


title: retrospective, acute leukemia, AL_020

source_name: Pericardial fluid

value: Pericardial fluid


title: NSPC_tent-5_polyA_2

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

description:
Nanopore Direct RNA Sequencing of C. elegans nspc/tent-5 mutant strain at L4 stage, biological replicate 2
polya_statistics_nspc_mutants.xlsx

data_processing:
Illumina RNA-seq were performed in external companies. FastQ files were then mapped to WBCel235 reference genome using STAR aligner (v2.7.10a) and processed with samtools (v1.961). Read counts were obtained with featureCounts from the Subread package (v2.0.665, using options -Q 10 -p -C -B). Differential expression analysis was conducted using DESeq2 Bioconductor package (v1.28) with default settings.
Nanopore Direct RNA Sequencing was performed with the MinION device, followed by basecalling with Guppy 6.0.0 (ONT), mapping to WBCel235 reference (MiniMap v2.17 (25) with options -k 14 -ax map-ont –secondary = no), and processing with samtools v1.9. Lengths of poly(A) tails were estimated with Nanopolish (v0.13.2).
Assembly: WBcel235
Supplementary files format and content: Excel files with raw number of counts for Illumina RNA sequencing and poly(A) tails statistics for Nanopore direct RNA sequencing

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Strains were cultured at 20°C (or 15°C for ablation experiments) on nematode growth medium (NGM) plates seeded with E. coli HB101 (or HT115 expressing corrensponding RNAi vector) as a food source.

extract_protocol:
Populations of worms were collected and washed three times with 50 mM NaCl. Worm pellets were resuspended in 1 ml TRI Reagent (Sigma-Aldrich), vortexed for 15 minutes at room temperature, and stored at -80°C until further processing. RNA extraction was performed according to the manufacturer’s protocol for TRIzol-based isolation, with additional purification using KAPA Pure magnetic beads (RNA to beads ratio: 1:3 v/v). RNA quality and integrity were confirmed using the Agilent TapeStation system.
Total RNA samples for Illumina RNA sequencing were sent to Center for New Technology (Poland) or Genewiz (Germany) and libraries were prepared with the use of internal protocols. Sequencing libraries for Nanopore direct RNA sequencing were prepared using the DRS Kit (Oxford Nanopore Technologies, SQK- RNA002) according to the manufacturer’s protocol. In each library, total RNA isolated from worms (1,5 - 2 μg depending on the amount of isolated RNA) was mixed with 2 ng of in vitro transcribed poly(A) standards.

value: whole worm

value: nspc/tent-5 double mutant

value: ADZ130 (this study)

tag: developmental stage

value: grown at 20℃ on NGM plates seeded with E. coli HB111


title: cnr.ta1.ctrl.h3k27ac.rep2

value: TA1del GATA3 (126-444aa)

value: H3K27Ac [Millipore, MABE647]


title: cnr.ta1.ctrl.h3k27ac.rep1

value: basal breast cancer line


title: retrospective, acute leukemia, AL_021


title: D-1099

description: Library name: D-1099

value: quadriceps


title: NSPC_tent-5_polyA_1

description:
Nanopore Direct RNA Sequencing of C. elegans nspc/tent-5 mutant strain at L4 stage, biological replicate 1
polya_statistics_nspc_mutants.xlsx

value: grown at 20℃ on NGM plates seeded with E. coli HB110


title: D-1098

description: Library name: D-1098


title: cnr.ta1.ctrl.h3k4me1.rep3


title: D-1097

description: Library name: D-1097


title: tent-5_polyA_2

description:
Nanopore Direct RNA Sequencing of C. elegans tent-5 mutant strain at L4 stage, biological replicate 2
polya_statistics_nspc_mutants.xlsx

value: tent-5 mutant

value: tent-5(tm3504) I (NBRP)

value: grown at 20℃ on NGM plates seeded with E. coli HB108


title: retrospective, acute leukemia, AL_016

value: Peripheral Blood


title: tent-5_polyA_1

description:
Nanopore Direct RNA Sequencing of C. elegans tent-5 mutant strain at L4 stage, biological replicate 1
polya_statistics_nspc_mutants.xlsx

value: grown at 20℃ on NGM plates seeded with E. coli HB107


title: cnr.ta1.ctrl.fra1.rep3

value: Control/Uninduced

value: FRA1 [Abcam, ab252421]


title: cnr.ta1.ctrl.fra1.rep2


title: D-1096

description: Library name: D-1096


title: cnr.ta1.ctrl.h3k27ac.rep3


title: retrospective, acute leukemia, AL_015

value: Bone Marrow

value: retrospective, acute leukemia


title: D-1095

description: Library name: D-1095


title: cnr.ta1.ctrl.flag.rep3

value: FLAG M2 SIGMA [SIGMA, F1804]


title: nspc_polyA_2

description:
Nanopore Direct RNA Sequencing of C. elegans nspc mutant strain at L4 stage, biological replicate 2
polya_statistics_nspc_mutants.xlsx

value: whole worm

value: nspc mutant

value: ADZ114 (this study)

value: grown at 20℃ on NGM plates seeded with E. coli HB105


title: retrospective, acute leukemia, AL_014


title: cnr.ta1.ctrl.fra1.rep1

value: basal breast cancer line

value: TA1del GATA3 (126-444aa)


title: cnr.ta1.ctrl.flag.rep2


title: WT_polyA_2

description:
Nanopore Direct RNA Sequencing of C. elegans wild-type strain at L4 stage, biological replicate 2
polya_statistics_nspc_mutants.xlsx

value: wild type

value: N2 Bristol (CGC)

value: grown at 20℃ on NGM plates seeded with E. coli HB102


title: nspc_polyA_1

description:
Nanopore Direct RNA Sequencing of C. elegans nspc mutant strain at L4 stage, biological replicate 1
polya_statistics_nspc_mutants.xlsx

value: grown at 20℃ on NGM plates seeded with E. coli HB104


title: D-1094

description: Library name: D-1094

value: quadriceps


title: retrospective, acute leukemia, AL_018


title: retrospective, acute leukemia, AL_013


title: cnr.ta1.ctrl.flag.rep1


title: WT_polyA_1

description:
Nanopore Direct RNA Sequencing of C. elegans wild-type strain at L4 stage, biological replicate 1
polya_statistics_nspc_mutants.xlsx

value: grown at 20℃ on NGM plates seeded with E. coli HB101


title: retrospective, acute leukemia, AL_011


title: D-1092

description: Library name: D-1092


title: retrospective, acute leukemia, AL_017

value: Peripheral Blood


title: retrospective, acute leukemia, AL_010


title: D-1091

description: Library name: D-1091


title: atac.wt.treatment_dmso_4ul.dox

data_processing:
Adapters were clipped from raw read pairs with TrimGalore v0.6.6.
Read pairs were mapped to the hg38 reference assembly with bowtie2 v2.4.5 using default settings, then filtered with samtools v1.19.2 for minimum MAPQ of 30.
Duplicate mapped fragments were then removed by MarkDuplicate from the Picard tool suite v.2.27.1 with parameter REMOVE_DUPLICATES=TRUE.
For treated samples (BRM14, DMSO, or lentivirus AFOS or empty), replicates were merged prior to calling peaks with macs2 v2.2.9.1 (parameters: --nomodel -q 0.0001 -f BAMPE).  For untreated samples, peaks calls with macs2 were made for individual samples, then filtered to retain only those with intersecting peak calls in all three biological replicates.
Final peaks for analysis were established by concatenating within a given experimental subset, merging with bedtools v2.30.0, and filtering to remove exclusion list regions (ENCODE) and non-canonical chromosomes.
Fragments at peaks were counted by the featureCounts function of subread v2.0.3 with parameters "-p -countReadPairs".
Genomic coverage tracks were generated by deeptools bamCoverage v3.5.3 with parameters "--normalizeUsing RPGC --binSize 10 --ignoreDuplicates --effectiveGenomeSize 2913022398".
Assembly: hg38
Supplementary files format and content: Fragment counts per peak in tab-delimited text format.
Supplementary files format and content: Normalized genomic coverage tracks in bigWig format; *merged files are linked to the corresponding rep1 sample records

extract_protocol:
ATAC-seq samples were generated as previously described (Orlando et al. 2020) with the following modifications: 50,000 cells per reaction, omni-ATAC was performed for cell lysis steps (Corces et al. 2017, Grandi et al. 2022) and Tn5 to volume ratio was 1:10.
ATAC-seq libraries were generated by PCR amplification for 5 cycles followed by qPCR for determining remaining cycle numbers (~1/3 curve). Following DNA purification with Qiagen MinElute kit, final libraries were double-sided size selected (0.5X and 1.8X) with AMPure beads.

