title: PD fluid3

description: PD fluid_3

value: Peritoneal tissue

value: Endothelial

value: WT


title: D3 T3M4-sgTP63-187e7-rep2

status: Public on Dec 06 2023

type: SRA

city: Cold Spring Harbor

first: Diogo

last: Maia e Silva

state: NY

address: 1 Bungtown Road

country: USA

institute: Cold Spring Harbor Laboratory

library_source: transcriptomic

data_processing:
For RNA-seq, sequencing reads were mapped onto reference human genome hg38 using STAR v2.7.9a with default settings. HTSeq-counts was used to generate raw gene counts, and DESeq2 was then used to perform differential expression analysis.
For ChIP-Seq, reads were mapped to hg38 with bowtie2 2.4.2 with very-sensitive setting. Bam files are then sorted with Samtools 1.11 with default settings, and used to call peaks with MACS2. Bedtools 2.30.0 was used to intersect and merge peaks
Deeptools v3.5.0 was used to generate BigWig files that were then visualized in the UCSC genome browser with the hg38 genome. HOMER v4.11 was used to assign the closest annotated ORFs to each peak and for motif discovery.
For CRISPR amplicon sequencing, raw reads were aligned to each sgRNA library to generate count files with MAGeCK.
For scRNA-seq experiments, data was genetically demultiplexed using cellsnp-lite 1.2.3 and Vireo 0.5.8, aligned to the human genome and assigned to cells using Cell Ranger 7.1.0, and downstream analyzed using Seurat 4.3.0.1.
Assembly: hg38
Supplementary files format and content: Htseq-count matrix for RNA-Seq. H5 Seurat files for scRNA-seq. Bigwig files for ChIP-Seq. Mageck count files for CRISPR libraries.

molecule: total RNA

organism: Homo sapiens

growth_protocol: Human cancer cell lines were cultured according to vendor recommendations in RPMI or DMEM 10% FBS supplemented with pen-strep.

extract_protocol:
For RNA-seq experiments, total RNA was isolated using TRIzol (Thermo Fisher, 15596026) according to the manufacturer’s instructions. For scRNA-seq experiments, cells were single cell captured and barcoded using the 10X Chromium chemistry. For ChIP-seq experiments, lysates were clarified from crosslinked, sonicated nuclei and protein-DNA complexes were immunoprecipitated with specific antibodies. For CRISPR libraries, genomic DNA was isolated using phenol-chloroform extraction and directly used for library preparation.
RNA-seq and ChIP-seq ibraries were constructed using  Illumina TruSeq RNA library prep kit v2 (Illumina, RS-122-2001) or  Illumina TruSeq ChIP library prep kit (Illumina, IP-202-1012) based on the manufacturer’s instructions. scRNA-seq libraries were biult using 10X Genomics NextGEM Single-Cell 3' Library Kit. CRISPR libraries were prepared using sgRNA flanking primers described in the article and 1 step PCR amplification.

tag: cell type

value: human pancreatic cancer cell line

tag: cell line

tag: genotype

tag: time


title: NCI-H1975_siFRA1_DMSO_rep1

city: Zurich

first: Michael

last: Hottiger

address: Winterthurerstrasse 190

department: DMMD

country: Switzerland

institute: University of Zurich

data_processing:
For the analysis, demultiplexing was performed using the Illumina bcl2fastq Conversion Software. Individual library sizes ranged from 22.5 million to 39.2 million reads. RNA sequencing analysis was performed using the SUSHI framewor, encompassing the following steps: Read quality was inspected using FastQC, and sequencing adaptors were removed using fastp; Alignment of the RNA-Seq reads using the STAR aligner and with the GENCODE human genome build GRCh38.p13 (Release 37) as the referenc; the counting of gene-level expression values using the ‘featureCounts’ function of the R package Rsubread; differential expression using the generalized linear model as implemented by the DESeq2 Bioconductor R package, and; GO term pathway analysis using both the hypergeometric over-representation test via the ‘enricher’ function and gene-set enrichment analysis via the ‘GSEA’ function, of the clusterProfiler Bioconductor R package. For the GSEA-based pathway analysis, we included a gene set from the MSigDB Hallmark, KEGG, and Wiki pathways. All R functions were executed on R version 4.1.2 (R Core Team, 2020) and Bioconductor version 3.14
Assembly: GRCh38.p13 (Release 37)
Supplementary files format and content: DESeq2 computed mean of normalized count of all samples based on sequencing depth

source_name: lung

growth_protocol: NCI-H1975 cells were grown in complete DMEM medium supplemented with 10% FCS and 1% P/S. 2x10^5 cells were seeded into 6-well plates.

extract_protocol:
Total RNA was extracted from quadruplicate experiments using the RNAeasy Plus Mini Kit (Qiagen) according to the manufactures protocol.
The quality of the isolated RNA was determined with a Fragment Analyzer (Agilent). The TruSeq Stranded mRNA kit (Illumina) was used in the succeeding steps. Briefly, total RNA samples (100-1000ng) were poly-A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired, and adenylated before the ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using the Fragment Analyzer (Agilent). The product is a smear with an average fragment size of approximately 260bp. The libraries were normalized to 10nM in Tris-Cl 10 mM pH=8.5 with 0.1% Tween20. According to standard protocol, the Novaseq 6000 (Illumina) was used for cluster generation and sequencing. The sequencing configuration was single-end 100bp.

treatment_protocol: NCI-H1975 cells were reverse transfected with the control siRNA (siSCR, 10uM) or a siRNA targeting FRA1 (10uM) using RNAiMAX (Thermo Fisher). To avoid cytotoxicity, the medium was exchange 12h following the transfection. 42h after the transfection DMSO or RBN-2397 (100uM) were added to the respective samples for 6h.

tag: tissue

value: lung

value: non-small cell lung cancer

value: FRA1 knockdown

tag: treatment

value: siFRA1 48h,DMSO 6h


title: D3 T3M4-sgTP63-51e1-rep2


title: C1

city: Guangzhou

first: Huiyun

last: Ye

address: 1838 North Guangzhou Ave

country: China

institute: Southern Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

organism: Mus musculus

source_name: kidney

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

value: control

tag: strain

value: PCOS mouse

tag: strain background


title: T3

value: DHT


title: NCI-H1975_siSCR_RBN-2397_rep4

value: SCR transfection

value: siSCR 48h,RBN-2397 6h


title: C3


title: T2


title: NCI-H1975_siFRA1_DMSO_rep2


title: 3KO 2h post sporulation induction, replicate 2

city: Warsaw

first: Agata

middle: L.

last: Starosta

address: Pawińskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

description:
3KO2r_2
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx

library_source: other

data_processing:
FastQC reports were utilized to assess raw data quality.
Following this step, the removal of adapters and low-quality sequences was performed using TrimGalore! software
The Bowtie tool was employed to eliminate sequences corresponding to tRNA and rRNA using genome reference data.
For RIBO-seq data, filtering was applied, retaining only sequences between 15-32 nucleotides in length.
After preprocessing, the FastQC tool was used for quality control.
Length distribution plots were created to analyze the read length distribution of the RIBO-seq data.
The clean and trimmed data was mapped to the genome using STAR, with a tolerance of up to 4% mismatch in read length and exclusion of splicing. The resulting BAM files were sorted and indexed using the sambamba software. Unique mapped reads were counted using featureCounts, employing gene and UTR annotations from the BSGatlas database, with a minimum overlap of 4 nucleotides.
Subsequently, the normalization of read counts was carried out using the Transcripts Per Million (TPM) method for CDS, UTR, and combined data.
Differential gene expression analysis was carried out on RNA-seq and RIBO-seq data using the DEBrowser tool and the DESeq2 library.
Assembly: NC_000964.3
Supplementary files format and content: XLSX files include raw counts for each sample (CDS and UTRs)
Supplementary files format and content: XLSX files include raw counts for each sample (CDS only)
Supplementary files format and content: XLSX files include TPM values for each sample (CDS and UTRs)
Supplementary files format and content: XLSX files include TPM values for each sample (CDS only)
Supplementary files format and content: XLSX file includes differential expression results between 3KO and WT for each time-point
Library strategy: RIBO-seq

molecule: other

organism: Bacillus subtilis

source_name: strain 168

growth_protocol: The B. subtilis 168 strain served as the wild type, and other strains were derived from it. The strains were cultured overnight in LB medium at 30 °C with shaking, then diluted to OD600=0.1 in CH medium. They were grown until OD600 reached 0.5 – 0.6 at 37 °C with shaking. Sporulation was induced by changing the medium to sporulation medium, following the method by Sterlini and Mandelstam (1968), with the modification that cells were harvested by filtration. Filters were then transferred into the culture flasks, and the sporulation medium was supplemented with 3% v/v of the culture in the CH medium at OD600=0.5-0.6 to promote sporulation.

extract_protocol:
RNA was isolated from sporulating WT and 3KO strains. Cultures were harvested hourly for seven hours into sporulation, beginning at T0 (prior to sporulation induction), resulting in a total of eight timepoints. Before harvesting, cultures were treated with 0.3 mM chloramphenicol. Cells were collected by filtration and flash frozen in liquid nitrogen. Purification of mRNA, ribosomal footprint isolation and library preparation was performed as described earlier. Briefly, frozen pellets were ground using mortar and pestle with the addition of aluminum oxide and lysis buffer. The extracted total RNA was used for purification of mRNA and ribosomal footprint isolation. rRNA depletion was performed to yield mRNA which was then fragmented by alkaline hydrolysis. Ribosomal footprint isolation was performed by MNase digestion of the total RNA followed by size selection using polyacrylamide gel electrophoresis.
The obtained mRNA fragments and ribosomal footprints were end-repaired (dephosphorylation of 3'ends followed by phosphorylation of 5' ends) and used for preparation of cDNA sequencing libraries with NEBNext Multiplex Small RNA Library Prep Set for Illumina, according to the manufacturer's guidelines. Sequencing was performed on an Illumina NextSeq500 by Genomed S.A. (Warsaw, Poland) and Genome Facility at CeNT (Warsaw, Poland); single-end 50bp reads were sequenced.

value: strain 168

tag: library type

value: RIBO-seq

value: bacterial cells


title: D3 T3M4-sgTP63-187e7-rep1


title: NCI-H1975_siFRA1_DMSO_rep4


title: 3KO 3h post sporulation induction, replicate 2

description:
3KO3r_2
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: 3KO 1h post sporulation induction, replicate 1

description:
3KO1r_1
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: NCI-H1975_siSCR_RBN-2397_rep3


title: D3 T3M4-sgTP63-187e4-rep3


title: Traf6cko_CD8_TILs_Rep2

city: Wuhan

first: shuan

last: ran

state: Hubei

address: Jiefang Road 1277

department: Department of Cardiovascular Surgery

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

data_processing:
Clean reads were mapped to the mm10 (UCSC) mouse genome with  subjunc (subread v2.0.1) with default parameters.
Transcripts were assembled Expression quantitation using featureCounts (subread v2.0.1) with mouse annotation (release_M20) from Gencode
Differential gene expression was calculated using the DESeq2 package (v1.30.1) package of the R (version 4.0.4) software
Assembly: mm10
Supplementary files format and content: Comma-Separated Row counts for each sample

source_name: CD8+ T Cell

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
DNase I was used to digest double-stranded and single-stranded DNA in total RNA, then, magnetic beads were purified to recover the reaction products, RNase H or Ribo-Zero method (human, mouse, plants) (Illumina, USA) was used to remove the rRNA. Purified mRNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand Reaction System by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to carry out end repair. The cDNA fragments with adapters were amplyfied by PCR, and the products were purified by Ampure XP Beads. Library was validating on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products above were heated denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on NovaSeq 6000 platform .

