title: human dissection 6

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

country: Japan

institute: Kobe University Graduate School of Medicine

description: 10x Genomics

data_processing: Cell Ranger Single Cell Software (v 6.1.2) by 10X Genomics against the GRCh38 human reference genome or the mm10 murine reference genome with default parameter

source_name: aorta

extract_protocol: Each sample was washed, cut into small pieces, and digested in enzymatic digestion buffer with 3 mg/ml collagenase type II (LS004176, Worthington), 0.15 mg/ml collagenase type XI (H3506, Sigma), 0.25 mg/ml soybean trypsin inhibitor (LS003571, Worthington), 0.1875 mg/ml elastase lyophilized (LS002292, Worthington), 0.24 mg/ml hyaluronidase type I (H3506, Sigma), and 2.38 mg/ml 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES, H4034, Sigma) in PBS with Ca2+ and Mg2+ at 37 °C for 60 minutes while shaking.

value: aorta


title: 20-6t2_S13

status: Public on Mar 01 2024

type: SRA

city: Rotterdam

first: Paul

last: Hengeveld

address: Dr Molewaterplein 40

department: Immunology

country: Netherlands

institute: Erasmus MC

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
20-6t2_S13_L001

library_source: genomic

data_processing:
Raw FASTQ files were uploaded to the ARResT/Interrogate immunoprofiler for annotation and initial exploratory analysis. The full productive IGH repertoire for each sample was downloaded in .csv format and processed in R (R Core Team, 2020) during further analysis.
Assembly: GRCh38
Supplementary files format and content: Tab delimited tekst file containing: sample,QC.status,scenario,rearrangements,raw.count,w.junction.count,w.junction.percent,artefacts.count,artefacts.percent,usable.count,usable.percent,w.most.pop.cln.s..count,w.most.pop.cln.s..percent,uniq.usable.seq.count,clonotypes.count,diversity..norm.ed..count,effective.species.count,R1.Q.mean.stdev.count,R2.Q.mean.stdev.count,joined.normally.count,joined.normally.percent,joined.loosely.count,joined.loosely.percent,total.joined.count,total.joined.percent,saved.from.unjoined.count,saved.from.unjoined.percent,low.quality..ee.nt...0.01..count,low.quality..ee.nt...0.01..percent,short...50nt..count,short...50nt..percent,annotated.count,annotated.percent,w.TR.receptor.count,w.TR.receptor.percent,w.B.chain.count,w.B.chain.percent,w.VJ.Vb..Db..Jb.count,w.VJ.Vb..Db..Jb.percent,w.VJ.Vb..Db..Jb.cln

molecule: genomic DNA

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
gDNA was available from the HOVON-139/GIVE trial. 2-12 ug DNA was amplified through multiplex PCR of IGHV-IGHD-IGHJ gene rearrangements following the EC-NGS leader primer protocol. After amplification, PCR products were purified on Agencourt AMPURE beads (Beckman Coulter, Brea, CA, USA) and eluted using H2O. The purified product was checked for primer dimers using the Agilent Tapestation (Agilent,Santa Clara, CA, USA).
The intitial multiplex PCR already attached the indexes to the PCR products, so library construction was simply pooling the purified PCR product in equilmolar fashion.

tag: tissue

value: PBMCs

tag: sample type

value: HOVON139/GIVE post-Tx

tag: patient number

tag: timepoint

value: 6 months after randomization


title: mutant zb10, 16DAP endosperm, rep3

city: Chengdu

first: Qiang

last: Huang

state: SC

address: No.211, Huimin Road, Wenjiang District

country: China

institute: sichuan agriculture university

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: Read count extraction and normalization
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Zea mays

source_name: endosperm

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 fllowing manufacturer's protocols.

value: endosperm

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: ESC timecourse_0-72hours

city: Boston

first: Edroaldo

last: Lummertz da Rocha

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

country: USA

institute: Boston Children's Hospital

description:
Library index for LIB1 (ESC 0hr) is: ATAGAGAG , LIB2 (ESC 24hr) is: AGAGGATA, LIB3 (ESC 48hr) is:CTCCTTAC and LIB4 (ESC 72hr) is TATGCAGT.
Single-cell RNA-seq data of ESCs under totipotent culture conditions (0 hours)

data_processing:
Raw sequencing files were processed using a standard indropseq pipeline available at https://github.com/indrops/indrops
Quality control, normalization, graph-based clustering, gene signatures were performed using CellRouter
The project yaml file to be used with the indrops pipeline available at https://github.com/indrops/indrops can be provided upon request
We used scImpute to account for drop-out rates in single-cell RNA-seq data
Processed data for LIB2 (ESC 24hr) and LIB3 (ESC 48hr) not provided because not used in manuscript.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file containing gene expression counts

organism: Mus musculus

source_name: Embryonic Stem Cells

growth_protocol: ESCs were grown in standard feeder free culture condition containing serum and supplemented with Leukemia Inhibitory Factor.