treatment_protocol: To investigate changes in chromatin accesibility by ATAC-seq following WT or TA1del-GATA3 expression, cells were induced with +/- DOX (1 ug/mL) for 24 hr.To determine the effect of AP-1 binding on chromatin accesibilty changes by WT GATA3, cells were transduced with lentivirus containing empty vector or AFOS (dominant negative AP-1 that inhibits binding) for 48 hrs prior to DOX induction for 24 hrs. To determine the effect of ATPase function by SWI/SNF on WT GATA3 dependent chromatin accesibility, cells were treated concurrently +/- DOX (1 ug/ml) and either DMSO (8 uL) or BRM014 (8 uM) for 24 hrs.

value: WT GATA3 (1-444aa)

value: DOX

value: DMSO (4ul)


title: retrospective, acute leukemia, AL_009

value: Bone Marrow

value: retrospective, acute leukemia


title: D-1090

description: Library name: D-1090


title: atac.wt.treatment_dmso_2ul.dox

value: DMSO (2ul)


title: Injury_1

city: Haikou

first: Yue

last: Hong

address: 58 Renmin Road

department: School of Life and Health Sciences

institute: Hainan University

description:
Library name: Injury-50
10X genomics

library_source: transcriptomic single cell

data_processing:
The reads were mapped onto the rabbit genome using a standard CellRanger pipeline. A raw unique molecular identifier (UMI) count matrix was generated after Cell Ranger processing, then the matrix was converted into a Seurat object by R package Seurat. Low-quality cells with UMI numbers <500, gene numbers <200, or mitochondrial genes > 15% were filtered and the rest of cells were retained for downstream analysis.
Assembly: mOryCun1.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Oryctolagus cuniculus

source_name: urothelium

growth_protocol: Normal samples were harvested from bladder mucosa under homeostasis.

extract_protocol:
A 2.0×2.0 cm area of mucosa was extracted from rabbit bladder, then finely cut into 1mm^3 pieces with blade and digested with dissociation buffer (Ham’s F12, 1 mg/ml collagenase Ⅱ (Gibco), 100 µg/ml Pen/Strep) for 1-2 hour at 37 °C with gentle rocking. Dissociated cells were washed thoroughly in cold wash buffer (Ham’s F12, 5% fetal bovine serum, 100 µg/ml Pen/Strep) before proceeding to scRNA preparation.
The single cell suspensions from normal and injured bladder tissues were procceded to scRNA-seq, according to instruction manual of the Chromium Single Cell 3’ Reagent Kits v3. Cellular suspensions were loaded on the Chromiu Controller (10x Genomics, Pleasanton) to generate Gel Bead-In-Emulsions (GEMs). Barcoded sequencing libraries were conducted following the instruction manual of the Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics). Following the library preparation, the sequencing was performed with paired-end sequencing of 150nt each end on one lane of NovaSeq 6000 per sample.

treatment_protocol: Injury samples were taken at Day 10 after the introduction of a focal mucosal resection, corresponding to a stage where the injured area was just completely covered by de novo urothelium.

value: urothelium

value: injury


title: Injury_2

description:
Library name: Injury-51
10X genomics


title: Normal_2

description:
Library name: Normal-55
10X genomics

value: normal


title: retrospective, acute leukemia, AL_008


title: retrospective, acute leukemia, AL_007


title: Normal_1

description:
Library name: Normal-54
10X genomics


title: D-1093

description: Library name: D-1093


title: atac.wt.treatment_dmso_05ul.dox

value: basal breast cancer line

value: DMSO (0.5ul)


title: HD68_TAK_H3K27ac

city: Montpellier

first: Denis

last: Tempé

address: 1919 route de Mende

country: France

institute: CNRS

description:
Library name: HD68_TAK_H3K27ac
PE100

data_processing:
Libraries were sequenced by 100 bp paired-end DNB-Seq sequencing (BGI)
Image analysis and base calling were performed by BGI.
Reads were processed using nf-core/cutandrun version 3.2.2 with Spike-in normalization. Preprocessing included FastQC quality control, TrimGalore for adapter trimming, and bowtie2 for alignment to the reference genome.
Peak calling was performed with MACS2 in narrow mode.
Consensus peak set was determined from peaks present in at least 2 samples among 4.
Differential enrichment was computed using DiffBind R package on consensus peak set with Spike-in normalization.
Assembly: hg38/GRCh38p12
Supplementary files format and content: bw.bed
Library strategy: CUT&RUN

source_name: blood

growth_protocol: PBMCs were purified from either buffy coat of healthy blood donors using density-based centrifugation method (Histopaque 1077- H8889 Sigma-Aldrich). Myeloid cells were purified from PMBCs using CD33+ microbeads (Miltenyi Biotech 130-045-501) according to manufacturer guidelines. The flow through, depleted from CD33+ cells, was then processed using negative selection NK cells isolation Kit (Miltenyi Biotech 130-092-657). Purified NK cells were cultured in RPMI medium + 10% fetal calf serum.

extract_protocol:
100,000 NK cells per sample were subjected to CUT&RUN protocol. DNA fragments were purified using Monarch PCR and DNA Cleanup Kit (T1030L).
Sequencing libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit (Illumina, catalog #E7645) with fragments amplification for 15 cycles and purification using cleanNGS beads (CleanNA, catalog #CNGS-0001). Libraries were quality-checked and quantified by capillary electrophoresis (Fragment Analyzer, NGS HS kit).

treatment_protocol: Purified NK cells were treated with TAK-981 (100 nM) for 6 h.

value: blood

value: natural killer

tag: chip antibody


title: D-1089

description: Library name: D-1089


title: HD68_NT_IgG

description:
Library name: HD68_NT_IgG
PE100

value: IgG

value: DMSO


title: atac.wt.treatment_dmso_1ul.dox

value: DMSO (1ul)


title: retrospective, acute leukemia, AL_003


title: atac.wt.treatment_dmso_8ul.dox

value: DMSO (8ul)


title: CG

city: Handan

first: Jia

last: Cui

address: 19 Taiji Road

institute: Hebei University of Engineering

description: Library name: Sample 1

data_processing:
ABI genome assembly
raw data for splice removal and removal of low quality sequences, The parameter is ~fastp -i sample.R1.fastq -I sample.R2.fastq -o out.R1.fastq -p sample.R2.fastq -q 20-l 100-n 10
The clean reads were mapped to the reference genome using HISAT2
Read count extraction and normalization were performed using ABI genome assembly
Assembly: NCBI_GCF_000003625.3_OryCun2.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: ovary

extract_protocol:
A total of 150 female IRA rabbits (35 days old) were randomly divided into three groups, and kept in environmental control rooms for four weeks. The rabbits in the control group (CG) were kept under an NH3 concentration of < 3 ppm. The two treatment groups were kept under NH3 concentrations of 10 ppm (low ammonia concentration, LAC) and 30 ppm (high ammonia concentration, HAC). The oocyte complexes cumulus of the ovarian were taken after slaughter and frozen in liquid nitrogen for examination.
Approximately 5ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero Gold rRNA Removal Kit (Illumina, cat.MRZG12324, San Diego, USA). After removing ribosomal RNAs, the left RNAs were fragmented (NEBNext® Magnesium RNA Fragmentation Module, cat.E6150S, USA) into short fragments using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H(NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection (300-600bp) was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min;8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec;and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000following the vendor's recommended protocol.

value: ovary

value: cumulus oocyte complex

value: NH3 concentration < 3 ppm


title: atac.wt.treatment_dmso_025ul.dox

value: WT GATA3 (1-444aa)

value: DOX

value: DMSO (0.25ul)


title: LAC

description: Library name: Sample 2

value: NH3 concentration = 10 ppm


title: HD68_NT_H3K27ac

description:
Library name: HD68_NT_H3K27ac
PE100


title: retrospective, acute leukemia, AL_004

value: Peripheral Blood

value: retrospective, acute leukemia


title: atac.wt.treatment_brm014_4uM.dox

value: basal breast cancer line


title: HD67_NT_H3K27ac

description:
Library name: HD67_NT_H3K27ac
PE100


title: atac.wt.treatment_brm014_2uM.dox


title: atac.wt.treatment_brm014_8uM.dox


title: HD67_TAK_H3K27ac

description:
Library name: HD67_TAK_H3K27ac
PE100


title: nspc_RNAi_2

description:
Illumina RNA Sequencing of C. elegans wild-type strain after RNAi silencing with nspc-7/14/20 vector, biological replicate 2
raw_counts_rnai.xlsx

molecule: polyA RNA

value: whole worm

value: wild type

value: N2 Bristol (CGC)

value: mix population

value: grown at 20℃ on NGM plates seeded with E. coli HT115 expressing nspc-7/14/20 RNAi vector


title: retrospective, acute leukemia, AL_005

value: Bone Marrow


title: HAC

description: Library name: Sample 3

value: NH3 concentration = 30 ppm


title: retrospective, acute leukemia, AL_001


title: nspc_RNAi_1

description:
Illumina RNA Sequencing of C. elegans wild-type strain after RNAi silencing with nspc-7/14/20 vector, biological replicate 1
raw_counts_rnai.xlsx


title: retrospective, acute leukemia, AL_002


title: LPP_Levia3_6mo

type: RNA

city: North Grafton

first: Jillian

last: Richmond

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

hyb_protocol: Hybridizations were performed per Nanostring manufacturer's protocol overnight for 18h in a BioRad C1000 touch thermocycler

scan_protocol: Cartridges were run on a Nanostring Sprint machine

data_processing:
Data were analyzed with nSolver software version 4.0
Counts

label: fluorescent probe

source_name: scalp biopsy

label_protocol: Probe labeling was performed per Nanostring manufacturer's protocol

extract_protocol: RNA was isolated from 30 micron curls from archival skin biopsies using Qiagen FFPE RNEasy kit with Deparaffinization solution per the manufacturer's instructions.