value: CD8+ T Cell


title: D3 T3M4-sgTP63-187e4-rep2


title: 3KO 1h post sporulation induction, replicate 2

description:
3KO1r_2
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: 3KO 0h, prior to sporulation induction, replicate 2

description:
3KO0r_2
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: D3 T3M4-sgTP63-51e1-rep1


title: T1


title: NCI-H1975_siSCR_RBN-2397_rep2


title: D3 T3M4-sgRPA3-1e2-rep2


title: WT_CD8_TILs_Rep1


title: 1616_Spleen

city: Milwaukee

last: Pisano

state: Wisconsin

address: 8701 W Watertown Plank Rd MFRC 6033

department: Medicine

institute: Medical College of Wisconsin

data_processing:
Adapters were trimmed using TrimGalore v0.4.0
Trimmed reads were mapped to Gencode Fasta transcriptome GRCm39
Counts were imported into R using tximeta, with differential expression performed using DESeq2
Assembly: Gencode GRCm39
Supplementary files format and content: Transcripts per million (TPM) table for all samples in csv format

source_name: Spleen

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen, 74106)
TruSeq Stranded Total RNA

treatment_protocol: After isolation from tissue activated B cells were activated with 1ug/ml LPS for 16hrs

value: Spleen

value: Malignant Plasma Cell


title: NCI-H1975_siSCR_RBN-2397_rep1


title: D3 T3M4-sgROSA26-rep3

value: human pancreatic cancer cell line


title: KARR-seq K562 siYBX3 G1 Rep 2

city: Farmington

first: Youzhi

last: Cheng

state: Connecticut

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

data_processing:
KARR-seq: For paired end FASTQ formatted files, SeqPrep (commit: 575507b) was first used to merge overlapping read pairs (2 x 150 bp) into single end reads. Unmerged read pairs were discarded. The resulting single end results were then aligned to mm10, hg19 or dm3 reference genome using STAR (v2.5.2a) as well as the species' corresponding RefSeq transcripts. The pre-merging step was skipped for single-end FASTQ files, and directly aligned using STAR. The following STAR parameters were used to recover gapped and chimeric reads (--runMode alignReads --outFilterMultimapNmax 100 --outSAMattributes all --alignIntronMin 1 --scoreGapNoncan -4 --scoreGapATAC -4 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --limitOutSJcollapsed 10000000 --limitIObufferSize 1500000000). Only chimeric reads (CIGAR N gap between mapped segments of the read) were kept, spliced sites filtered and interaction pairs tabulated. Pairix was used to index the interaction pairs file.
Assembly: mm10,hg19,dm3
Supplementary files format and content: Processed files are bgzipped text files that follows the 4DN-standard pairs file format (pairix)
Library strategy: KARR-seq

source_name: human bone marrow cells

growth_protocol: HEK293T and HepG2 cells were cultured in DMEM (Gibco 11995) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco) at 37 ˚C with 5% CO2.

extract_protocol:
Resuspend cell pellets in 410 µL 25 mM K3BO3, with 50 µL 10% SDS, 30 µL proteinase K, 10 µL RNase inhibitor. The mixture was shaken at 55 ˚C for 2 h and was subjected to phenol-chloroform extraction and ethanol precipitation. Extracted RNA were used for enrichment, end repair, and proximity ligation.
Libraries were conctructed by using the SMARTer Stranded Total RNA-seq kit v2 – pico input mammalian.

treatment_protocol: Cells were crosslinked in 1% formaldehyde for 10 min and then quenched with 125 mM glycine for 5 min. Cells were incubated 30 min in lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, 5 mM EDTA) supplemented with 20 mM N3-kethoxal, proteinase inhibitor, and RNase inhibitor, and was collected by centrifuging. The cell pellet was then washed and shook in lysis buffer supplemented with 12.5 µM G1-DBCO-biotin dendrimer at 1,000 rpm at 37 ˚C for 1 h. After the reaction, cells were collected and washed once as above.

value: bone marrow cells

value: Knockdown YBX3


title: WT 7h post sporulation induction, replicate 2

description:
WT7r_2
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx

value: WT


title: D3 T3M4-sgTP63-187e7-rep3


title: 1615_Spleen


title: WT_CD8_TILs_Rep2


title: WT 5h post sporulation induction, replicate 2

description:
WT5r_2
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: NCI-H1975_siSCR_DMSO_rep1

value: lung

value: non-small cell lung cancer

value: siSCR 48h,DMSO 6h


title: NCI-H1975_siSCR_DMSO_rep4


title: D3 T3M4-sgRPA3-1e2-rep3


title: Traf6cko_CD8_TILs_Rep1


title: WT 7h post sporulation induction, replicate 1

description:
WT7r_1
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: D3 T3M4-sgROSA26-rep2


title: D3 T3M4-sgTP63-187e4-rep1


title: NCI-H1975_siSCR_DMSO_rep3


title: KARR-seq K562 siControl G1 Rep 2

value: Knockdown control


title: WT 5h post sporulation induction, replicate 1

description:
WT5r_1
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: WT 4h post sporulation induction, replicate 2

description:
WT4r_2
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: 1614_Spleen


title: NCI-H1975_siSCR_DMSO_rep2


title: 3KO 0h, prior to sporulation induction, replicate 1

description:
3KO0r_1
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: WT 6h post sporulation induction, replicate 2

description:
WT6r_2
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: WT 6h post sporulation induction, replicate 1

description:
WT6r_1
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: WT 4h post sporulation induction, replicate 1

description:
WT4r_1
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: 1616_MLN

source_name: Mesenteric lymph node

value: Mesenteric lymph node


title: D3 T3M4-sgRPA3-1e2-rep1


title: D3 T3M4-sgPCNA-3e2-rep2


title: D3 T3M4-sgPCNA-3e2-rep1


title: KARR-seq A549 Mock G1 Rep 1

source_name: human epithelial cells

value: epithelial cells


title: 1613_Spleen


title: 1612_Spleen


title: KARR-seq HepG2 in vivo Total RNA G1 Rep 1

source_name: human liver cells

value: liver cells


title: 1615_MLN


title: 1611_Spleen


title: KARR-seq K562 siYBX3 G1 Rep 1


title: D3 T3M4-sgROSA26-rep1


title: D3 T3M4-sgPCNA-3e2-rep3


title: D3 T3M4-sgNT-4-rep3


title: KARR-seq A549 Mock G1 Rep 2


title: 1614_MLN


title: 1610_MLN


title: WT 3h post sporulation induction, replicate 1

description:
WT3r_1
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx

value: strain 168


title: 1613_MLN


title: WT 2h post sporulation induction, replicate 2

description:
WT2r_2
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx

value: RIBO-seq


title: KARR-seq HepG2 in vivo Total RNA G1 Rep 2


title: CFTR knockout H1 ES-derived salivary gland epithelial progenitors,rep3

city: Beijing

first: Shuang

last: Yan

address: zizhuyuanstreet

institute: Peking University

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean data was generated by quality control and then mapped to the reference genome (GRCh38_release95) using Hisat2.
Quantification of gene expression levels were measured by fragments per kilobase of transcript per million fragments mapped (FPKM) from Florea L,. F1000Res. 2013. In the equation, cDNA Fragments represents the number of PE reads mapped to the specific transcript; Mapped Fragments (Millions) is the number of all mapped reads, which is counted as 10^6; Transcript Length(kb) is the length of transcript in unit of 10^3 b.
Assembly: GRCh38_release95
Supplementary files format and content: tab-delimited list files include FPKM values for each Sample

growth_protocol: The hESC lines H1(H1 ES) were maintained under feeder-free conditions and passaged on Matrigel™ (1:160 dilution) coated plates in mTeSR™ medium (STEMCELL) and 1% penicillin/streptomycin  in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from CFTR knockout SGEPs and wild type SGEP at day 16 using RNeasy mini kit (Qiagen) following the manufacturer’s instructions. RNA concentration and quality were measured by NanoDrop 2000 and the Agilent Bioanalyzer 2100 system.
Sequencing libraries were prepared using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The SGEP were generated by differentiation of CFTR knockout and wild type hESCs at day 16. Briefly, the colonies of hESCs were isolated and cell aggregates were plated in low-cell adhesion plates (day 0). EBs was harvested at day 3 and transferred to tissue-treated cell culture plates to allow cell adherent for 2 additional days without disturbing. Cells were then cultured in differentiation medium plus 10 pM BMP4 from day 5 to day 10. RA was applied to the cultures at day 10 for 2 days at a final concentration of 1 μM, followed by a 4-day treatment of 6 μM CHIR99021.

value: human embryonic stem cell

value: CFTR knockout

value: salivary gland epithelial progenitors' differentiation

value: Day 16


title: 1609_MLN

value: Malignant Plasma Cell


title: D3 T3M4-sgCDK1-6e1-rep3

value: human pancreatic cancer cell line


title: D3 T3M4-sgNT-4-rep2


title: H1 ES-derived salivary gland epithelial progenitors,rep2


title: WT 1h post sporulation induction, replicate 2

description:
WT1r_2
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx

value: bacterial cells


title: WT 2h post sporulation induction, replicate 1

description:
WT2r_1
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx

value: WT


title: D3 T3M4-sgNT-4-rep1


title: H1 ES-derived salivary gland epithelial progenitors,rep3


title: KARR-seq K562 siControl G1 Rep 1

value: bone marrow cells


title: 1611_MLN


title: WT 3h post sporulation induction, replicate 2

description:
WT3r_2
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: D3 T3M4-sgNT-3-rep3


title: D3 T3M4-sgCDK1-6e1-rep2


title: Quiescent_3

value: Spleen

value: B Cell


title: WT 1h post sporulation induction, replicate 1

description:
WT1r_1
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: 1610_Spleen


title: D3 T3M4-sgNT-3-rep2


title: H1 ES-derived salivary gland epithelial progenitors,rep1


title: WT 0h, prior to sporulation induction, replicate 1

description:
WT0r_1
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: D3 T3M4-sgNT-3-rep1


title: WT 0h, prior to sporulation induction, replicate 2

description:
WT0r_2
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: O-ASCs-3

city: shanghai

first: bo

last: wang

address: 130 Meilong Rd.