extract_protocol:
RNA was purified and proccessed for indrop according to the protocol from Klein et al (Cell, 2015, doi:10.1016/j.cell.2015.04.044)
RNA libraries were prepared for sequencing by the indrop core facility at Harvard Medical School. We used library version v3 where R1 is the biological read. R2 carries the first half of the gel barcode, R3 carries the library index and R4 the second half of the gel barcode, the UMI and a fraction of the polyA tail. Library index for LIB1 (ESC 0hr) is:ATAGAGAG , LIB2 (ESC 24hr) is: AGAGGATA, LIB3 (ESC 48hr) is:CTCCTTAC and LIB4 (ESC 72hr) is TATGCAGT.

treatment_protocol: ESCs grown in standard conditions were treated with the chemicals described for the LBPXTSb reprogramming condition, for either 24, 48 or 72 hours.

value: ESC

value: totipotent culture conditions

tag: time

value: mixed sample (non-demultiplexed) representing timepoints 0h, 24h, 48h, 72h


title: 20-3t4_S7

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
20-3t4_S7_L001

value: Venetoclax ramp-up


title: Scer, 24 hr fixation, optimal growth, FAIRE Input

city: Canberra

first: Erin

middle: Elizabeth

last: Hahn

state: ACT

address: Clunies Ross

department: National Research Collections Australia

country: Australia

institute: CSIRO

data_processing:
Genome preparation : We performed repeat masking with RepeatMasker v.4.1.0 (http://www.repeatmasker.org) through two rounds of masking, first with default settings and with standard Illumina adapters using -e rmblast enabled.
Alignment: For deduplication with the IDT library unique molecular identifiers (UMIs), we converted the Fastq files to BAM format using FastqToSam (PICARD v 2.9.2), extracted the UMIs with ExtractUmisFromBam (FGBio v. 1.3.0) and restored the files to FastQ format with SamToFastq (PICARD). We aligned raw reads using kalign (ngskit4b tool suite version 200218) with options -c25 -l25 -d50 -U4. We removed PCR and optical duplicates using MarkDuplicates (PICARD) enabling REMOVE_DUPLICATES=TRUE and utilising UMIs. We computed and corrected for GC-bias with deepTools version 3.5.1 using an effective genome size of 12,157,105 bp.
Peak analysis: We analysed regional occupancy after quantile normalisation of sequencing depth differences between treatment and control to calculate differential occupancy values with the dtriple function in DANPOS3. We analysed all alignments both as individual samples and as pools of three replicates. For profiling the effect of FAIRE and MNase treatment, we used a corresponding input control. For differential peak analyses, we ran pooled heat-shocked cultures versus pooled optimal growth conditions as input control.
Assembly: S288C R64/sacCer3
Supplementary files format and content: WIG files are provided for all individual samples and DANPOS3 comparions with input controls and between conditions

organism: Saccharomyces cerevisiae

source_name: BJ5464 (delta-URA3)

growth_protocol: We grew Saccharomyces cerevisiae strain BJ5464 auxotroph ΔURA3 in 500 mL Yeast Extract-Peptone-Dextrose (YPD) medium to OD600 = 0.75 at 28°C.