tag: disease status

value: LPP

value: Levia

tag: time


title: LPP_Levia3_baseline

value: baseline


title: atac.wt.treatment_brm014_05uM.dox

value: WT GATA3 (1-444aa)


title: WT_RNAi_3

description:
Illumina RNA Sequencing of C. elegans wild-type strain after RNAi silencing with empty vector, biological replicate 3
raw_counts_rnai.xlsx

value: grown at 20℃ on NGM plates seeded with E. coli HT115 expressing empty RNAi vector


title: WT_RNAi_2

description:
Illumina RNA Sequencing of C. elegans wild-type strain after RNAi silencing with empty vector, biological replicate 2
raw_counts_rnai.xlsx


title: atac.wt.treatment_brm014_025uM.dox

value: DOX


title: LPP_Theradome4_6mo

value: Theradome


title: NK_NT_rep4

description:
Library name: NT_4
PE100

data_processing:
Libraries were sequenced by 100 bp paired-end DNB-Seq sequencing (BGI)
Image analysis and base calling were performedby BGI.
Reads were processed using nf-core/atacseq v2.1.2 with default parameters. Preprocessing included FastQC quality control, TrimGalore for adapter trimming, and BWA for alignment to the reference Genome.
Assembly: hg38/GRCh38p12
Supplementary files format and content: bigWig

extract_protocol:
100,000 NK cells were washed once with ice cold PBS and lysed with cold lysis buffer (containing 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 (Sigma-I8896)). After lysis, Nuclei were harvested by centrifugation and DNA was digested with Tagment DNA Enzyme 1 (Illumina, 15027865) for 30 min at 37°C. Tagmented DNA fragments were purified using Monarch PCR and DNA Cleanup Kit (T1030L).
Tagmented DNA fragments were amplified for 11 cycles by PCR using Q5 High Fidelity DNA Polymerase (NEBNext Ultra II Q5 - M0544) and Ad1 and Ad2 primers.

value: blood

value: natural killer

value: DMSO


title: NK_NT_rep3

description:
Library name: NT_3
PE100


title: nspc_RNAi_3

description:
Illumina RNA Sequencing of C. elegans wild-type strain after RNAi silencing with nspc-7/14/20 vector, biological replicate 3
raw_counts_rnai.xlsx

value: whole worm


title: LPP_Theradome4_baseline


title: WT_RNAi_1

description:
Illumina RNA Sequencing of C. elegans wild-type strain after RNAi silencing with empty vector, biological replicate 1
raw_counts_rnai.xlsx

value: wild type


title: Monocyte, C1q, n2

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

data_processing:
ChIP sequencing data was aligned to human genome hg38 with BWA. Samtools was used to filter reads with a quality score lower than 20, and PCR duplicates were removed with Picard. Peaks were identified with MACS 2.2.6 in paired-end mode and ‘call-summits’ enabled at a false discovery rate of 0.01. A union of all identified peaks was generated with BEDTools, which was used to count reads per peak in each sample. Count matrix data was loaded to R programming language and differential H3K4me3 loci were identified by using R package edgeR. The confident H3K4me3 signals (Counts per million (CPM) > 1 in more than 2 samples) were used for downstream analysis and Trimmed Mean of M-values (TMM) normalization was performed. Then it was adjusted for differences between donors by an additive linear model with donor as the blocking factor and the dispersion was estimated. The differential H3K4me3 signals were identified by fitting negative binominal generalized linear models. The H3K4me3 signals with p value < 0.01 were subjected to gene ontology analysis. The annotation of H3K4me3 signals were performed with R packages ChIPSeeker and clusterProfiler.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

source_name: Monocytes

extract_protocol:
Monocytes were resuspended in RPMI culture medium and fixed using formaldehyde (1% final concentration, Sigma Aldrich) for 10 minutes at room temperature. Unreacted formaldehyde was quenched with 125 mM glycine and incubated for 5 minutes at room temperature. Cells were washed twice in PBS containing protease inhibitor cocktail (Roche) and 1 mM PMSF (Roche), and subsequently snap frozen in liquid nitrogen. Cell pellets were stored at -80°C for further use. Cells were sonicated at a concentration of 15 million cells/mL using a Bioruptor pico sonicator (Diagenode; 10-20 cycles, 30s on, 30s off), at 4°C. Immunoprecipitation was performed using the MagnaChIP kit (Merck Millipore) according to manufacturer’s instruction. In short, 500,000 cells were incubated overnight with 1 mg H3K4me3 (Diagenode) and protein A magnetic beads at 4°C. Beads and chromatin/antibody mixture were washed four times for 5 minutes at 4°C. After washing chromatin was eluted and proteins were degraded using proteinase K. DNA was purified using spin columns and eluted in millliQ.
ChIP-seq libraries were prepared using the Kapa Hyper Prep Kit according to manufacturer’s protocol, with the following modifications. 2.5 mL of the NEXTflex adaptor stock (600 nM, Bio Scientific) was used for adaptor ligation of each sample. Libraries were amplified with 12-15 PCR cycles followed by a double post-amplification clean-up used to ensure proper removal of adapters. Samples were analyzed for purity using a High Sensitivity DNA Chip on a Bioanalyzer 2100 system (Agilent). Libraries were paired-end sequenced to a read length of 50 bp on an Illumina NextSeq500.

value: Monocytes

value: H3K4me3 (Diagenode #pab-003-050)


title: Monocyte, RPMI, n2

value: RPMI control


title: SQ109 treated sample 3

city: Blacksburg

first: Ramu

last: Anandakrishnan

state: VA

address: 1410 Prices Fork Rd., Lab 101

department: Biomedical Sciences

institute: Edward Via College of Osteopathic Medici

description: Library name: B3

data_processing:
Perform alignments with HISAT2 to the reference.
Filtered and normalized gene expression levels were calculated from the aligned reads using HTSeq v.2.0.8
Differential gene expression was calculated by linear modeling and Bayesian statistics using the limma v.3.49.1
Assembly: C. neoformans var. grubii H99 GCF_000149245.1
Supplementary files format and content: Tab separated file containing gene expression counts by sample

organism: Cryptococcus neoformans H99

source_name: Fungal

extract_protocol:
Exponential C. neoformans H99 cells from YPD culture were pelleted, washed three times with saline, and adjusted to a final density of ~1 x106 CFU/mL in RPMI medium. Individual aliquots were treated with SQ109 (2 μg/mL) or DMSO (control) for 3 hrs at 35 °C under agitation. Treated yeast cells were collected, and RNA extraction was performed using RiboPureTM-Yeast Kit (Ambion, AM1926, MA, USA) following manufacture guidelines [61, 63]. The quality of RNA samples was validated using NanoDrop One spectrophotometer (Thermo Fisher Scientific, DE, USA).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library.