institute: East China University of Science and Technology

data_processing:
The qualified dsDNA samples were sequenced using Illumina Nova Seq 6000 platform (San Diego, USA)
Raw sequencing reads were mapped to GRCh38 assembly of the human genome using Tophat2, version 2.0.10
Fragments per kilobase of exon model per million mapped reads (FPKM) were computed using Stringtie and normalized with TMM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: mesenchymal stem cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
dsDNA library was constructed using VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme) and purified using VIHTS DNA Clean Beads (Vazyme) according to the manufacturer’s instructions

value: mesenchymal stem cells


title: slide_2_P88-81 | 009 | CD31

city: Brisbane

first: Akhilandeshwari

last: Ravichandran

state: Queensland

address: 60 Musk Avenue

country: Australia

institute: Queensland University of Technology

description:
FFPE Spatial transcriptomics
qcdata.csv
normdata.csv

data_processing:
*library strategy: GeoMx Seq
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27”
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1“
Assembly: sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx Hs_R_NGS_WTA_v1.0 file
Supplementary files format and content: Processed data files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: rawdata: raw count data, normdata: normalised count data

source_name: Breast

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR. After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

value: Breast

tag: cell

value: Endothelial cell

tag: tissue type

value: Normal-adjacent

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: Quiescent_1

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: D6 KLM1-sgROSA26-rep2

tag: cell line

tag: time


title: O-ASCs-1


title: Activated_5

value: Activated B Cell

value: Stimulation with 1ug/ml LPS for 16 hours


title: L-ASCs-3


title: D6 KLM1-sgROSA26-rep1


title: RsbQS96A_mock_rep2

city: Perth

first: Muhammad

last: Kamran

state: WA

address: 35 Stirling Hwy, Crawley WA

department: School of Molecular sciences

institute: The University of Western Australia

description:
WT_mock_vs_RsbQS96A_mock
RsbQS96A_mock_vs_RsbQS96A_treated
rsbQ_mock_vs_RsbQS96A_mock

data_processing:
libraries were generated using the Illumina Stranded TotalRNAwith Ribo-Zero Plus product which is a rRNA depletion workflow as per manufacturers instructions
Adapter trimming, read mapping onto the Bacillus subtilis subsp. subtilis str. 168 (GCA_000009045) reference genome and read counts were carried out with kallisto
Differentially expressed genes (DEGs) analysis was done by DEseq2 using R studio.
Assembly: Bacillus subtilis subsp. subtilis str. 168 (GCA_000009045)
Supplementary files format and content: MS Excel files report log2FoldChange

source_name: bacterial cell

growth_protocol: approximately of 500 µl (1:100) of the starter culture was inoculated into a prewarmed 50 ml liquid LB and grown in a shaker incubator (Innova 42, New Brunswick Scientific) at 185 RPM and 37°C.

extract_protocol:
Cultures were harvested at OD ranging from 1.4 to 1.5 and immediately centrifuged at 10,000xg for 2 minutes using a Heraeus Multifuge X3R Centrifuge. The resulting pellet was then rapidly transferred to liquid nitrogen. RNA was extracted using the Spectrum Plant Total RNA kit (Sigma-Aldrich).
Paired-end libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturers' protocol.

treatment_protocol: Treatment solutions (DMSO and  rac-GR24) were added directly to the flasks by manual pipetting at an optical density (OD 600) ranging from 1.0 to 1.1.

tag: strain

value: bacterial cell

value: DMSO

tag: bacterial growth


title: RsbQS96A_treated_rep3

description:
rsbQ_treated_vs_RsbQS96A_treated
RsbQS96A_mock_vs_RsbQS96A_treated

value: 10 µM dGR24


title: Quiescent_4


title: CFTR knockout H1 ES-derived salivary gland epithelial progenitors,rep1

value: human embryonic stem cell

value: CFTR knockout

value: salivary gland epithelial progenitors' differentiation

value: Day 16


title: RsbQS96A_treated_rep2


title: D3 T3M4-sgCDK1-6e1-rep1

value: human pancreatic cancer cell line


title: RsbQS96A_treated_rep1


title: RsbQS96A_mock_rep3


title: O-ASCs-2


title: Quiescent_2

value: WT


title: D6 KLM1-sgNT-4-rep3


title: CFTR knockout H1 ES-derived salivary gland epithelial progenitors,rep2


title: rsbQ_treated_rep3

description:
rsbQ_mock_vs_rsbQ_treated
rsbQ_treated_vs_RsbQS96A_treated

value: rsbQ


title: Activated_3

value: Spleen


title: D6 KLM1-sgROSA26-rep3


title: Activated_2


title: Activated_4


title: L-ASCs-2

value: mesenchymal stem cells


title: Patient 9_CD4_remainder

city: Krume

first: Koichi

last: Ohshima

state: Fukuoka

address: Asahimachi 67

department: Pathology

country: Japan

institute: Kurume University

description: Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

data_processing:
NovaSeq-derived FASTQ files for each sample were compiled for each compartment using the bcl2fastq program of Illumina, and then demultiplexed and converted to digital count conversion (DCC) files using the GeoMx DnD pipeline (v.1) of Nanostring according to manufacturer’s pipeline.
DCC files were imported back into the GeoMx DSP instrument for QC and data analyses using GeoMx DSP Control Center software (version 2.5.1.145) (Nanostring Technologies).
To ensure good data quality, we calculated the 75th percentile of the gene counts (that is, geometric mean across all non-outlier probes for a given gene) for each AOI, and normalized to the geometric mean of the 75th percentile across all AOIs to give the upper quartile (Q3) normalization factors for each AOI. The distribution of these Q3 normalization factors were then checked for outliers.
Assembly: N/A
Supplementary files format and content: text files include values for each sample
Library strategy: GeoMx Seq

source_name: GeoMx_Slide_3_3re | 004 | CD4 remainder

extract_protocol:
For GeoMx DSP sample collections, entire slides were imaged at 20X magnification. AOIs were segmented using CD30 and CD4 markers. CD30+ large cells were defined as HRS-like cells (CD30+). CD4+ cells within 20μm from CD30+ HRS-like cells were defined as 'contour'. The remaining CD4+ cells were defined as 'remainder'. A total of 12 AOIs from 4 samples were segmented and exposed to 385?nm light (UV), releasing the indexing oligonucleotides which were collected with a microcapillary and deposited into a 96-well plate for subsequent processing. The indexing oligonucleotides were dried overnight and resuspended in 110 μl of DEPC-treated water.
Sequencing libraries were generated by PCR from the photo-released indexing oligos and AOI-specific Illumina adapter sequences. Unique i5 and i7 sample indexes were added. Each PCR reaction used 4 μl of indexing oligonucleotides, 4 μl of indexing PCR primers, 2 μl of Nanostring 5X PCR Master Mix. Thermocycling conditions were 37 °C for 30 min, 50 °C for 10 min, 95 °C for 3 min; 18 cycles of 95 °C for 15 s, 65 °C for 1 min, 68 °C for 30 s; and 68 °C for 5 min. PCR reactions were pooled and purified twice using AMPure XP beads (Beckman Coulter, A63881), according to the manufacturer's protocol.

treatment_protocol: Slide preparation was followed the GeoMx DSP slide preparation user manual (MAN-10087-04). In summary, FFPE tissue microarray section of 4-µm were mounted on positively charged histology slides. Sections were incubated at 65 °C for 1 hour. Slides were deparaffinized and antigen retrieval was performed in Tris-EDTA pH 9.0 at 100°C for 15 min at low pressure. The RNA probe mix (Whole Transcriptome Atlas (https://nanostring.com/products/geomx-digital-spatial-profiler/geomx-rna-assays/geomx-whole-transcriptome-atlas/), a pool of in situ hybridization probes with UV photocleavable oligonucleotide barcodes) was placeed on each section. Slides were incubated for hybridization overnight at 37°C in a Hyb EZ II hybridization oven (Advanced Cell Diagnostics). After hybridization, tissues were stained with CD30 (clone Ber-H2, dilution 1:10, Cell Marque) and CD4 (clone EPR6855, 1:20, Abcam) and located on the GeoMx Digital Spatial Profiler (DSP).

value: Lymph node

tag: slide name

tag: roi number

tag: segment type

tag: patient id

value: patient 9

tag: sample identifier

tag: disease

value: Hodgkin-like ATLL


title: D6 KLM1-sgNT-4-rep2


title: rsbQ_treated_rep1


title: Activated_1

value: Activated B Cell


title: L-ASCs-1


title: rsbQ_treated_rep2


title: D6 KLM1-sgNT-4-rep1


title: D6 KLM1-sgNT-3-rep3


title: rsbQ_mock_rep3

description:
WT_mock_vs_rsbQ_mock
rsbQ_mock_vs_rsbQ_treated
rsbQ_mock_vs_RsbQS96A_mock


title: RsbQS96A_mock_rep1


title: D6 KLM1-sgNT-3-rep1


title: Patient 9_CD4_contour

source_name: GeoMx_Slide_3_3re | 004 | CD4 contour


title: rsbQ_mock_rep1


title: IL6Myc-5 rep3

source_name: Cell Line

value: Cell Line

value: Mouse Myeloma Cell Line


title: D6 KLM1-sgNT-3-rep2


title: IL6Myc-5 rep1


title: Patient 8_CD4_contour

source_name: GeoMx_Slide_3_3re | 001 | CD4 contour

value: patient 8


title: IL6Myc-4 rep3


title: Patient 9_CD30

source_name: GeoMx_Slide_3_3re | 004 | CD30


title: rsbQ_mock_rep2

value: bacterial cell

value: DMSO


title: Patient 8_CD4_remainder

source_name: GeoMx_Slide_3_3re | 001 | CD4 remainder


title: WT_treated_rep2

value: 10 µM dGR24


title: D6 KLM1-sgMED12-4-rep3


title: D6 KLM1-sgMED12-4-rep2


title: Patient 8_CD30

source_name: GeoMx_Slide_3_3re | 001 | CD30


title: WT_treated_rep3


title: IL6Myc-4 rep2


title: Patient 2_CD4_remainder

source_name: GeoMx_Slide_3_3re | 003 | CD4 remainder

value: patient 2


title: IL6Myc-4 rep1


title: WT_mock_rep3

description:
WT_mock_vs_WT_reated
WT_mock_vs_rsbQ_mock
WT_mock_vs_RsbQS96A_mock


title: WT_treated_rep1


title: IL6Myc-5 rep2


title: D6 KLM1-sgMED12-3-rep3


title: D6 KLM1-sgMED12-3-rep2


title: IL6Myc-3 rep3


title: Patient 2_CD30

source_name: GeoMx_Slide_3_3re | 003 | CD30


title: IL6Myc-2 rep3


title: Patient 43_lt51

type: RNA

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

country: Italy

institute: Azienda USL- IRCCS di Reggio Emilia

description: Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol

hyb_protocol: RNA was hybridized to capture and reporter probes using the NanoString nCounter system according to the manufacturer's protocol. Each reporter probe provided by the manufacturer was labeled with a flourescent barcode specific for each transcript.

scan_protocol: Scanning was conducted using the NanoString Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files. The data were normalized using 3 HK genes (COG7, DNAJC14, ERCC3). Raw values correspond to the number of copies of each molecular barcode representative of a specific transcript.
Mean count of negative controls plus two standard deviations was subtracted only from coding genes counts to eliminate negative background. Then normalization on synthetic positive controls was conducted by multiplying the count of each gene for a correction factor. This factor was calculated for each sample as the ratio between the quadratic mean of positive controls counts and the mean of quadratic means in all samples. In order to performed CodeSet Content normalization on housekeeping genes, three reference genes were selected among the 15 available in the panel based on the lowest coefficients of variation (CV= ratio between standard deviations and mean counts across all samples). Finally, CodeSet Content normalization was performed by multiplying genes counts for a further correction factor calculated on reference genes as described for positive technical controls.

label: Molecular barcode on reporter probe

source_name: Anaplastic Large Cell Lymphoma

label_protocol: RNA was not labeled, but it was pre-processed following the NanoString manufacturer's protocol.

extract_protocol: Formalin-fixed, paraffin-embedded (FFPE) tissues of ALCL were reviewed by different pathologists. For RNA purification, five 5um FFPE slides were cut for each tumor. Total RNA was extracted by Maxwell® RSC RNA FFPE kit (Promega). RNA quantity and quality were assessed by NanoDrop2000 (Thermo Fisher Scientific). For samples that reached the quality standards (A260/A280 ≥ 1.7 and A260/A230 ≥ 1.8), we evaluated the expression profile of  39 genes by a NanoString Custom Panel called VF_150921 (NanoString Technologies).

treatment_protocol: Specimens from ALCL affected patients were included in this study.