extract_protocol:
We pelleted the fixed cells (4,000 × g, 5 min, 4°C), washed twice with Phosphate Buffered Saline, pH 7.4 (PBS), then resuspended in 10 mL cold Glycine Tris EDTA (GTE; 100 mM glycine, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA) buffer and incubated at 4°C with rocking for 24 hr.    We isolated nuclei by harvesting fixed cells (4,000 × g, 5 min, 4°C), washed twice with cold milliQ water, and resuspended in 2 mL Spheroplast Buffer (SB; 1M Sorbitol, 50 mM Tris, pH 7.5 with freshly added 10 mM b-mercaptoethanol).We obtained spheroplasts by adding Zymolase 20T (MP Biomedicals) to 0.25 mg/mL and incubating at 28°C for 2 hr. We harvested fixed spheroplasts (1,500 × g, 10 min, 4°C), washed twice with cold SB and resuspended in 10 mL. We aliquoted spheroplasts such that each aliquot contained a volume of cells from 4 mL and 10 mL of original culture for the short (15 min and 1 hr) and long (6 hr and 24 hr) cultures, respectively. We collected more cells from longer fixation timepoints to account for lower expected DNA recovery due to heavy fixation. We pelleted spheroplasts (1,500 × g, 10 min, 4°C), removed the supernatant and froze the tubes at -80°C.  gDNA and RNA extraction from unfixed yeast   We extracted gDNA and RNA from unfixed cells frozen at -80°C. For gDNA, we resuspended cells in 200 mL SB, added Zymolase 20T to 0.25 mg/mL and 1 mL RNase A and incubated at 37°C for 30 min. We harvested spheroplasts (3,000 × g, 10 min, 4°C), resuspended in 100 mL PBS plus 0.01 M EDTA, added 2 mL of proteinase K (20 mg/mL) and incubated at 56°C for 45 min in a thermal mixer with agitation at full speed (1,400 rpm). We purified gDNA using phenol:chloroform:isoamyl alcohol (25:24:1) extraction and concentrated the gDNA on beads as described in Small fragment-optimised bead purification of DNA, eluting in 20 mL 10 mM Tris, pH 8.0. For RNA, we resuspended three aliquots per culture in 450 mL RLT Buffer and followed the manufacturer’s instructions for the Qiagen RNeasy plant mini kit, eluting in 30 mL nuclease-free water.   MNase treatment:  We resuspended triplicate aliquots of each fixation timepoint (heat shock and optimal growth) in 200 mL MNase Digestion Buffer (DB; 0.5 mM spermidine, 0.075% Nonidet P40, 50 mM NaCl, 10 mM Tris pH 8.0, 5 mM MgCl2, 5 mM CaCl2 plus freshly added cOmplete EDTA-free protease inhibitor cocktail (Merck)), added 0.5 U of micrococcal nuclease (Worthington Biochemical Corporation) and incubated the tubes for 7 min in a 37°C water bath. We quenched the reaction with 50 μL Quenching Solution (QS; 4% Triton X-100, 1.2% SDS, 600 mM NaCl, 12 mM EDTA) and incubated the tubes on ice for 10 min. We collected digested chromatin by centrifuging (14,000 × g, 10 min, 4°C) and removing the supernatant to a new tube. We digested the supernatant with proteinase K at a final concentration of 0.1 mg/mL and incubated at 56°C for 2 hr. We purified DNA with two phenol:chloroform:isoamyl alcohol (25:24:1) extractions, RNase treatment (1 μL RNase A and incubation at room temperature for 30 min) between extractions one and two followed by Small fragment-optimised bead purification of DNA, resuspending in 20 mL 10 mM Tris, pH 8.0 and fully de-crosslinking at 65°C overnight.    FAIRE treatment: We resuspended four aliquots from each fixation timepoint ( heat shock and optimal growth) in 1 mL Chromatin Shearing Buffer (CSB; 10 mM Tris-HCl pH 8.0, 0.1% SDS, 1 mM EDTA) and transferred each to a 1 mL Covaris milliTUBE. We sonicated the tubes in a Covaris E220 focused-ultrasonicator on settings PIP 420, duty factor 30%, cycles per burst 200 for 7 min (short fixation time points) or 12 min (long fixation time points). After clarifying the lysate by centrifugation (5,500 × g, 15 min, 4°C), we set aside one tube per sample type at this point as an input control. With the remaining tubes, we performed phenol:chloroform:isoamyl alcohol (25:24:1) extraction with back-extraction of the organic phase with addition of 150 mL 10 mM Tris, pH 8.0 followed by an additional extraction. To the aqueous and input control tubes, we added 10 mL RNase A and incubated at room temperature for 30 min followed by addition of 2 mL proteinase K and incubation at 55°C for 1 hr. We de-crosslinked overnight with incubation at 65°C and concentrated the DNA via Small fragment-optimised bead purification of DNA, resuspending in 20 mL 10 mM Tris, pH 8.0.
xGen cfDNA & FFPE DNA Library Prep Kit (IDT)

treatment_protocol: Splitting the culture into equal volumes, one underwent 37°C heat stress for 20 minutes. We added formaldehyde (1%) to both optimal and heat shock flasks and incubated with slow shaking at room temperature. At 15 min, 1 hr, 6 hr and 24 hr we collected aliquots and quenched fixation with addition of glycine to 0.125 M followed by gentle shaking at room temperature for 15 min.