value: Fungal

value: SQ109 treated


title: nspc_daf-16_3

description:
Illumina RNA Sequencing of C. elegans nspc/daf-16 mutant strain at L4 stage, biological replicate 3
raw_counts_nspc_mutants.xlsx

value: nspc/daf-16 double mutant

value: ADZ131 (this study)

value: grown at 20℃ on NGM plates seeded with E. coli HB118


title: SQ109 treated sample 2

description: Library name: B2


title: Monocyte, C1q, n1


title: NK_TAK981_rep4

description:
Library name: TAK_4
PE100


title: LPP_Levia1_baseline

value: LPP

value: Levia

value: baseline


title: LPP_Levia1_6mo


title: atac.wt.treatment_brm014_1uM.dox

value: basal breast cancer line

value: WT GATA3 (1-444aa)

value: DOX


title: nspc_daf-16_2

description:
Illumina RNA Sequencing of C. elegans nspc/daf-16 mutant strain at L4 stage, biological replicate 2
raw_counts_nspc_mutants.xlsx

value: grown at 20℃ on NGM plates seeded with E. coli HB117


title: SQ109 treated sample 1

description: Library name: B1


title: Monocyte, RPMI, n1


title: LPP_Plaquenil5_6mo

value: Plaquenil


title: nspc_daf-16_1

description:
Illumina RNA Sequencing of C. elegans nspc/daf-16 mutant strain at L4 stage, biological replicate 1
raw_counts_nspc_mutants.xlsx

value: whole worm

value: grown at 20℃ on NGM plates seeded with E. coli HB116


title: Untreated sample 3

description: Library name: A3


title: NK_TAK981_rep3

description:
Library name: TAK_3
PE100

value: blood

value: natural killer


title: daf-16_3

description:
Illumina RNA Sequencing of C. elegans daf-16 mutant strain at L4 stage, biological replicate 3
raw_counts_nspc_mutants.xlsx

value: daf-16 mutant

value: daf-16(mu86) I (CGC)

value: grown at 20℃ on NGM plates seeded with E. coli HB115


title: LPP_Plaquenil5_baseline


title: Monocyte, C1q, n4

value: Monocytes

value: H3K4me3 (Diagenode #pab-003-050)


title: LPP_Plaquenil1_6mo

value: LPP


title: Untreated sample 2

description: Library name: A2

value: Fungal


title: Monocyte, RPMI, n4

value: RPMI control


title: daf-16_2

description:
Illumina RNA Sequencing of C. elegans daf-16 mutant strain at L4 stage, biological replicate 2
raw_counts_nspc_mutants.xlsx

value: grown at 20℃ on NGM plates seeded with E. coli HB114


title: Untreated sample 1

description: Library name: A1


title: LPP_Plaquenil1_baseline

value: baseline


title: Monocyte, C1q, n3


title: daf-16_1

description:
Illumina RNA Sequencing of C. elegans daf-16 mutant strain at L4 stage, biological replicate 1
raw_counts_nspc_mutants.xlsx

value: grown at 20℃ on NGM plates seeded with E. coli HB113


title: LPP_Theradome3_6mo

value: Theradome


title: Single cell RNAseq: Day 28

city: Milwaukee

first: Xiaolong

last: Ma

state: Wisconsin

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

description:
Library name: Sample 9
10x Genomics

data_processing:
Single cell RNAseq: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Bulk RNAseq: The aligment were done by STAR v2.7.11b, and transcripts count were done by FeatureCounts under Subread v2.0.8  package.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cell line

growth_protocol: Human iPS cultures were propagated in StemFit Basic03 medium (Ajinomoto, Tokyo, Japan) on 6-well plates coated with Laminin iMatrix-511 E8 fragment (0.5 μg/cm2; AMSBio) for a minimum of three passages before initiation of differentiation.

extract_protocol:
SEAM cultures at Day 0, 14 and 28 were lifted in 0.05% Trypsin-EDTA (Life Technologies) followed by gentle mechanical dissociation in Accumax (STEMCELL Technologies). Dissociated cells were filtered through a 70 μm mesh membrane (Miltenyi Biotec) to achieve a single cell suspension. Magnetically labelled apoptotic and dead cells were removed using a Dead Cell Removal kit (Miltenyi Biotec) and MACS separation column. Cell concentration and viability were determined using a CellDrop FL Automated Cell Counter (DeNovix) prior to proceeding with either the 10X Genomics single cell protocol or total RNA extraction.
Approximately 10,000 cells were used to generate a single cell library at each time point using the Chromium Next GEM Single Cell 3’ Reagent kit (v3.1, Dual Index; 10X Genomics), following the manufacturer’s protocol. Total RNA from two biological replicates from each time point were sent to Psomagen, Inc. (Rockville, MD) for library preparation and sequencing. Only samples with an RNA integrity number (RIN) ≥ 7 were considered for cDNA library preparation. cDNA libraries were generated using TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), which included an rRNA suppression step.

treatment_protocol: To induce differentiation of SEAM cultures, human iPS cells were seeded (350 cells/cm2) across LN511E8-coated (0.5 μg/cm2) 6-well plates and cultivated in StemFit Basic03 medium for 7 days prior to changing to differentiation medium. Differentiation medium consisted of GMEM (Life Technologies) supplemented with 10% knockout serum replacement (Life Technologies), 1 mM sodium pyruvate (Sigma), 0.1 mM non-essential amino acids (Life Technologies), 2 mM L-glutamine (Life Technologies), 1% penicillin-streptomycin solution (Life Technologies), and 55 μM 2-mercaptoethanol (Life Technologies). Differentiation medium was exchanged every other day. SEAM cultures were cultivated for 28 days under these differentiation conditions.

value: cell line

value: iPSCs [201B7]

value: Day 28

value: ATCC ACS-1023; KYOU-DXR0109B

value: female


title: nspc_tent-5_3

description:
Illumina RNA Sequencing of C. elegans nspc/tent-5 mutant strain at L4 stage, biological replicate 3
raw_counts_nspc_mutants.xlsx

value: whole worm

value: nspc/tent-5 double mutant

value: ADZ130 (this study)

value: grown at 20℃ on NGM plates seeded with E. coli HB112


title: Monocyte, RPMI, n3

value: Monocytes

value: H3K4me3 (Diagenode #pab-003-050)


title: Single cell RNAseq: Day 14

description:
Library name: Sample 8
10x Genomics

value: Day 14


title: LPP_Theradome3_baseline

value: LPP


title: nspc_tent-5_2

description:
Illumina RNA Sequencing of C. elegans nspc/tent-5 mutant strain at L4 stage, biological replicate 2
raw_counts_nspc_mutants.xlsx

value: grown at 20℃ on NGM plates seeded with E. coli HB111


title: Monocyte, C1q, RNA-seq, n3

data_processing:
RNA bulk sequencing was performed by Single Cell Discoveries (Utrecht, The Netherlands) with a sequencing depth of 20 million reads/sample. Library preparation was performed according to the CEL-seq2 protocol. Sequencing was performed on a Nextseq500 (Illumina).
Assembly: hg38
Supplementary files format and content: RNAseqcountsC1q text file includes raw files for each sample

extract_protocol:
RNA was isolated from 1*106 monocytes using RNeasy Mini kit (Qiagen) including DNAse I digestion according to manufacturer’s instructions.
RNA bulk sequencing was performed by Single Cell Discoveries (Utrecht, The Netherlands) with a sequencing depth of 20 million reads/sample. Library preparation was performed according to the CEL-seq2 protocol. Sequencing was performed on a Nextseq500 (Illumina).


title: nspc_tent-5_1

description:
Illumina RNA Sequencing of C. elegans nspc/tent-5 mutant strain at L4 stage, biological replicate 1
raw_counts_nspc_mutants.xlsx

value: grown at 20℃ on NGM plates seeded with E. coli HB110


title: Single cell RNAseq: Day 0

description:
Library name: Sample 7
10x Genomics

value: Day 0


title: LPP_Plaquenil2_6mo

value: Plaquenil


title: Bulk RNAseq: Day 28, biol rep 2

description:
Library name: Sample 6
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression
TRscSEAMD28R2

value: cell line


title: Monocyte, RPMI, RNA-seq, n3

value: RPMI control


title: tent-5_3

description:
Illumina RNA Sequencing of C. elegans tent-5 mutant strain at L4 stage, biological replicate 3
raw_counts_nspc_mutants.xlsx

value: tent-5 mutant

value: tent-5(tm3504) I (NBRP)

value: grown at 20℃ on NGM plates seeded with E. coli HB109


title: Bulk RNAseq: Day 28, biol rep 1

description:
Library name: Sample 5
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression
scSEAMD28

value: iPSCs [201B7]

value: Day 28

value: ATCC ACS-1023; KYOU-DXR0109B

value: female


title: Monocyte, C1q, RNA-seq, n2

value: Monocytes


title: LPP_Theradome1_6mo

value: Theradome


title: Monocyte, RPMI, RNA-seq, n2


title: tent-5_2

description:
Illumina RNA Sequencing of C. elegans tent-5 mutant strain at L4 stage, biological replicate 2
raw_counts_nspc_mutants.xlsx

value: whole worm

value: grown at 20℃ on NGM plates seeded with E. coli HB108


title: Bulk RNAseq: Day 14, biol rep 2

description:
Library name: Sample 4
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression
TRscSEAMD14R2