tag: Sex

value: F

tag: age

tag: alk phenotype

value: neg


title: Patient 44_lt52

value: M


title: IL6Myc-3 rep2

tag: tissue


title: WT_mock_rep2

tag: cell type

value: WT


title: D6 KLM1-sgMED12-2-rep3

value: human pancreatic cancer cell line

tag: genotype


title: D6 KLM1-sgMED12-3-rep1


title: Patient 1_CD4_remainder

source_name: GeoMx_Slide_3_3re | 002 | CD4 remainder

value: patient 1


title: Patient 42_lt50


title: D6 KLM1-sgMED12-4-rep1


title: Patient 2_CD4_contour

source_name: GeoMx_Slide_3_3re | 003 | CD4 contour

value: Lymph node


title: D6 KLM1-sgMED12-2-rep1


title: IL6Myc-3 rep1


title: WT_mock_rep1

tag: treatment


title: D6 KLM1-sgMED12-2-rep2

tag: cell line


title: Patient 1_CD4_contour

source_name: GeoMx_Slide_3_3re | 002 | CD4 contour


title: Patient 1_CD30

source_name: GeoMx_Slide_3_3re | 002 | CD30


title: IL6Myc-1 rep3


title: IL6Myc-2 rep2


title: IL6Myc-2 rep1


title: D6 KLM1-sgMED12-1-rep3

tag: time


title: D6 KLM1-sgMED12-1-rep2


title: KARR-seq K562 siSRSF1 Nuclear G1 Rep 2

description: G1_kethoxal-K562-siSRSF1-Nuclear_B17_R02

data_processing:
library strategy: KARR-seq
KARR-seq: For paired end FASTQ formatted files, SeqPrep (commit: 575507b) was first used to merge overlapping read pairs (2 x 150 bp) into single end reads. Unmerged read pairs were discarded. The resulting single end results were then aligned to mm10, hg19 or dm3 reference genome using STAR (v2.5.2a) as well as the species' corresponding RefSeq transcripts. The pre-merging step was skipped for single-end FASTQ files, and directly aligned using STAR. The following STAR parameters were used to recover gapped and chimeric reads (--runMode alignReads --outFilterMultimapNmax 100 --outSAMattributes all --alignIntronMin 1 --scoreGapNoncan -4 --scoreGapATAC -4 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --limitOutSJcollapsed 10000000 --limitIObufferSize 1500000000). Only chimeric reads (CIGAR N gap between mapped segments of the read) were kept, spliced sites filtered and interaction pairs tabulated. Pairix was used to index the interaction pairs file.
Genome_build: mm10,hg19,dm3
Supplementary_files_format_and_content: Processed files are bgzipped text files that follows the 4DN-standard pairs file format (pairix)

source_name: KARR-seq K562 siSRSF1 Nuclear G1

value: bone marrow cells

value: Knockdown SRSF1, nuclei were used

tag: molecule subtype

value: nuclear RNA


title: Patient 41_lt48


title: Patient 40_lt45


title: KARR-seq K562 Arsenite Total G1 Rep 2

source_name: KARR-seq K562 Arsenite Total G1

value: Cells treated with sodium arsenite


title: IL6Myc-1 rep2

value: Cell Line

value: Mouse Myeloma Cell Line


title: Patient 39_lt44


title: Patient 38_lt42


title: IL6Myc-1 rep1


title: KARR-seq K562 siSRSF1 Total G1 Rep 2

source_name: KARR-seq K562 siSRSF1 Total G1

value: Knockdown SRSF1


title: Patient 37_lt40

value: pos


title: D6 KLM1-sgMED12-1-rep1


title: KARR-seq K562 Arsenite Total G1 Rep 1


title: D3 KLM1-sgTP63-87e10-rep3


title: KARR-seq K562 in vivo Nuclear G1 Rep 2

source_name: KARR-seq K562 in vivo Nuclear G1

value: Cell nuclei were used


title: KARR-seq K562 siSRSF1 Total G1 Rep 1


title: 6780_2_6743_1_FB_pool_of_18_mouse_NMM_tumors_TACTTTAGCT-CAAATAACTC_S13

city: Amsterdam

first: Maarten

last: Slagter

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
Multiplexed library of multiple experimental conditions
Feature barcoding

data_processing:
Barcode processing, gene counting and aggregation was performed using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38
Supplementary files format and content: 10x Genomics CellRanger output

source_name: NRAS-mutated mouse melanoma (NMM)

growth_protocol: NMM Tumor cells were harvested from  Rag-/- mice, manually minced and enzymatically digested in RPMI medium (Gibco) supplemented with 5 Wünsch units/ml TH Liberase/ml (Roche) 25 μg/ml DNase I (Roche) for 20 min at 37 °C under continuous shaking. Cells were harvested and filtered through a 70-μm strainer (Falcon) and single-cell suspensions were stained with IR-Dye (Invitrogen) and TotalSeq Hastag antibodies (TotalSeq-A, Biolegend). Cells from each sample were combined at equal numbers, and CFP+ (i.e. bystander) tumor cells were sorted from this cell pool on a FACSaria Fusion (BD biosciences).

extract_protocol:
Cells were harvested and diluted to a final concentration of 1,000 cells/μl in 1xPBS containing 0.04% weight/volume BSA.
The Chromium Controller platform of 10X Genomics was used for single cell partitioning and barcoding. Per single cell suspension, each cell’s transcriptome was barcoded during reverse transcription, pooled cDNA was amplified and Single Cell 3’ Gene Expression libraries and Cell Hashing libraries via Feature barcode technology were prepared, according to the manufacturer’s protocol (CG000183, CG000206 and CG000317, 10X Genomics). All libraries were quantified on a 2100 Bioanalyzer Instrument following the Agilent Technologies Protocol (Agilent DNA 7500 kit, G2938-90024). Sequence library pools were composed and quantified by qPCR, according to the KAPA Library Quantification Kit Illumina® Platforms protocol (KR0405, KAPA Biosystems)
NovaSeq Illumina sequencing was used for paired-end sequencing of the Single Cell 3’ Gene Expression library and Cell Hashing libraries, at a sequencing depth of between 20,000-60,000 reads /cell and approximately 3,500 genes/cell. Novaseq 6000 paired-end sequencing was performed using 28 cycles for Read 1, 10 cycles for each Read i7 and i5, and 90 cycles for Read 2, using the NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) (20028316, Illumina)

value: NRAS-mutated mouse melanoma (NMM)

value: Melanoma

value: NRAS mutated


title: 6780_1_6743_1_GE_pool_of_18_mouse_NMM_tumors_CTTGCATAAA-AAGCCCTGAT_S12

description:
Multiplexed library of multiple experimental conditions
Experimental conditions (separated by ';'): Ag-GAS + T; Ag-GAS + T; Ag-GAS + T; Ag-GAS + T; Ag-GAS + T; Ag-GAS + T; Mix PBS; Mix PBS; Mix PBS; Mix PBS; Mix PBS; Mix PBS; Mix + T; Mix + T; Mix + T; Mix + T; Mix + T; Mix + T


title: KARR-seq K562 in vivo Nuclear G1 Rep 1


title: Patient 36_lt22

value: F

value: neg


title: Patient 35_lt21

value: M


title: TS5

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

data_processing:
Preprocessing: Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.15 (HannonLab, 2010; Martin, 2011). Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using using FastX 0.0.14 and ShortRead 1.40.0 (Morgan et al, 2009). With Bowtie2 2.3.3.1 we identified and removed reads that align to phix_illumina (Langmead & Salzberg, 2012).
Mapping: The preprocessed reads were aligned with STAR aligner v2.5.2b to the reference genome of Mus musculus (GRChm38.82) (AD et al, 2013).  Default STAR aligner parameter settings were used, except for ‘--outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate’. Using Samtools 1.5, reads with a mapping quality smaller than 20 were removed from the alignments (Li et al, 2009).
Counting: The number of reads in the alignments that overlap with gene features were counted with featureCounts 1.5.3 (Liao et al, 2014). Following parameters were chosen: -Q 0 -s 2 -t exon -g gene_id. We removed genes for which all samples had less than 1 count-per-million. Raw counts were further corrected within samples for GC-content and between samples using full quantile normalization, as implemented in the EDASeq package from Bioconductor (Risso et al, 2011).
Assembly: Mus_musculus.Ensembl.GRCm.38.82
Supplementary files format and content: .xlsx file includes Raw counts and FPKM values for each Sample.

source_name: Lung tissue

growth_protocol: The human osteosarcoma cell line 143B was cultured in Eagle’s minimum essential medium (EMEM), supplemented with 10% heat-inactivated fetal bovine serum (FBS), 0.015 mg/ml 5-bromo-2’-deoxyuridine (BrdU), 1.0 mM sodium pyruvate (Gibco), and 1% antibiotic-antimycotic (Gibco). The cells were maintained under standard adherent conditions in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using TRIzol reagent following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using the library prep kit TruSeq (protocol version: # 1000000040498 v00 October 2017)  and the sequencing kit NovaSeq6000 SP Flowcell 100 cycles.

treatment_protocol: Mice were treated with the 143B cell-derived secretome by daily i.p. injection for one week or implanted subcutaneously with the 143B OS cells for a primary tumour formation.