value: Day 14


title: Monocyte, C1q, RNA-seq, n1


title: LPP_Theradome1_baseline

value: LPP

value: baseline


title: tent-5_1

description:
Illumina RNA Sequencing of C. elegans tent-5 mutant strain at L4 stage, biological replicate 1
raw_counts_nspc_mutants.xlsx

value: grown at 20℃ on NGM plates seeded with E. coli HB107


title: Bulk RNAseq: Day 14, biol rep 1

description:
Library name: Sample 3
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression
scSEAMD14

value: cell line


title: LPP_Levia5_6mo

value: Levia


title: Monocyte, RPMI, RNA-seq, n1

value: RPMI control


title: Bulk RNAseq: Day 0, biol rep 2

description:
Library name: Sample 2
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression
TRscUNDIFFR2

value: Day 0


title: nspc_3

description:
Illumina RNA Sequencing of C. elegans nspc mutant strain at L4 stage, biological replicate 3
raw_counts_nspc_mutants.xlsx

value: nspc mutant

value: ADZ114 (this study)

value: grown at 20℃ on NGM plates seeded with E. coli HB106


title: LPP_Levia5_baseline


title: nspc_2

description:
Illumina RNA Sequencing of C. elegans nspc mutant strain at L4 stage, biological replicate 2
raw_counts_nspc_mutants.xlsx

value: grown at 20℃ on NGM plates seeded with E. coli HB105


title: Bulk RNAseq: Day 0, biol rep 1

description:
Library name: Sample 1
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression
scUNDIFF

value: iPSCs [201B7]

value: ATCC ACS-1023; KYOU-DXR0109B

value: female


title: nspc_1

description:
Illumina RNA Sequencing of C. elegans nspc mutant strain at L4 stage, biological replicate 1
raw_counts_nspc_mutants.xlsx

value: whole worm

value: grown at 20℃ on NGM plates seeded with E. coli HB104


title: MCF-7 Tamoxifen-resistant (TR) breast cancer cells condition medium treated rep 2

city: RENDE

first: INES

last: BARONE

state: Please select an option below

address: VIA P BUCCI

department: Pharmacy and Health and Nutritional Sciences

country: Italy

institute: UNIVERSITY OF CALABRIA

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-quality sequence by using cutadapt software (version 2.5).
The sample was mapped on reference Human (from GenCode (Release 37 - GRCh38.p13)) genome, using the bioinformatics tool STAR (version 2.7.5c), with the standard parameters for paired reads.
The quantification of transcripts expressed for each sequenced samples was performed using featureCount algorithm (version 2.0). Reads that had a sum read count less than 10 were excluded, in all samples used.
the DESeq2 algorithm was used to detected the differentially expressed genes.
Assembly: HG38-Gencode (Release 37 - GRCh38.p13)
Supplementary files format and content: Matrix table with raw counts for every sample
Supplementary files format and content: tab-delimited text files include normalized values (median of ratio of gene counts) for each Sample.

source_name: not applicable

growth_protocol: not applicable

extract_protocol:
Total RNA was extracted using the RNAeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: not applicable

value: not applicable

value: BREAST CANCER  EPITHELIAL CELLS

value: conditioned medium derived from 3T3L1 mature adipocytes


title: LPP_Levia6_baseline

value: LPP

value: baseline


title: MCF-7 Tamoxifen-resistant (TR) breast cancer cells condition medium treated rep 1


title: BT16 cells, IgG, TM, CUT&RUN

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

description:
IgG_TMNegcontr_6
PLX270348_assay_data.csv
PLX085833_assay_data.csv
PLX268514_assay_data.csv

data_processing:
FASTQ files were processed using the nf-core-cutandrun pipeline (v3.1).
Adapter sequences were removed with Trim Galore.
Reads were aligned with Bowtie2 to GRCh38 (NCBI, p.14, release 110) and duplicates were removed for only control samples using picard.
Peaks were called with macs27 (normalization mode: CPM), and were defined as regions where at least one of the target samples significantly exceeds its matched IgG control for a given genomic region.
Consensus peaks were merged across all samples using BEDTools and annotated to the nearest gene transcriptional start site using HOMER.
Peak counts were generated using featureCounts.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text files include raw consensus peaks for each Sample
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: ATRT

growth_protocol: BT16 ATRT cells were cultured in RPMI medium (Life Technologies, Gibco #11875-093) supplemented with 10% fetal bovine serum (FBS; Atlanta Biologicals, Inc. #S11550) and 1% penicillin/streptomycin (Life Technologies, Gibco #15140-122).  Cells were cultured at 37 °C with 95% air and 5% CO2.

extract_protocol:
CUTANA protocol (ChIC/CUT&RUN kit Version 3) was used for CUT&RUN assay. Cleavage under target and release using nuclease (CUT&RUN) beads were prepared using 10 ul/sample of CUTANA Concavalin A Conjugated Paramagnetic Beads (EpiCypher, SKU:21-1401). Beads were transferred to a 1.5 ml tube and placed in a magnetic separation rack, supernatant was removed, and beads were washed 2 times with 100 ul/sample of cold Bead Activation Buffer (20 mM HEPES pH7.9, 10 mM KCl 1 mM CaCl2, 1 mM MnCl2). Beads were then resuspended in 10 ul/sample of cold Bead Activation Buffer, and aliquot 10 ul/sample of activated bead slurry into 8-strip tube and kept on ice. BT16 ATRT cells were collected using 0.05% trypsin, washed with 100 ul/sample of Wash Buffer (20 mM HEPES pH7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmplete EDTA-free Protease Inhibitor (1187358001)) at room temperature, and centrifuged at 600 g for 3 min, for a total of two washes. Cells were resuspended in 100 ul/sample RT Wash Buffer, and then an aliquot of 100 ul washed cells was added to each 8-strip tube containing 10 ul of activated beads and mixed by pipetting. Cells were incubated with bead slurry for 10 min at RT. Tube strip was placed on a magnetic separation rack until slurry cleared and the supernatant was removed. 50 ul of cold Antibody Buffer was added to each sample and mixed by pipetting; 1ul of antibody IgG (Rabbit IgG Negative Control, EpiCypher, 13-0042 K), H3K4me3 (Positive Control, EpiCypher, 13-0041), H3K27Ac (Cell Signaling, #8173), H3K27me3 (Cell Signaling, #9733), was added to each sample, mixed and incubated on a nutator overnight at 4 °C. The tube was placed on a magnet until slurry cleared, and the supernatant was removed. While beads were on magnet, 250 ul of cold Digitonin Buffer was added directly onto beads of each sample and then pipetted to remove supernatant, for a total of 2 washes. 50 ul of cold Digitonin Buffer was added to each sample and mixed. 2.5ul of CUTANA pAG-MNase (20Xstock) was added to each sample, mixed, and incubated for 10 min at RT. Tube was placed on a magnet and supernatant was removed. The beads were washed 2 times with cold Digitonin Buffer. Supernatant was removed, and 50 ul of cold Digitonin Buffer was added to each sample and mixed. Tubes were placed on ice, and 1 ul of 100 mM CaCl2 was added to each sample and mixed, and then incubated on nutator 2 hrs at 4 °C. 33 ul/sample of Stop buffer containing 0.5 ng/sample of E. coli spike-in DNA, was added to the samples, mixed by pipetting, and incubated for 10 min at 37 °C in a thermocycler. Tubes were placed on a magnet stand until slurry cleared, and the supernatant was transferred to a 1.5 ml tube. Finally, the DNA was purified using CUTANA DNA Purification Kit (EpiCypher, 14-0050) according to the manufacturer instructions, and 1 ul of DNA was used for quantification by Qubit.
The NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #E7645S) with Dual Index Primers (NEB #E7600) were used to library preparation for ChIPseq and CUT&Run samples sequencing.   For the NEBNext end prep, 1x TE was added to the DNA to get final volume of 50 ul and mixed with 3ul of NEBNext Ultra II End Prep Enzyme Mix and 7ul of NEBNext Ultra II End Prep Reaction Buffer, placed in thermocycler with heated lid set to 75 °C and run the program 30 minutes at 20°C, 60 minutes at 50 °C and hold at 4 °C. The adaptor ligation reaction was performed with 60u l of Prep Reaction Mixture, 2.5ul of NEBNext Adaptor for Illumina diluted following the manufacture recommendations, 30 ul of NEBNext Ultra Ligation Master Mix and 1ul of NEBNext Ligation Enhancer, incubated at 20 °C for 15 min with heated lid off. 3 ul of USER Enzyme was added to the reaction and incubated at 37 °C for 15 min with heated led set to 47 °C. For the cleanup of the adaptor-ligated DNA without size selection, 1.1x of AMPure XP Beads were added to the Adaptor Ligation reaction and samples were incubated for 5min at room temperature. Tubes were placed on a magnetic stand to separate beads from supernatant, after 5 min, supernatant was removed, and beads were washed 2 times with 200ul of 80% freshy prepared ethanol. Beads were air dried for up 5 min while tubes were on magnet with lid open. DNA was eluted from the beads by adding 17 ul of 0.1XTE buffer.  For the PCR enrichment of adaptor-ligated DNA step, to 15 ul of the Adaptor Ligated DNA fragments was added 25ul of NEBNext Ultra Q5 Master Mix, 5 ul of Index primer i7 and 5ul Universal PCR Primer i5, and PCR amplification was performed following the cycling conditions: 98 °C for 45s, 98 °C 15s and 60 °C 10s for 16 cycles, 72 °C for 1 min and hold at 4 °C. Followed by a Clean Up of the PCR reaction using AMPure XP Beads.  The DNA was quantified using Qubit and the quality and size of libraries were checked with the Bioanalyzer and sent for sequencing at the Genomics Shared Resource (sequencing core) of CU Anschutz Medical Campus.