value: Lung tissue

value: Osteosarcoma cells

value: Athymic Swiss nude (Foxn1nu/nu) mice

value: Subcutaneous injection into the lower flank of 143B Luc+ cells


title: TS6


title: D3 KLM1-sgTP63-87e10-rep1

value: human pancreatic cancer cell line


title: D3 KLM1-sgTP63-51e1-rep3


title: D3 KLM1-sgTP63-51e1-rep2


title: KARR-seq K562 in vitro G1 Rep 2

source_name: KARR-seq K562 in vitro G1

value: bone marrow cells

value: RNA were refolded in vitro


title: Patient 34_lt47


title: Patient 33_lt39


title: KARR-seq K562 siSRSF1 Nuclear G1 Rep 1

description: G1_kethoxal-K562-siSRSF1-Nuclear_B17_R01

value: Knockdown SRSF1, nuclei were used

value: nuclear RNA


title: D3 KLM1-sgTP63-187e7-rep3


title: KARR-seq K562 in vitro G1 Rep 1


title: Patient 32_lt38


title: KARR-seq K562 in vivo G1 Rep 2

source_name: KARR-seq K562 in vivo G1


title: TS3


title: TS2


title: D3 KLM1-sgTP63-51e1-rep1


title: KARR-seq K562 in vivo G1 Rep 1


title: TS1


title: D3 KLM1-sgTP63-187e7-rep2


title: Patient 31_lt37


title: Patient 30_lt36


title: MC5

value: Daily intraperitoneal injection of 143B cells-derived secretome


title: D3 KLM1-sgTP63-87e10-rep2


title: MC6


title: KARR-seq HepG2 HT G1 Rep 2

source_name: KARR-seq HepG2 HT G1

value: liver cells

value: Cells treated with harringtonine


title: D3 KLM1-sgTP63-187e7-rep1


title: Patient 28_lt34


title: Patient 29_lt35


title: D3 KLM1-sgTP63-187e4-rep2


title: MC4


title: D3 KLM1-sgTP63-187e4-rep3


title: KARR-seq HepG2 HT G1 Rep 1


title: D3 KLM1-sgTP63-187e4-rep1


title: MC3


title: Patient 27_lt32


title: KARR-seq HepG2 CHX G1 Rep 1

source_name: KARR-seq HepG2 CHX G1

value: Cells treated with cycloheximide


title: MC2


title: Patient 26_lt31


title: D3 KLM1-sgRPA3-1e2-rep3


title: KARR-seq HepG2 siDDX3X G1 Rep 2

source_name: KARR-seq HepG2 siDDX3X G1

value: Knockdown DDX3X


title: MC1


title: D3 KLM1-sgRPA3-1e2-rep2


title: CTR5


title: Patient 25_lt30

value: F


title: KARR-seq HepG2 CHX G1 Rep 2


title: KARR-seq HepG2 siControl G1 Rep 1

source_name: KARR-seq HepG2 siControl G1

value: Knockdown control


title: KARR-seq HepG2 siControl G1 Rep 2


title: CTR4


title: CTR2


title: Patient 23_lt28

source_name: Anaplastic Large Cell Lymphoma

value: pos


title: Patient 24_lt29

value: neg


title: KARR-seq HepG2 siDDX3X G1 Rep 1


title: Patient 22_lt27

value: M


title: D3 KLM1-sgRPA3-1e2-rep1


title: D3 KLM1-sgROSA26-rep2


title: KARR-seq HepG2 in vitro G1 Rep 2

source_name: KARR-seq HepG2 in vitro G1


title: D3 KLM1-sgROSA26-rep3


title: D3 KLM1-sgROSA26-rep1


title: KARR-seq HepG2 in vitro G1 Rep 1


title: KARR-seq F123 kethoxal (-) G3 Rep 1

source_name: KARR-seq F123 kethoxal (-) G3

value: embryonic stem cells


title: CTR1

value: Lung tissue

value: Athymic Swiss nude (Foxn1nu/nu) mice


title: Patient 21_lt26


title: KARR-seq HepG2 in vivo G1 Rep 2

source_name: KARR-seq HepG2 in vivo G1


title: D3 KLM1-sgPCNA-3e2-rep3

value: human pancreatic cancer cell line


title: Patient 19_lt24


title: D3 KLM1-sgPCNA-3e2-rep2


title: KARR-seq HepG2 in vivo G1 Rep 1


title: KARR-seq F123 dendrimer (-) G3 Rep 1

source_name: KARR-seq F123 dendrimer (-) G3


title: KARR-seq F123 dendrimer (-) kethoxal (-) G3 Rep 1


title: D3 KLM1-sgPCNA-3e2-rep1


title: Patient 18_lt23


title: KARR-seq HEK293T in vitro G1 Rep 2

source_name: KARR-seq HEK293T in vitro G1

value: kidney cells

value: RNA were refolded in vitro


title: KARR-seq F123 biotin (-) G3 Rep 1

source_name: KARR-seq F123 biotin (-) G3


title: D3 KLM1-sgNT-4-rep3


title: Patient 17_lt20


title: Patient 16_lt19


title: KARR-seq HEK293T in vitro G1 Rep 1


title: KARR-seq F123 ligation (-) G3 Rep 1

source_name: KARR-seq F123 ligation (-) G3


title: KARR-seq HEK293T in vivo G1 Rep 2

source_name: KARR-seq HEK293T in vivo G1


title: D3 KLM1-sgNT-4-rep2


title: KARR-seq F123 in vivo G3 Rep 1

source_name: KARR-seq F123 in vivo G3


title: Patient 15_lt17


title: KARR-seq HEK293T in vivo G1 Rep 1


title: Patient 14_lt15


title: OA-DLM

first: Hao

last: Sun

state: Guangdong

address: Zhongshan 2nd Road

department: Joint surgery

institute: First Affiliated Hospital of Sun Yat-sen University,

description: Single-cell RNA

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 40%;    Cell Gene Number < 10000;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV file contain counts for each sample

source_name: meniscus

extract_protocol: RNA libraries were generated by BD Rhapsody singel cell RNA-seq and prepared for sequencing using standard Illumina protocols

treatment_protocol: human meniscus tissues were cut into small pieces, and then digested by 4 mg/mL protease for 1 hour and 0.25 mg/mL collagenase P for 4 to 6 hours.

value: Discoid lateral meniscus

tag: condition

value: osteoarthritis


title: OA-CON

description: Single-cell RNA

value: osteoarthritis lateral meniscus


title: Patient 20_lt25


title: D3 KLM1-sgNT-4-rep1

data_processing:
For RNA-seq, sequencing reads were mapped onto reference human genome hg38 using STAR v2.7.9a with default settings. HTSeq-counts was used to generate raw gene counts, and DESeq2 was then used to perform differential expression analysis.
For ChIP-Seq, reads were mapped to hg38 with bowtie2 2.4.2 with very-sensitive setting. Bam files are then sorted with Samtools 1.11 with default settings, and used to call peaks with MACS2. Bedtools 2.30.0 was used to intersect and merge peaks
Deeptools v3.5.0 was used to generate BigWig files that were then visualized in the UCSC genome browser with the hg38 genome. HOMER v4.11 was used to assign the closest annotated ORFs to each peak and for motif discovery.
For CRISPR amplicon sequencing, raw reads were aligned to each sgRNA library to generate count files with MAGeCK.
For scRNA-seq experiments, data was genetically demultiplexed using cellsnp-lite 1.2.3 and Vireo 0.5.8, aligned to the human genome and assigned to cells using Cell Ranger 7.1.0, and downstream analyzed using Seurat 4.3.0.1.
Assembly: hg38
Supplementary files format and content: Htseq-count matrix for RNA-Seq. H5 Seurat files for scRNA-seq. Bigwig files for ChIP-Seq. Mageck count files for CRISPR libraries.


title: KARR-seq F123 ribo-depletion (-) Rep 1

source_name: KARR-seq F123 ribo-depletion (-)


title: KARR-seq F123 in vitro G1 Rep 2

source_name: KARR-seq F123 in vitro G1


title: D3 KLM1-sgNT-3-rep2


title: D3 KLM1-sgNT-3-rep3


title: Patient 13_lt14


title: D3 KLM1-sgNT-3-rep1


title: KARR-seq F123 in vitro G1 Rep 1


title: Patient 11_lt9


title: Patient 12_lt13


title: D3 KLM1-sgCDK1-6e1-rep3


title: KARR-seq F123 in vivo G1 Rep 2

source_name: KARR-seq F123 in vivo G1


title: Input-ubp5, rep2

city: Galway

first: Sara

last: Farrona

address: University Road

country: Ireland

institute: National University of Ireland Galway

library_source: genomic

data_processing:
Raw data with adapter sequences and low-quality sequences was filtered using SOAPnuke software developed by BGI with following parameters: -n 0.01 -l 20 -q 0.4 --cutAdaptor -Q 2 -G --polyX 50 --minLen 100.
The reads were mapped to the Arabidopsis genome (TAIR10) using using STAR v2.7.8a with parameters align intron max as 1 and align ends type as EndToEnd. Duplicated reads were removed using Picard tool MarkDuplicates option and only uniquely mapped reads were retained for further analysis.
Peaks were called uing MACS v3.0.0 with the significance cut-off q-value <=0.01 and narrowPeaks files were generated.
Bigwig files were generated using deepTools bamCoverage with RPGC normalisation.
Assembly: TAIR10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Seedlings (12 DAG)

growth_protocol: Sterilised seeds were sown on Murashige & Skoog medium (MS Base) supplemented with 1% Sucrose, 0.1% MES, 0.8 % agar with pH adjusted to 5.6, stratified at 4°C for three days and placed to Percival tissue culture cabinet under a 16:8 h light: dark (21°C/18°C) regime. Seedlings were collected 12 days after germination (DAG).

extract_protocol:
Chromatin was extracted from 1% formaldehyde fixed tissue and fragmented using a Bioruptor® Pico (Diagenode) in fragments of 200–500 bp. For IP the antibodies used were H2Aub (Cell Signalling Technology D27C4) and H3K27me3 (Millipore 07-449).
BGISEQ platform Chip-seq library preparation:  1) End repair and adapter ligation:Fill the ends of IP/Input DNA followed by 5' phosphorylation. A 3' sticky-end with an overhanging A is formed, which could ligate with an overhanging T at the 3' end of the bubble adapter;  2)PCR amplification: PCR amplify the ligated products with specific primers;  3)Single-strand separation and circularization: Separate PCR products into single-strands by thermal denaturation. Then circularize the single-stranded DNA through a bridge primer to obtain single-stranded circular DNA library;  4)Sequencing: Amplified products DNA Nanoballs (DNBs) are used for sequencing.

value: Seedlings (12 DAG)

tag: ecotype

tag: antibody


title: Input-ubp5, rep3


title: D3 KLM1-sgCDK1-6e1-rep2

last: Maia e Silva

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

extract_protocol:
For RNA-seq experiments, total RNA was isolated using TRIzol (Thermo Fisher, 15596026) according to the manufacturer’s instructions. For scRNA-seq experiments, cells were single cell captured and barcoded using the 10X Chromium chemistry. For ChIP-seq experiments, lysates were clarified from crosslinked, sonicated nuclei and protein-DNA complexes were immunoprecipitated with specific antibodies. For CRISPR libraries, genomic DNA was isolated using phenol-chloroform extraction and directly used for library preparation.
RNA-seq and ChIP-seq ibraries were constructed using  Illumina TruSeq RNA library prep kit v2 (Illumina, RS-122-2001) or  Illumina TruSeq ChIP library prep kit (Illumina, IP-202-1012) based on the manufacturer’s instructions. scRNA-seq libraries were biult using 10X Genomics NextGEM Single-Cell 3' Library Kit. CRISPR libraries were prepared using sgRNA flanking primers described in the article and 1 step PCR amplification.


title: KARR-seq F123 in vivo G1 Rep 1


title: Patient 10_lt8


title: Patient 9_lt7


title: Input-ubp5, rep1


title: KARR-seq F123 G7 Rep 2

source_name: KARR-seq F123 G7


title: D3 KLM1-sgCDK1-6e1-rep1


title: Input-Col, rep3


title: 6575_3_6489_1_FB_sample_pool_of_24_samples_with_combinations_ATCCGCCGAA_S3

data_processing:
Barcode processing, gene counting and aggregation was performed using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Cellranger-GRCh38-3.0.0
Supplementary files format and content: 10x Genomics CellRanger output

growth_protocol: Cells were cultured at 37°C/ 5% CO2 in IMDM (Gibco) supplemented with 10% FCS (Sigma), 100 U/ml penicillin (Roche), 100 μg/ml streptomycin (Roche), and GlutaMax (Gibco, 1x).

extract_protocol:
Cells were harvested and diluted to a final concentration of 1,000 cells/μl in 1xPBS containing 0.04% weight/volume BSA.
The Chromium Controller platform of 10X Genomics was used for single cell partitioning and barcoding. Per single cell suspension, each cell’s transcriptome was barcoded during reverse transcription, pooled cDNA was amplified and Single Cell 3’ Gene Expression libraries and Cell Hashing libraries via Feature barcode technology were prepared, according to the manufacturer’s protocol (CG000183, CG000206 and CG000317, 10X Genomics). All libraries were quantified on a 2100 Bioanalyzer Instrument following the Agilent Technologies Protocol (Agilent DNA 7500 kit, G2938-90024). Sequence library pools were composed and quantified by qPCR, according to the KAPA Library Quantification Kit Illumina® Platforms protocol (KR0405, KAPA Biosystems)
NextSeq HIGH sequencing was used for paired-end sequencing of the Single Cell 3’ Gene Expression library and Cell Hashing libraries, respectively, at a sequencing depth of between 20,000-60,000 reads /cell and approximately 3,500 genes/cell. NextSeq 550 paired-end sequencing was performed using 28 cycles for Read 1, 10 cycles for Read i7, and 54 cycles for Read 2, using the NextSeq 500/550 High Output Kit v2.5 (75 Cycles) (20024906, Illumina) and NextSeq 500/550 Mid Output Kit v2.5 (150 Cycles) (20024904, Illumina).

treatment_protocol: Cells were treated with tumor-cell T-cell coculture supernatant at various dilutions and exposure durations in vitro

value: Ovarian carcinoma


title: KARR-seq F123 G7 Rep 1


title: 6575_1_6489_1_GE_sample_pool_of_24_samples_with_combinations_GCGCTTATGG_S1

description:
Multiplexed library of multiple experimental conditions
Experimental conditions (separated by ';'): Unstimulated in vitro - 2h; SN - 2h; 1/5 SN - 2h; 1/25 SN - 2h; 1/125 SN - 2h; 1/625 SN - 2h; Unstimulated in vitro - 6h; SN - 6h; 1/5 SN - 6h; 1/25 SN - 6h; 1/125 SN - 6h; 1/625 SN - 6h; Unstimulated in vitro - 12h; SN - 12h; 1/5 SN - 12h; 1/25 SN - 12h; 1/125 SN - 12h; 1/625 SN - 12h; Unstimulated in vitro - 24h; SN - 24h; 1/5 SN - 24h; 1/25 SN - 24h; 1/125 SN - 24h; 1/625 SN - 24h


title: Patient 6_lt4


title: KARR-seq F123 G3 Rep 2

source_name: KARR-seq F123 G3


title: 6547_3_6489_1_FB_sample_pool_of_24_samples_with_combinations_ATCCGCCGAA_S3


title: H3K27me3-ubp5, rep2


title: KARR-seq F123 G5 Rep 1

source_name: KARR-seq F123 G5


title: H3K27me3-ubp5, rep1


title: Input-Col, rep1


title: KARR-seq F123 G3 Rep 1


title: Patient 5_lt3

source_name: Anaplastic Large Cell Lymphoma


title: Patient 4_lt2


title: KARR-seq F123 G1 Rep 2

source_name: KARR-seq F123 G1


title: 6391_1_6369-GE_TTCTCGATGA_S1

description:
Library consisting of multiple experimental conditions
Gene expression data. Experimental conditions (separated by ';'): Unstimulated in vitro - 2h;1 ng/ml IFNy - 2h;10 ng/ml IFNy - 2h;100 ng/ml IFNy - 2h;Unstimulated in vitro - 6h;1 ng/ml IFNy - 6h;10 ng/ml IFNy - 6h;100 ng/ml IFNy - 6h;Unstimulated in vitro - 12h;1 ng/ml IFNy - 12h;10 ng/ml IFNy - 12h;100 ng/ml IFNy - 12h;Unstimulated in vitro - 24h;1 ng/ml IFNy - 24h;10 ng/ml IFNy - 24h;100 ng/ml IFNy - 24h;Unstimulated in vitro - 24h - frozen;100 ng/ml IFNy - 24h - frozen

treatment_protocol: Cells were treated with  IFNy at various concentrations and exposure durations in vitro

value: IFNy-sensing reporter, CFP+


title: 6547_1_6489_1_GE_sample_pool_of_24_samples_with_combinations_GCGCTTATGG_S1


title: Patient 7_lt5


title: Patient 3_lt12


title: Input-Col, rep2


title: Patient 2_lt11


title: KARR-seq F123 G1 Rep 1


title: Patient 8_lt6

value: F


title: H2Aub-ubp5, rep3


title: H3K27me3-Col, rep1


title: KARR-seq F123 G5 Rep 2


title: ductal_KPTS_cultured_RNAseq_4

city: San Antonio

first: Pei

last: Wang

state: TX

address: 7703 Floyd Curl Dr

department: Cell Systems & Anatomy

institute: University of Texas Health San Antonio

data_processing:
Alignment was performed using TopHat 2.1.1 and gene expression was quantified using HTSeq 0.11.1.
Assembly: hg38
Supplementary files format and content: read_table.txt.gz is tab delimited table of read counts per gene for all samples.
Supplementary files format and content: TPM_table.txt.gz is tab delimited table of transcripts per million per gene for all samples

source_name: exocrine pancreas

extract_protocol:
Total RNA was extracted using Zymo Direct-zol RNA Miniprep Kit as per manufacturer instructions.
RNAseq libraries prepared using Illumina Stranded mRNA Prep Ligation kit as per manufacturer instructions.

treatment_protocol: "K" genotype cells have enforced expression of oncogenic KRAS-G12V and "KPTS" genotype cells have KRAS-G12V and CRISPR/Cas9 knockout of P16, P53, and SMAD4 .

value: exocrine pancreas

value: ductal

value: KPTS

value: monolayer culture


title: Patient 1_lt10

value: M

value: neg


title: H2Aub-ubp5, rep2


title: No_glucose_HA_CHIP

city: MIAMI

first: Julio

middle: C

last: Barredo

state: Florida

address: 1580 NW 10th ave room

institute: University of Miami

data_processing:
Raw reads were trimmed for adapters using Cutadapt (v1.15 –nextseq-trim=20 –m 18).
Fastq files were aligned to hg38 human using BWA (v0.7.13) with parameters aln -q 5 -l 32 -k 2, and deduplicated using Picard Mark Duplicates (v2.10.6).
Peaks were called using narrow peaks by macs2 (v2.1.1.20160309). ChIPseeker (v1.14.0) and R (v3.4.1) were used for genomic annotation. Peak overlaps were determined by merging peaks list from a given comparison and intersecting individual peak files to the combined list by at least 1 bp. Signal bigwig files were CPM normalized.
Assembly: hg38
Supplementary files format and content: bigWig (except for Input sample).

source_name: CCRF-CEM

growth_protocol: CCRF-CEM/HA-AMPKa2 cells were grown in RPMI + 10% FBS.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Cells were grown in ctrl or no glucose medium for 24 hours.

value: CCRF-CEM

value: T cell leukemia

value: Glucose deprivation for 24h

tag: chip antibody


title: ductal_KPTS_cultured_RNAseq_3


title: ductal_KPTS_cultured_RNAseq_2


title: H2Aub-ubp5, rep1


title: 6391_2_6369-FB_ATTTACCGCA_S2

description:
Library consisting of multiple experimental conditions
Feature barcoding


title: H3K27me3-Col, rep2


title: CTRL_HA_CHIP

value: No treatment


title: ductal_KPTS_cultured_RNAseq_1


title: H2Aub-Col, rep3


title: CTRL_input


title: miRNA_MCD mice-2

city: Nankoku

first: Shuji

last: Sakamoto

state: Kochi

address: Oko-cho, Kohasu

department: Science Research Center

institute: Kochi University

hyb_protocol: The biotin-labeled RNA was hybridized with a miRNA 4.1 Array Strip  (ThermoFisher Scientific).

scan_protocol: The array was scanned by the GeneAtlas system (Affymetrix, MA, USA) to measure the intensities of the microarray spots.

data_processing:
The intensities of the spots were analyzed by the Transcriptome Analysis Console (TAC) software (ThermoFisher Scientific).
processed data file contains avegae log2 RMA+DABG signal for ND and MCD with statistics.

label: biotin

source_name: Wild-type mice fed with MCD

label_protocol: Biotin-labeled RNA was generated with Flash-Tag Biotin HSR RNA Labeling Kit (ThermoFisher Scientific, MA, USA).

growth_protocol: Mice were maintained at 19-25 ºC with 55 % ± 25 % humidity under a 14-hour light/10-hour dark cycle in specific-pathogen-free are.

extract_protocol: Total RNA was prepared from the liver of mice fed with ND or MCD by miRNeasy mini kit (QIAGEN, Hilden, Germany).

treatment_protocol: Wild type male C57BL/6J mice at 6 weeks of age were randomly assigned into two groups (normal diet or MCD groups). Mice were fed with normal diet (ND) or MCD for 20 weeks.

tag: strain

value: male

value: Liver


title: No glucose rep2

data_processing:
Reads were aligned to the hg38 transcriptome and ERCC spike-in indexes using RSEM (v1.3.0) and STAR (v2.6.0c) with Gencode annotations.
Differentially expressed genes were determined by DESeq2 (v1.18.1, Fold Change > 1.5 or < -1.5, q value < 0.05) after gene counts were corrected based on ERCC variances using RUVseq (v1.12.0).
Supplementary files format and content: hg38
Supplementary files format and content: data_matrix_ctrl_no_glucose.txt: Matrix table for all genes expression.

extract_protocol:
RNA was extracted from cells using the RNeasy plus kit (Qiagen).
Libraries were prepared using Illumina’s TruSeq Stranded Total RNA library preparation kit. Libraries were sequenced on a 75 bp single-end run using the NextSeq 500 High-Output Kit (75-cycle; 400 M flow cell).


title: colon tissues, DSS+BV2

city: Changsha

first: Xing

last: Wu

address: 138 Tongzipo Road, Changsha, Hunan 410013, P.R. China

department: Department of Gastroenterology

institute: The Third Xiangya Hospital of Central South University

data_processing:
Data filtering: The raw data was filtered with SOAPnuke (v1.5.2) by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 10%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 50%, afterwards clean reads were obtained and stored in FASTQ format.
Reference genome mapping：The clean data were mapped to the reference genome by HISAT (v2.1.0)
Reference gene mapping: The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5).The expression level of genes was calculated by RSEM (v1.2.8)
The reference genome was GCF_000001635.26_GRCm38.p6
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Colon

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep kit following manufacture's  protocols.

value: Colon

value: DSS+BV


title: colon tissues, DSS+BV1


title: colon tissues, DSS+BV3


title: colon tissues, DSS3

value: DSS


title: H2Aub-Col, rep1

value: Seedlings (12 DAG)


title: No_glucose_input


title: miRNA_MCD mice-1


title: miRNA_ND mice-2

source_name: Wild-type mice fed with normal diet


title: colon tissues, DSS2


title: No glucose rep1


title: UBP-GFP, rep2

data_processing:
Raw data with adapter sequences and low-quality sequences was filtered using SOAPnuke software developed by BGI with following parameters: -n 0.01 -l 20 -q 0.4 --cutAdaptor -Q 2 -G --polyX 50 --minLen 100.
The reads were mapped to the Arabidopsis genome (TAIR10) using Bowtie2 2.4.5 using default parameters. Duplicated reads were removed using Picard tool MarkDuplicates option and only uniquely mapped reads were retained for further analysis.
Peaks were called uing MACS v3.0.0 with the significance cut-off q-value <=0.01 and narrowPeaks files were generated.
Bigwig files were generated using deepTools bamCoverage with RPGC normalisation.
Assembly: TAIR10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
12-DAG seedlings were ground in liquid N2 to fine powder and resuspended in nuclei isolation buffer (60 mM HEPES pH 8.0, 1 M Sucrose, 5 mM KCl, 5 mM MgCl2, 5 mM EDTA, 0.6% Triton X-100, 0.4 mM PMSF, pepstatin and complete protease inhibitors (Roche). Then, the samples were cross‐linked with 25 mM ethylene glycol bis succinimidyl succinate (EGS) by rotating for 20 min and with 1% formaldehyde by rotating for 10 min. The crosslinking of samples was stopped by 2M glycine for 10 min at room temperature. The chromatin was isolated and sheared into 200–500 bp fragments by sonication. For IP, the sonicated chromatin was incubated with 20 μl of anti‐GFP antibody (Thermo Fisher #A11122) overnight at 4°C while gentle rotating.
BGISEQ platform Chip-seq library preparation:  1)End repair and adapter ligation:Fill the ends of IP/Input DNA followed by 5' phosphorylation. A 3' sticky-end with an overhanging A is formed, which could ligate with an overhanging T at the 3' end of the bubble adapter;  2)PCR amplification: PCR amplify the ligated products with specific primers;  3)Single-strand separation and circularization: Separate PCR products into single-strands by thermal denaturation. Then circularize the single-stranded DNA through a bridge primer to obtain single-stranded circular DNA library;  4)Sequencing: Amplified products DNA Nanoballs (DNBs) are used for sequencing.