treatment_protocol: BT16 ATRTcells were treated with TM with dose 20uM for 24 hrs or with DMSO which was used for control.

value: ATRT

tag: cut&run antibody

value: IgG (EpiCypher, 13-0042 K)

value: TM


title: LPP_Plaquenil2_baseline

value: Plaquenil


title: BT16 cells, IgG, DMSO, CUT&RUN

description:
IgGDMSONegcontr_1
PLX270348_assay_data.csv
PLX085833_assay_data.csv
PLX268514_assay_data.csv

value: DMSO


title: WT_3

description:
Illumina RNA Sequencing of C. elegans wild-type strain at L4 stage, biological replicate 3
raw_counts_nspc_mutants.xlsx

value: wild type

value: N2 Bristol (CGC)

value: grown at 20℃ on NGM plates seeded with E. coli HB103


title: WT_2

description:
Illumina RNA Sequencing of C. elegans wild-type strain at L4 stage, biological replicate 2
raw_counts_nspc_mutants.xlsx

value: grown at 20℃ on NGM plates seeded with E. coli HB102


title: MCF-7 Tamoxifen-resistant (TR) breast cancer cells untreated rep 3

value: untreated


title: LPP_Levia2_6mo

value: Levia


title: WT_1

description:
Illumina RNA Sequencing of C. elegans wild-type strain at L4 stage, biological replicate 1
raw_counts_nspc_mutants.xlsx

value: whole worm

value: grown at 20℃ on NGM plates seeded with E. coli HB101


title: BT16 cells, H3K27ac, TM, CUT&RUN

description:
H3K27ac_TM_10
PLX268514_assay_data.csv

value: H3K27ac (Cell Signaling, #8173)


title: LPP_Levia2_baseline


title: active_exp3_3

description:
Illumina RNA Sequencing of C. elegans active miniSOG strain after illumination, third experiment, biological replicate 3
raw_counts_ablation.xlsx

value: nspc-10p::active miniSOG

value: ADZ83 (this study)

value: young adult

value: grown at 15℃ on NGM plates seeded with E. coli HB101 ; illuminated 5x10min with blue light at L3 stage


title: LPP_Theradome2_6mo

value: LPP

value: Theradome


title: BT16 cells, H3K27ac, DMSO, CUT&RUN

description:
H3K27ac_DMSO_5
PLX268514_assay_data.csv

value: ATRT


title: MCF-7 Tamoxifen-resistant (TR)  breast cancer cells untreated rep 2

value: not applicable

value: BREAST CANCER  EPITHELIAL CELLS


title: LPP_Theradome2_baseline

value: baseline


title: IPF119 siCBX5 TGF-beta

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression from fibroblasts from IPF patient 119, transfected with siCBX5 siRNA and grown in medium containing TGF-beta.

data_processing:
STAR (version 2.6.0c) was used to align sequence reads to human genome build hg38.
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 1.6.2) and Ensembl annotation build 100 (uniquely aligned proper pairs, same strand).
Variance-stabilizing-transformed (VST) expression values were computed using the DESeq2 R package (version 1.23.10).
Assembly: hg38
Supplementary files format and content: counts.txt: 60646 x 12 matrix of counts produced by Subread featureCounts
Supplementary files format and content: RPKM.txt: 60646 x 12 matrix of reads per kilobase per million reads (RPKM) expression values

source_name: fibroblast

growth_protocol: IPF-derived fibroblast cells were maintained in MEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol: Total RNA was isolated from IPF cells using the Quick-RNA Miniprep Kit (Zymo Research, Irvine, CA, USA).

treatment_protocol: IPF cells were cultured and transfected with scrambled control siRNA or siCBX5 for 48 hours followed by 24 hours of TGFβ treatment.

value: fibroblast

tag: patient

tag: sirna

value: TGF-beta


title: MCF-7 Tamoxifen-resistant (TR) breast cancer cells condition medium treated rep 3

tag: cell line

tag: cell type

value: conditioned medium derived from 3T3L1 mature adipocytes


title: BT16 cells, H3K27me3, TM, replicate 2, CUT&RUN

description:
H3K27me3cellsignab_TM_9
PLX085833_assay_data.csv

value: H3K27me3 (Cell Signaling, #9733)

tag: treatment

value: TM


title: LPP_Levia6_6mo

value: Levia


title: active_exp3_2

description:
Illumina RNA Sequencing of C. elegans active miniSOG strain after illumination, third experiment, biological replicate 2
raw_counts_ablation.xlsx

tag: tissue

value: whole worm

tag: genotype


title: LPP_Levia4_6mo


title: BT16 cells, H3K27me3, DMSO, replicate 2, CUT&RUN

description:
H3K27me3cellsignab_DMSO_4
PLX085833_assay_data.csv

value: DMSO


title: IPF108 siCBX5 TGF-beta

description: Gene expression from fibroblasts from IPF patient 108, transfected with siCBX5 siRNA and grown in medium containing TGF-beta.


title: LPP_Levia4_baseline


title: BT16 cells, H3K27me3, TM, replicate 1, CUT&RUN

description:
H3K27me3Epiab_TM_8
PLX085833_assay_data.csv


title: IPF114 siCBX5 TGF-beta

description: Gene expression from fibroblasts from IPF patient 114, transfected with siCBX5 siRNA and grown in medium containing TGF-beta.


title: active_exp3_1

description:
Illumina RNA Sequencing of C. elegans active miniSOG strain after illumination, third experiment, biological replicate 1
raw_counts_ablation.xlsx

value: nspc-10p::active miniSOG

value: ADZ83 (this study)


title: BT16 cells, H3K27me3, DMSO, replicate 1, CUT&RUN

description:
H3K27me3Epiab_DMSO_3
PLX085833_assay_data.csv


title: inactive_exp3_3

description:
Illumina RNA Sequencing of C. elegans inactive miniSOG strain after illumination, third experiment, biological replicate 3
raw_counts_ablation.xlsx

value: nspc-10p::inactive miniSOG

value: ADZ74 (this study)

value: young adult

value: grown at 15℃ on NGM plates seeded with E. coli HB101 ; illuminated 5x10min with blue light at L3 stage


title: IPF119 Scr TGF-beta

description: Gene expression from fibroblasts from IPF patient 119, transfected with scrambled siRNA and grown in medium containing TGF-beta.

value: scrambled


title: LPP_Plaquenil4_6mo

value: LPP

value: Plaquenil


title: inactive_exp3_2

description:
Illumina RNA Sequencing of C. elegans inactive miniSOG strain after illumination, third experiment, biological replicate 2
raw_counts_ablation.xlsx


title: BT16 cells, H3K4me3, TM, CUT&RUN

description:
H3K4me3_TMpositivecontr_7
PLX270348_assay_data.csv

value: ATRT

value: H3K4me3 (EpiCypher, 13-0041)


title: inactive_exp3_1

description:
Illumina RNA Sequencing of C. elegans inactive miniSOG strain after illumination, third experiment, biological replicate 1
raw_counts_ablation.xlsx


title: LPP_Plaquenil4_baseline

value: baseline


title: IPF114 Scr TGF-beta

description: Gene expression from fibroblasts from IPF patient 114, transfected with scrambled siRNA and grown in medium containing TGF-beta.

value: fibroblast

value: TGF-beta


title: MCF-7 Tamoxifen-resistant (TR) breast cancer cells untreated rep 1

value: not applicable

value: BREAST CANCER  EPITHELIAL CELLS

value: untreated


title: BT16 cells, H3K4me3, DMSO, CUT&RUN

description:
H3K4me3_DMSOpositivecontr_2
PLX270348_assay_data.csv

value: DMSO


title: In vitro, IR adipocyte exosome treated, biological replicate 1

first: Gerald

middle: V

last: Denis

address: 72 East Concord Street

description:
Library name: T_IR_1
invitro_rsem_expected_counts.tsv

data_processing:
Sequencing reads were processed using the nf-core rnaseq pipeline.
Reads were quality trimmed using Trimmomatic to remove adapters and low-quality bases.
Quality-checked reads were aligned to the mouse reference genome using STAR aligner.
Gene expression counts were generated using featureCounts based on the GRCm38/mm10 annotation.
Differential gene expression analysis was performed using DESeq2 to compare Control and Experimental groups.
Assembly: GRCm39/mm39 mouse reference genome.
Supplementary files format and content: Tab-delimited text files containing raw gene counts for each sample.
Supplementary files format and content: Tab-delimited text files containing normalized expression values for each sample.

source_name: In vitro

growth_protocol: Murine 4T1 cells as a TNBC model and murine 3T3-L1 pre-adipocytes to be differentiated into mature adipocytes were obtained from the American Type Culture Collection. The 4T1 cells and 3T3L1 cells were cultured in RPMI1640 and DMEM medium, respectively, supplemented with 10% fetal bovine serum (FBS), and 100 units/mL penicillin, 10 μg/mL streptomycin (Corning), and incubated at 37°C with 100% humidity and 5% CO2.

extract_protocol:
Total RNA was extracted from 4T1 cells treated with IS and IR adipocyte derived exosome using the RNeasy Plus Mini Kit (QIAGEN, Cat. No. 74136), following the manufacturer's protocol. Exosomal RNA was extracted from culture media using the exoRNA Easy Kit(Qiagen, Cat. No. 77144).  RNA integrity was assessed using an Agilent 2100 Bioanalyzer.
Libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep Kit, as per the manufacturer's protocol. Final libraries were checked for quality using an Agilent Bioanalyzer and quantified using a Qubit fluorometer.

treatment_protocol: 4T1 cells were treated with exosomes isolated from IS and IR adipocytes on Day 0 and cultured for 72 hours until 70% confluency was reached.

value: In vitro

value: Mammary adenocarcinoma cells

value: Insulin resistant adipocyte derived exosomes


title: LPP_Plaquenil3_6mo


title: WT_exp3_3

description:
Illumina RNA Sequencing of C. elegans wild-type strain after illumination, third experiment, biological replicate 3
raw_counts_ablation.xlsx

value: whole worm

value: wild type

value: N2 Bristol (CGC)

value: young adult


title: BT16 cells, TM, replicate 4, RNA-seq

data_processing:
FASTQ files were processed using the nf-core-rnaseq pipeline (v3.12.0) (auto strandedness).
Adapter sequences were removed withTrim Galore.
Reads were aligned with STAR to GRCh38 (NCBI, p.14, release 110) and quantified to gene counts using RSEM.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text files includes raw counts for each Sample

extract_protocol:
Ribonucleic acid was isolated from treated cells using a QIAGEN miRNAeasy kit Cat#217004 (Qiagen, Valencia, CA, USA). 500ng total RNA was used.
Libraries were prepared and sequenced by Genomics and Microarray Core Facility (University of Colorado Denver). Universal Plus™ mRNA-Seq library kit with NuQuant (Tecan) was used. Libraries were sequenced on an Illumina NovaSEQ X. High-quality base calls at Q30R ≥80% were obtained with 40M paired end reads.

treatment_protocol: BT16 ATRTcells were treated with TM with dose 30um for 72 hrs or with DMSO which was used for control.

value: TM

tag: condition

value: Treated


title: IPF119 siCBX5 control

description: Gene expression from fibroblasts from IPF patient 119, transfected with siCBX5 siRNA and grown in control medium.

value: control


title: LPP_Plaquenil3_baseline

value: LPP

value: Plaquenil

value: baseline


title: WT_exp3_2

description:
Illumina RNA Sequencing of C. elegans wild-type strain after illumination, third experiment, biological replicate 2
raw_counts_ablation.xlsx

value: grown at 15℃ on NGM plates seeded with E. coli HB101 ; illuminated 5x10min with blue light at L3 stage


title: BT16 cells, TM, replicate 3, RNA-seq

value: ATRT


title: IPF114 siCBX5 control

description: Gene expression from fibroblasts from IPF patient 114, transfected with siCBX5 siRNA and grown in control medium.

value: fibroblast


title: WT_exp3_1

description:
Illumina RNA Sequencing of C. elegans wild-type strain after illumination, third experiment, biological replicate 1
raw_counts_ablation.xlsx


title: BT16 cells, TM, replicate 2, RNA-seq


title: IPF108 siCBX5 control

description: Gene expression from fibroblasts from IPF patient 108, transfected with siCBX5 siRNA and grown in control medium.


title: IFE-1 CLIP Replicate 2 (input)

city: Indianapolis

first: Scott

middle: T

last: Aoki

state: Indiana

address: 635 Barnhill Drive MS-4071

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

description: Library name: IFE-1 Rep-2 Input

data_processing:
Fastq raw sequencing files were assessed for quality and filtered to remove adapters by fastp (v0.21.0). Barcodes were subsequently removed and reads deduplicated. Paired reads were merged with Ngmerge (v0.03). Processed reads were mapped to the C. elegans genome using STAR (v2.7.10b). Custom perl scripts were used to identify RNA start sites and read coverage. Targets were identified using the CLIPPER software package.
Assembly: WBcel235
Supplementary files format and content: bam
Supplementary files format and content: bigwig

source_name: Whole organism

growth_protocol: Large synchronized populations of IFE-1::3xFLAG worms were generated by standard bleaching protocol and allowed to develop for 72 hours on NGM plates seeded with HB101 bacteria as a food source.

extract_protocol:
Homogenized samples were treated with 250 U of RNase I (Ambion) at 37°C for 10 minutes with constant shaking at 1200 rpm prior to immunoprecipitation. Briefly, upon RNase I digestion, 2% of 5 mg worm lysate was taken as inputs and the rest of the lysate was incubated with 100 µl of anti-FLAG magnetic beads (Sigma) with a final concentration of 1:5 dilution of wash buffer (20 mM Tris-HCl (pH 7.5), 10 mM MgCl2, 5 mM NaCl, 0.2% Tween-20) for 1 hour. IP samples were washed once with high-salt wash buffer (50 mM Tris-HCl (pH 7.5), 1 M NaCl, 1 mM EDTA, 0.1% SDS, 1% NP-40) and washed twice with the wash buffer. T4 PNK Minus reaction was performed on bead using T4 PNK Minus (NEB) at 37°C for 20 minutes with constant shaking at 1200 rpm, followed by 1x wash with high-salt wash buffer and 3x wash with wash buffer. IP samples were subjected to Fast AP (Thermo Scientific) reaction at 37°C for 10 minutes with constant shaking at 1200 rpm and PNK reaction with T4 PNK (NEB) at 37°C for 20 minutes with constant shaking at 1200 rpm without removing the FastAP reaction mixture. IP samples were washed 1x with high-salt wash buffer and 3x with wash buffer. 3’ RNA adapter (CLASHInvRiL19) was ligated on bead using T4 RNA ligase (high-concentration, NEB) at RT for 75 minutes on a rotator. IP samples were washed 1x with wash buffer, 1x with high-salt wash buffer, and 2x with wash buffer. All input and IP samples were denatured using 4xNuPAGE™ sample buffer (Invitrogen) at 65°C for 10 minutes and resolved in NuPAGE™ 4-12% Bis-Tris gel (Invitrogen) at 150 V for 75 minutes, followed by transfer to nitrocellulose membrane at 30 V for overnight. After confirming the position of IFE-1 protein by western blot using FLAG antibody (Sigma), regions above IFE-1 protein (up to ~250 kDa) were excised for proteinase K (NEB) treatment at 37°C for 40 minutes with constant shaking at 1200 rpm. RNA was isolated from proteinase K treatment reaction using Zymo RNA clean & concentrator kit (Zymo Research). Upon RNA isolation, input samples were also treated with FastAP (Thermo Scientific) for 10 minutes and T4 PNK (NEB) for 20 minutes, both at 37°C with constant shaking at 1200 rpm, followed by clean up using Zymo RNA clean & concentrator kit (Zymo Research).
3’ RNA adapter (CLASHInvRiL19) was ligated to input samples after incubation at 65°C for 2 minutes using T4 RNA ligase (high-concentration, NEB) at RT for 60 minutes with flicking every 15 minutes. Input samples were cleaned up using MyONE Silane beads (Invitrogen). Reverse transcription was performed for both IP and input samples after incubation at 65°C for 2 minutes using an RT primer (InvAR17) and then at 55°C for 20 minutes using Superscript IV (Invitrogen). The reaction was cleaned up using ExoSAP-IT (Applied Biosystems) and MyONE Silane beads (Invitrogen). Then, 5’ DNA adapter (Invrand10_3Tr3) was ligated after incubation at 70°C for 2 minutes and then at RT for overnight using T4 RNA ligase (high-concentration, NEB) and 5’ deadenylase (NEB). Samples were cleaned up using MyONE Silane beads (Invitrogen) and PCR amplified for 8 cycles (Input) and 13 cycles (IP) using Q5 High-Fidelity PCR master mix (NEB) and PCR forward and reverse primers with specific barcodes. Libraries were purified using Ampure XP beads (Beckman Coulter) and quantified using the D1000 high sensitivity screen tape system (Agilent, La Jolla, CA) before pooling. The pooled library was sequenced on NextSeq2000 (Illumina, San Diego, CA) at the center of bioinformatics and genomics (CGB) at Indiana University, Bloomington using paired-end sequencing.