title: CTRL_Pol_II_CHIP

value: RNA Pol II (cst)


title: UBP-GFP, rep1


title: miRNA_ND mice-1


title: Ctrl rep1


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 12h - 10X Multiome ATAC - replicate 5

status: Public on Dec 05 2023

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
10x Genomics
L1_rice_multiome_RNA_combined_with_ATAC.RData

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed using the Cell Ranger software. Data filtering was performed with Seurat
Assembly: Os-Nipponbare-Reference-IRGSP-1.0  and Sorghum bicolor v3.0.1
Supplementary files format and content: Seurat object
Library strategy: 10X-multiome (RNA + ATAC-seq)

organism: Oryza sativa

source_name: seedling

growth_protocol: 5 day old seedlings grown on soil were exposed to light and harvested at different time points during de-etiolation.

extract_protocol:
Fresh tissue from each time point was finely chopped, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter. To enrich the filtered solution for nuclei, an Optiprep (Sigma) gradient was used.
Library construction was performed according to the manufacturer's specification (Chromium Next GEM Single Cell Multiome ATAC Kit, 10x Genomics)

value: seedling


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 12h - 10X Multiome ATAC - replicate 6


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 12h - 10X Multiome ATAC - replicate 4


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 12h - 10X Multiome ATAC - replicate 3


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 0h - 10X Multiome ATAC - replicate 5


title: H2Aub-Col, rep2


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 0h - 10X Multiome ATAC - replicate 4


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 12h - 10X Multiome RNA - replicate 6

molecule: nuclear RNA


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 0h - 10X Multiome ATAC - replicate 3


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 12h - 10X Multiome RNA - replicate 5


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 12h - 10X Multiome RNA - replicate 3


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 0h - 10X Multiome RNA - replicate 5


title: Input


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 0h - 10X Multiome RNA - replicate 3


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 12h - 10X Multiome ATAC - replicate 2


title: Ctrl rep2


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 0h - 10X Multiome ATAC - replicate 1


title: colon tissues, DSS1


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 0h - 10X Multiome ATAC - replicate 2


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 0h - 10X Multiome RNA - replicate 2


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 12h - 10X Multiome ATAC - replicate 1


title: 7-day-old light grown rice seedlings - replicate 1 - BS Marker Line

description:
10x Genomics
L1_rice_mT_combined.Rdata

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed using the Cell Ranger software. Data filtering was performed with Seurat
Assembly: Os-Nipponbare-Reference-IRGSP-1.0  and Sorghum bicolor v3.0.1
Supplementary files format and content: Seurat object

growth_protocol: Oryza sativa spp. japonica cultivar Kitaake single copy homozygous T2 seeds were dehusked and sterilized in 10% (v/v) bleach for 30 min. After washing several times with sterile water, seeds were incubated for 2 days in sterile water at 29°C in the dark. Germinated seedlings were transferred to ½ strength Murashige and Skoog medium with 0.8% agar in magentas and grown for 5 days in the light in a growth chamber at temperatures of 28°C and 20°C during the day and night, respectively, and a photoperiod of 12 h light and 12 h dark.

extract_protocol:
Seedlings were chopped on ice in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.5 mM spermidine, 0.2 mM spermine, 0.01% Triton-X, 1x Roche complete protease inhibitors, 1% BSA, Protector RNase inhibitor) with a sharp razor blade. The suspension was filtered through a 70 mm filter and subsequently through a 35 mm filter. Nuclei were stained with Hoechst and FACS purified on an AriaIII instrument, using a 70 mm nozzle. Nuclei were collected in an Eppendorf tube containing BSA and Protector RNase inhibitor. Nuclei were sorted based on the mTurquoise2 fluorescent signal. Nuclei were collected in minimal Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, RNase inhibitor, 0.05% BSA).
Library construction was performed according to the manufacturer's specification (Chromium Next GEM Single Cell 3' HT Kit v3.0, 10x Genomics)


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 0h - 10X Multiome RNA - replicate 1


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 12h - 10X Multiome RNA - replicate 1


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 12h - 10X Multiome RNA - replicate 2


title: 7-day-old light grown rice seedlings - replicate 2 - BS Marker Line

description:
10x Genomics
L1_rice_mT_combined.Rdata


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 12h - 10X

description:
10x Genomics
L1_rice_combined.RData

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter. To enrich the filtered solution for nuclei, an Optiprep (Sigma) gradient was used. Enriched nuclei were then stained with Hoechst, before being FACS purified.
Library construction was performed according to the manufacturer's specification (Chromium Next GEM Single Cell 3' HT Kit v3.0, 10x Genomics)


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 8h - 10X

description:
10x Genomics
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 12h - 10X Multiome RNA - replicate 4


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 1h  - 10X

description:
10x Genomics
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 0h - 10X

description:
10x Genomics
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 0.5h - 10X

description:
10x Genomics
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 0h - 10X Multiome RNA - replicate 4


title: Cyc8-AA +Rap+Man_3(Biol rep 3)

city: Dublin 2

first: Alastair

last: Fleming

address: College Green

department: Microbiology Dept.

institute: Trinity College Dublin

data_processing:
Raw sequencing data was processed using fastp (version 0.20.0) software to remove poor quality bases (below Phred Quality 20) oradapter sequences.
Assembly: High quality sequence reads were mapped to the Saccharomyces cerevisiae S288c reference genome available on ENSEMBL using the STAR aligner(STAR v2.7.3). BAM files were generated as a result of this step.
Supplementary files format and content: Raw alignment counts for genes in a tab-delimited text file
Supplementary files format and content: Normalised counts and Differences in ratios (both generated using R/Bioconductor DESeq2 package) between the Flo+ Cyc8-AA experiment and the Flo- Cyc8-AA experiment. Provided in a tab-delimited text file

organism: Saccharomyces cerevisiae

source_name: log phase yeast cells

growth_protocol: All samples were grown in YPD (2% glucose) media at 30° C.

extract_protocol: Total RNA was extracted using the hot phenol method, followed by DNase treatment and purification using the RNeasy Minelute Cleanup Kit (Qiagen).

treatment_protocol: Rapamycin (1μg/ ml) and/ or mannose (025M) were added to the relevant samples at early  exponential growth phase (OD600 = ~0.3) and samples for RNA isolation were taken after 4 hours.

value: log phase yeast cells

value: Cyc8-AA made in HHY221 background (Mata tor1-1 fpr1::loxP-LEU2-loxP RPL13A2xFKBP12::loxP CYC8-FRB::HIS3)

value: Grown for 4 hours after the addition of rapamycin and mannose (final concentration = 1μg/ ml and 025M respectively)


title: Cyc8-AA +Rap+Man_2(Biol rep 2)


title: Cyc8-AA +Rap+Man_1 (Biol rep 1)


title: Cyc8-AA -Rap+Man_3(Biol rep 3)

value: Grown for 4 hours after the addition of mannose (final concentration = 025M)


title: Cyc8-AA -Rap+Man_1 (Biol rep 1)


title: ESC_TRE_DUX_TRIM33KO_pLV2_1_DOX_rep2

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

data_processing:
Basecalling was performed using bcl2fastq version 2.20.0
RNAseq reads were adapter trimmed using cutadapt v1.18
Trimmed reads were aligned to the mm10 genome with the GENCODE transcriptome annotation version M25 using STAR v2.7.6a (Dobin et al. 2013) with the following parameters: --outMultimapperOrder Random, --winAnchorMultimapNmax 100, --outFilterMultimapNmax 100,--runRNGseed 777
Transcript and transposable element expression was quantified using TEcount from tetoolkit v2.1.4 with "multi" mode enabled and the parameter --stranded "reverse"
Assembly: mm10
Supplementary files format and content: Processed data files represent count files obtained from TEcount. This file is a plain-text, tab-separated file with with the following information: Gene or TE, and raw counts.

source_name: Embryonic Stem Cells

growth_protocol: ESC were grown on 0.1% gelatin-coated plates or alternatively on a feeder layer of growth-arrested MEFs in high-glucose DMEM (Gibco) supplemented with 15% FBS, 1:500 LIF (made in house), 0.1 mM non-essential amino acids, 1% glutamax, 1mM Sodium Pyruvate, 55 mM β-mercaptoethanol, and 1% penicillin/streptomycin (all from ThermoFisher Scientific) at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated using Isolate II RNA Mini Kit (Bioline).
DNA libraries for RNAseq analysis were prepared using NEBNextUltraII Directional RNA Library Prep Kit for Illumina (New England Biolabs, NEB) and NEBNextrRNA Depletion Kit (Human/Mouse/Rat) (NEB) according to the manufacturer’s protocol. Sequencing was performed on the Illumina NextSeq550 (75bp pair-end reads).

treatment_protocol: DOX was added for 16 hours

value: Embryonic Stem Cells

value: DOX


title: ESC_TRE_DUX_TRIM33KO_pLV2_1_DOX_rep1


title: ESC_TRE_DUX_TRIM33KO_pLV2_1_rep2


title: ESC_TRE_DUX_WT_pLV2_2_rep1

value: WT


title: ESC_TRE_DUX_WT_pLV2_2_DOX_rep2


title: ESC_TRE_DUX_TRIM33KO_pLV2_1_rep1


title: ESC_TRE_DUX_WT_pLV2_2_DOX_rep1


title: ESC_TRE_DUX_TRIM24KO_pLV2_1_DOX_rep2


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 6h - 10X

description:
10x Genomics
L1_rice_combined.RData


title: ESC_TRE_DUX_TRIM24KO_pLV2_1_DOX_rep1


title: ESC_TRE_DUX_WT_pLV2_1_rep2


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 2h - 10X

description:
10x Genomics
L1_rice_combined.RData


title: ESC_TRE_DUX_WT_pLV2_1_DOX_rep1


title: ESC_TRE_DUX_TRIM24KO_pLV2_1_rep1


title: ESC_TRE_DUX_TRIM24KO_pLV2_1_rep2


title: ESC_TRE_DUX_WT_pLV2_1_DOX_rep2


title: 7-day-old rice seedlings undergoing deetiolation - timepoint 4h - 10X

description:
10x Genomics
L1_rice_combined.RData


title: Cyc8-AA -Rap+Man_2(Biol rep 2)


title: ESC_TRE_DUX_DUXBL_KO_1_rep2

growth_protocol: ESC were grown on 0.1% gelatin-coated plates or alternatively on a feeder layer of growth-arrested MEFs in high-glucose DMEM (Gibco) supplemented with 15% FBS, 1:500 LIF (made in house), 0.1 mM non-essential amino acids, 1% glutamax, 1mM Sodium Pyruvate, 55 mM β-mercaptoethanol, and 1% penicillin/streptomycin (all from ThermoFisher Scientific) at 37°C and 5% CO2. Mouse embryos were collected in MEM, HEPES supplemented with 0.1% PVA (MEM/PVA). Cumulus cells were removed by treatment with 1 mg/ml hyaluronidase in MEM/PVA. Embryos were transferred to KSOM at 37ºC in an atmosphere of 5% CO2, 5% O2 and 90% N2 until microinjection.

extract_protocol:
Total RNA was isolated using Isolate II RNA Mini Kit (Bioline).
DNA libraries for RNAseq analysis were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, NEB) and NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB) according to the manufacturer’s protocol. Sequencing was performed on the Illumina NextSeq550 (75bp pair-end reads).


title: ESC_TRE_DUX_DUXBL_KO_1_DOX_rep1


title: ESC_TRE_DUX_DUXBL_KO_1_DOX_rep2


title: ESC_TRE_DUX_WT_1_DOX_rep1


title: ESC_TRE_DUX_WT_1_rep2


title: ESC_TRE_DUX_WT_1_rep1


title: ESC_TRE_DUX_WT_1_DOX_rep2


title: ESC_TRE_DUX_DUXBL_KO_1_rep1


title: ESC_TRE_DUX_WT_pLV2_2_rep2


title: Control_WT_2_PB-TRE-3XFLAG-DUXBL_pCW57-DUX_NoDOX_FLAG_rep1

data_processing:
Basecalling was performed using bcl2fastq version 2.20.0
Data were processed using a modified version of Cut&RunTools (Zhu et al., 2019).  Reads were adapter trimmed using fastp v.0.20.0 (Chen et al., 2018).  An additional trimming step was performed to remove up to 6bp adapter from each read.
Trimmed reads were aligned to a hybrid mm10 and E. coli (MG1655) genome using bowtie2 (Langmead et al., 2012) with the ‘dovetail’ and ‘sensitive’ settings enabled.  Aligned fragments were segregated into mouse and carry-over (E. coli) subsets.
Normalized reads per genomic signal (RPGC) signal tracks were generated from the mouse alignments using the ‘bamCoverage’ utility from deepTools (Ramirez et al., 2016) with parameters  bin-size=25, smooth length=75, and with ‘center_reads’ and ‘extend_reads’ options enabled.
Assembly: mm10
Supplementary files format and content: bigwig files containing reads per genomic content (RGPC) normalized read density.
Library strategy: CUT&RUN

extract_protocol:
The CUT&RUN protocol was slightly modified from (Skene et al., 2018; Meers et al., 2019). In brief, cells were washed thrice with Wash Buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, Roche complete Protease Inhibitor tablet EDTA free) and bound to activated Concanavalin A beads (Polysciences) for 10 minutes at room temperature. Cells were then permeabilized in Digitonin Buffer (0.05 % Digitonin and 0.1% BSA in Wash Buffer) and incubated with corresponding antibodies at 4°C for 2 hours. For negative controls, Guinea Pig anti-Rabbit IgG (Antibodies-online) was used. Following antibody incubation, cells were washed with Digitonin Buffer and incubated with a hybrid protein A-protein G-Micrococcal nuclease (pAG-MNase) at 4°C for 1 hour. Samples were washed in Digitonin Buffer, resuspended in 150 μl Digitonin Buffer and equilibrated to 0°C on ice water for 5 minutes. To initiate MNase cleavage, 3 μl 100 mM CaCl2 was added to cells and after 1 hour of digestion, reactions were stopped with the addition of 150 μl 2x Stop Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02 % Digitonin, 50 μg/ml RNase A, 50 μg/ml Glycogen). Samples were incubated at 37°C for 10 minutes to release DNA fragments and centrifuged at 16,000 g for 5 minutes. Supernatants were collected and a mix of 1.5 μl 20% SDS / 2.25 μl 20 mg/ml Proteinase K was added to each sample and incubated at 65°C for 35 minutes. DNA was precipitated with ethanol and sodium acetate and pelleted by high-speed centrifugation at 4°C, washed, air-dried and resuspended in 10 μ 0.1x TE.
The entire precipitated DNA obtained from CUT&RUN was used to prepare Illumina compatible sequencing libraries. In brief, end-repair was performed in 50 μl of T4 ligase reaction buffer, 0.4 mM dNTPs, 3 U of T4 DNA polymerase (NEB), 9 U of T4 Polynucleotide Kinase (NEB) and 1 U of Klenow fragment (NEB) at 20°C for 30 minutes. End-repair reaction was cleaned using AMPure XP beads (Beckman Coulter) and eluted in 16.5 μl of Elution Buffer (10 mM Tris-HCl pH 8.5) followed by A-tailing reaction in 20 μl of dA-Tailing reaction buffer (NEB) with 2.5 U of Klenow fragment exo- (NEB) at 37°C for 30 minutes. The 20 μl of the A-tailing reaction were mixed with Quick Ligase buffer 2X (NEB), 3000 U of Quick Ligase (NEB) and 10 nM of annealed adaptor (Illumina truncated adaptor) in a volume of 50 μl and incubated at room temperature for 20 min. The adaptor was prepared by annealing the following HPLC-purified oligos: 5′-Phos/GATCGGAAGAGCACACGTCT-3′ and 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATC∗T-3′ (∗phosphorothioate bond). Ligation was stopped by adding 50 mM of EDTA, cleaned with AMPure XP beads and eluted in 14 μl of Elution Buffer. All volume was used for PCR amplification in a 50 μl reaction with 1 μM primers TruSeq barcoded primer p7, 5′-CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC∗T-3′ and TruSeq barcoded primer p5 5′-AATGATACGGCGACCACCGAGATCTACACXXXXXXXXACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3′ (∗ represents a phosphothiorate bond and XXXXXXXX a barcode index sequence), and 2X Kapa HiFi HotStart Ready mix (Kapa Biosciences). The temperature settings during the PCR amplification were 45 s at 98°C followed by 15 cycles of 15 s at 98°C, 30 s at 63°C, 30 s at 72°C and a final 5 min extension at 72°C. PCR reactions were cleaned with AMPure XP beads (Beckman Coulter), run on a 2% agarose gel and a band of 300bp approximately was cut and gel purified using QIAquick Gel Extraction Kit (QIAGEN). Library concentration was determined with KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems). Sequencing was performed on the Illumina NextSeq500 (75bp pair-end reads) or NextSeq2000 (60bp pair-end reads).

treatment_protocol: DOX for 16 hours, Pladienolide B for 24 hours

value: anti-FLAG (Sigma-Aldrich Cat# F1804, RRID:AB_262044)


title: Control_WT_2_PB-TRE-3XFLAG-DUXBL_DOX_FLAG_rep1


title: Control_WT_1_PB-TRE-3XFLAG-DUXBL_DOX_IgG_rep1

value: anti-IgG (Antibodies-Online, Cat# ABIN101961,RRID:AB_10775589)


title: Control_WT_2_FUGW-DUXBL_DUXBL_rep2

value: anti-DUXBL (Origene, Cat #TA331435, Lot number:QC6694-190621)


title: Control_WT_2_PB-TRE-3XFLAG-DUXBL_NoDOX_IgG_rep1


title: Control_WT_1_PB-TRE-3XFLAG-DUXBL_NoDOX_FLAG_rep1


title: ESC_TRE_DUX_WT_pLV2_1_rep1


title: Control_WT_2_FUGW-DUXBL_IgG_rep2


title: Control_WT_1_PB-TRE-3XFLAG-DUXBL_DOX_FLAG_rep1


title: Control_WT_2_FUGW_DUXBL_rep2


title: Control_WT_1_FUGW-DUXBL_IgG_rep1


title: Control_WT_2_FUGW_IgG_rep2


title: Control_WT_1_FUGW_IgG_rep1


title: Control_WT_1_FUGW_DUXBL_rep1


title: Control_WT_1_FUGW-DUXBL_DUXBL_rep1


title: Low Calorie, Day 5, 25C, WT, Rep 2, ZT20

city: Evanston

first: William

last: Kath

state: IL

address: 2145 Sheridan Rd

department: Engineering Sciences and Applied Mathematics

institute: Northwestern University

data_processing:
Single-end reads were quality-assessed with FastQC and then trimmed with Atropos version 1.1.31 using the options atropos -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --minimum-length 16
Reads were then aligned and quantified using STAR (version 2.7.10a_alpha_220818) using the options  --outFilterType BySJout --alignIntronMax 1000000  --quantMode GeneCounts TranscriptomeSAM
RSEM (version 1.3.1) was then used with options --strandedness none to produce tags-per-million (TPM) counts for each gene from transcriptome alignments.
Assembly: Ensembl Drosophila melanogaster BDGP6.32 reference (release 107)
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

organism: Drosophila melanogaster

source_name: fat body (FB)

growth_protocol: All the flies used for experiments were first raised on a standard yeast-cornmeal-molasses based diet under a light-dark (LD) 12:12h cycle. Young mated female (~3 days old) flies (w^{1118}: Bloomington stock number 5905, Clk-Jrk: backcrossed 7 times to w^{1118}) of ~24 hours cohorts were entrained at either 25C or 18C for 5 days in 12L:12D cycles on a standard or diluted diet (Control: 15% [w/v] Sucrose and Yeast, 15SY; Dietary Restriction: 5% [w/v] Sucrose and Yeast, 5SY).

extract_protocol:
To collect dissected fat body samples at 2-hour and 4-hour intervals from ZT0 (set to 8AM) to ZT22 set (set to 10PM) during the daytime only, flies were entrained in two separate incubators with inverse light:dark schedule (LD and DL). On the day of sampling, flies were directly dissected without dry ice to harvest fat tissues in the abdomen. Pinned flies were cut to remove organs in the abdomen (intestine, ovaries, malpighian tubules, etc). Fat tissues attached to epidermis was collected. Dissected fat body tissues from 10 flies were homogenized in pH 7.4 PBS for 2 min using a Kontes motor and pestle, and were incubated TRIzol LS Reagent (Thermo Fisher, Waltham, MA) for 15 min. RNA was extracted according to the manufacturer's instructions and residual DNA in the homogenized samples was removed by RNAse free DNase I (Thermo Fisher Scientific). Quality of RNA samples were checked with Agilent 2100 Bioanalyzer.
cDNA library was constructed with poly(A) selected mRNA using Truseq RNA library preparation kit and then sequenced at the Genomics Core Facility at the University of Chicago on Illumina HiSeq 2000 System.

value: fat body (FB)


title: Low Calorie, Day 5, 25C, WT, Rep 2, ZT22


title: Control_WT_2_PB-TRE-3XFLAG-DUXBL_pCW57-DUX_DOX_FLAG_rep1


title: Low Calorie, Day 5, 25C, WT, Rep 2, ZT18


title: Low Calorie, Day 5, 25C, WT, Rep 2, ZT14


title: Low Calorie, Day 5, 25C, WT, Rep 2, ZT16


title: Low Calorie, Day 5, 25C, WT, Rep 2, ZT08


title: Low Calorie, Day 5, 25C, WT, Rep 2, ZT12


title: Low Calorie, Day 5, 25C, WT, Rep 2, ZT10


title: Low Calorie, Day 5, 25C, WT, Rep 2, ZT04


title: Low Calorie, Day 5, 25C, WT, Rep 2, ZT02


title: Low Calorie, Day 5, 25C, WT, Rep 1, ZT24


title: Low Calorie, Day 5, 25C, WT, Rep 1, ZT22


title: Low Calorie, Day 5, 25C, WT, Rep 2, ZT24


title: Low Calorie, Day 5, 25C, WT, Rep 1, ZT18


title: Low Calorie, Day 5, 25C, WT, Rep 1, ZT12


title: Low Calorie, Day 5, 25C, WT, Rep 1, ZT14


title: Low Calorie, Day 5, 25C, WT, Rep 1, ZT16


title: Low Calorie, Day 5, 25C, WT, Rep 1, ZT10


title: Low Calorie, Day 5, 25C, WT, Rep 1, ZT20


title: Low Calorie, Day 5, 25C, WT, Rep 1, ZT08


title: Low Calorie, Day 5, 25C, WT, Rep 1, ZT04


title: Low Calorie, Day 5, 25C, WT, Rep 1, ZT06


title: Low Calorie, Day 5, 25C, WT, Rep 1, ZT02


title: High Calorie, Day 5, 25C, JRK mutant, Rep 2, ZT18


title: High Calorie, Day 5, 25C, JRK mutant, Rep 2, ZT22