treatment_protocol: Synchronized adults were washed four times in PBS buffer and then exposed to 25 mJ/cm2 UV radiation on 10-cm NGM plates, washed into 15-ml conical tubes, and spun down. Irradiated worms were slowly dripped into a prechilled mortar filled with liquid nitrogen, forming small frozen spheres. Frozen worm spheres were vigorously grinded for 5 minutes using a pre-chilled mortar and pestle. Liquid nitrogen was added periodically to keep samples frozen. Ground samples were collected and stored at -80°C until use.

value: Whole organism


title: active_exp2_3

description:
Illumina RNA Sequencing of C. elegans active miniSOG strain after illumination, second experiment, biological replicate 3
raw_counts_ablation.xlsx

data_processing:
Illumina RNA-seq were performed in external companies. FastQ files were then mapped to WBCel235 reference genome using STAR aligner (v2.7.10a) and processed with samtools (v1.961). Read counts were obtained with featureCounts from the Subread package (v2.0.665, using options -Q 10 -p -C -B). Differential expression analysis was conducted using DESeq2 Bioconductor package (v1.28) with default settings.
Nanopore Direct RNA Sequencing was performed with the MinION device, followed by basecalling with Guppy 6.0.0 (ONT), mapping to WBCel235 reference (MiniMap v2.17 (25) with options -k 14 -ax map-ont –secondary = no), and processing with samtools v1.9. Lengths of poly(A) tails were estimated with Nanopolish (v0.13.2).
Assembly: WBcel235
Supplementary files format and content: Excel files with raw number of counts for Illumina RNA sequencing and poly(A) tails statistics for Nanopore direct RNA sequencing

extract_protocol:
Populations of worms were collected and washed three times with 50 mM NaCl. Worm pellets were resuspended in 1 ml TRI Reagent (Sigma-Aldrich), vortexed for 15 minutes at room temperature, and stored at -80°C until further processing. RNA extraction was performed according to the manufacturer’s protocol for TRIzol-based isolation, with additional purification using KAPA Pure magnetic beads (RNA to beads ratio: 1:3 v/v). RNA quality and integrity were confirmed using the Agilent TapeStation system.
Total RNA samples for Illumina RNA sequencing were sent to Center for New Technology (Poland) or Genewiz (Germany) and libraries were prepared with the use of internal protocols. Sequencing libraries for Nanopore direct RNA sequencing were prepared using the DRS Kit (Oxford Nanopore Technologies, SQK- RNA002) according to the manufacturer’s protocol. In each library, total RNA isolated from worms (1,5 - 2 μg depending on the amount of isolated RNA) was mixed with 2 ng of in vitro transcribed poly(A) standards.

value: nspc-10p::active miniSOG

value: ADZ83 (this study)


title: IFE-1 CLIP Replicate 1 (input)

description: Library name: IFE-1 Rep 1 Input


title: BT16 cells, TM, replicate 1, RNA-seq


title: IPF119 Scr control

description: Gene expression from fibroblasts from IPF patient 119, transfected with scrambled siRNA and grown in control medium.

value: scrambled


title: active_exp2_2

description:
Illumina RNA Sequencing of C. elegans active miniSOG strain after illumination, second experiment, biological replicate 2
raw_counts_ablation.xlsx

value: whole worm


title: IPF114 Scr control

description: Gene expression from fibroblasts from IPF patient 114, transfected with scrambled siRNA and grown in control medium.


title: active_exp2_1

description:
Illumina RNA Sequencing of C. elegans active miniSOG strain after illumination, second experiment, biological replicate 1
raw_counts_ablation.xlsx


title: BT16 cells, DMSO, replicate 4, RNA-seq

value: DMSO

value: Vehicle


title: IFE-1 CLIP Replicate 1 (CLIP)

description: Library name: IFE-1 Rep 1 CLIP


title: IPF108 Scr control

description: Gene expression from fibroblasts from IPF patient 108, transfected with scrambled siRNA and grown in control medium.


title: IPF108 Scr TGF-beta

description: Gene expression from fibroblasts from IPF patient 108, transfected with scrambled siRNA and grown in medium containing TGF-beta.

value: TGF-beta


title: Mouse_p53WT_untreated_2

description: Library name: Sample 12

data_processing:
Raw sequencing reads were aligned to Mus musculus GRCm39 genome assemblies using STAR (version 2.7.3a, GCC 6.4.0-2.28) with default setting.
Following alignment, raw read counts were generated using HTSeq (version 0.12.3, foss-2018b, Python-3.6.6). The corresponding gene annotation files used in HTSeq were Mus_musculus.GRCm39.103.chr.gtf for mouse samples.
Differentially expressed genes (DEGs) were identified using DESeq2 (version 1.42.1) in R (version 4.3.3).
Normalized counts were obtained using RSEM (version 1.3.3)
Assembly: mm39 (Mus_musculus.GRCm39)
Supplementary files format and content: tab-delimited text file includes TPM values for each samples

source_name: E9.5 embryos

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit (QIAGEN, #74134) according to the manufacturer’s instructions. ~500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were generated using the Illumina RNA kit with PolyA selection, followed by sequencing on the Illumina HiSeq platform, producing 2 × 75 bp paired-end reads. Sequencing was conducted by the UAB Heflin Center for Genomic Core.

treatment_protocol: Pregnant mice carrying E9.5-stage embryos were placed at the closest position to the ionizing radiation source in an X-RAD 320 X-ray irradiator, exposing the embryos to 5 Gy/min of radiation for a total dose of 30 Gy.

value: E9.5 embryos

value: w/o ionizing radiation-irradiation


title: BT16 cells, DMSO, replicate 2, RNA-seq


title: inactive_exp2_3

description:
Illumina RNA Sequencing of C. elegans inactive miniSOG strain after illumination, second experiment, biological replicate 3
raw_counts_ablation.xlsx

value: nspc-10p::inactive miniSOG

value: ADZ74 (this study)

value: young adult


title: BT16 cells, DMSO, replicate 3, RNA-seq


title: Rubi g9242 knockout repeat 3

city: hangzhou

first: Chao

last: Liu

state: 浙江

address: 浙江省

institute: 浙江大学

description: Rubi g9242 knockout repeat 3

data_processing:
Trimmomatic v0.39   STAR v2.7.6a  featureCounts v1.6.0
Assembly: N.rubi.CDS, N.rubi.gff3
Supplementary files format and content: reads counts

organism: Nigrospora rubi

source_name: hyphae

growth_protocol: PDA growth

extract_protocol:
Flash-freeze fungal tissue in liquid nitrogen and homogenize. Mix with lysis buffer containing RNase inhibitors. Add chaotropic salt, vortex, and perform phenol-chloroform extraction. Centrifuge, collect the aqueous phase, and precipitate RNA with alcohol. Wash the pellet, air-dry, dissolve in RNase-free water, and verify RNA quality.
Start fungal library construction with high-quality RNA extraction and genomic DNA removal. Convert RNA to cDNA using reverse transcription, then fragment the cDNA for sequencing. Attach adapters to the fragments, amplify via PCR, and quantify the library with a bioanalyzer before sequencing.

treatment_protocol: To ascertain which genes were influenced in deletion mutants, we newly generated transcriptome data for deletion mutant vs control for each of three convergent genes (ΔNrURED, ΔNrGMF1, and ΔNrGLA) in N. rubi

value: hyphae

value: g9242 knockout


title: Rubi g9242 knockout repeat 2

description: Rubi g9242 knockout repeat 2


title: inactive_exp2_2

description:
Illumina RNA Sequencing of C. elegans inactive miniSOG strain after illumination, second experiment, biological replicate 2
raw_counts_ablation.xlsx

value: grown at 15℃ on NGM plates seeded with E. coli HB101 ; illuminated 5x10min with blue light at L3 stage