tag: strain

value: BJ5464 (delta-URA3)

value: Optimal growth

tag: fixation time

value: 24 hr


title: EF2P5

city: Hong Kong

first: Mingxi

last: WENG

state: Not Applicable

address: L408A, Laboratory Block, 21 Sassoon Road, Pokfulam, Hong Kong

country: Hong Kong

institute: School of Biomedical Sciences, The University of Hong Kong

data_processing:
Raw reads in fastq format were aligned to the hg38 transcriptome using RSEM and bowtie 2.0 (with options: rsem-calculate-expression --bowtie2 --bowtie2-sensitivity-level very_sensitive --no-bam-output --estimate-rspd --paired-end).
Gene level alignment results of samples were merged and annotated using glbase3.
Read counts per genes were calculated using RSEM and normalized to GC content using EDAseq. GC-normalized read counts no less than 20 in at least two samples were kept, leading to a final read count table.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files. The first column is the ensemble gene ID(ensg). The second column contains the official gene names (name). The rest of the columns contain the normalized read counts for each sample.

source_name: Pluripotent stem cells

growth_protocol: Human naive PSCs (NPSCs), including those reprogrammed from dermal fibroblasts and iEPSCs, were propagated in different naïve culture condition: EPSCM, PXGLM and HENSM on mitomycin C-treated ICR MEF feeders. Human iEPSCs were propagated in EPSCM. ROCK inhibitor (Y-27632, #) were added to culture medium at the day of cell-replating onto feeders. Human NPSCs and EPSCs were cultured in a humidified incubator at 37 ℃.

extract_protocol:
NPSCs and iEPSCs were incubated onto gelatin for 60 min at 37 degree to remove MEFs. Total RNA was extracted using TRIzol reagent (Invitrogen, #15596018) following the user guide quantified using a Nanodrop One spectrophotometer (Thermo Scientific).
mRNA is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment. ffective concentration of library was determined by Q-PCR. Finally, the qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume.

value: Pluripotent stem cells

value: hiEPSC

value: EPSCM


title: Scer, 15 min fixation, heatshock, FAIRE Input

value: Heatshocked

value: 15 min


title: 20-3t4_S27

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
20-3t4_S27_L001


title: mutant zb10, 16DAP endosperm, rep2


title: Scer, 6 hr fixation, optimal growth, FAIRE Input

value: 6 hr


title: human dissection 3 adventitia

description: 10x Genomics

library_source: transcriptomic single cell

value: aorta


title: human dissection 3 intima

description: 10x Genomics


title: 1-t5_S2

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
1-t5_S2_L001

value: PBMCs

value: HOVON139/GIVE post-Tx

value: End of induction treatment


title: Scer, 1 hr fixation, optimal growth, FAIRE Input

value: 1 hr


title: WT, 16DAP endosperm, rep3

value: endosperm

value: WT


title: mutant zb10, 16DAP endosperm, rep1


title: 19-6t4_S12

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
19-6t4_S12_L001

value: 12 months after randomization


title: Scer, 15 min fixation, optimal growth, FAIRE Input

value: BJ5464 (delta-URA3)


title: MCF7 cells, shRNF20-40, 1% O2 (biol rep 2)

city: Baltimore

first: YONGKANG

last: YANG

state: Maryland

address: Room 673, MRB, 725 North Broadway

department: ICE

institute: Johns Hopkins University

data_processing:
RNA-seq data were processed and interpreted using Genialis Expressions software (https://www.genialis.com).
Sequence quality checks were performed on raw and trimmed reads (FastQC), trimming and quality filtering of reads (BBDuk), mapping to reference human genome Ensembl v.92 (STAR), expression quantification (featureCounts), and expression normalisation (RNA.norm).
Assembly: GRCh38
Supplementary files format and content: Excel tables containing detailed information on RPKM values for each Sample

extract_protocol:
RNA was harvested using TRIzol (Invitrogen) and treated with DNase (Qiagen).
Library preparation and sequencing using the NovaSeq 6000 platform (Illumina) were performed by the Johns Hopkins Genetics Resources Core Facility High-Throughput Sequencing Center.

value: breast cancer cells

value: RNF20/40 knockdown


title: Scer, 1 hr fixation, heatshock, FAIRE Input


title: 19-6t2_S3

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
19-6t2_S3_L001

value: 6 months after randomization


title: MCF7 cells, shRNF20-40, 1% O2 (biol rep 1)


title: WT, 16DAP endosperm, rep2


title: Scer, Unfixed, heatshock, gDNA

value: Unfixed


title: 19-3t3_S26

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
19-3t3_S26_L001

value: Venetoclax ramp-up


title: WT, 16DAP endosperm, rep1


title: Scer, Unfixed, optimal growth, gDNA

value: Optimal growth


title: 19-3t3_S11

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
19-3t3_S11_L001


title: MCF7 cells, shRNF20-40, 20% O2 (biol rep 3)


title: Dve1 Light 6 days after fertilization replica 3

city: Sevilla

first: Gabriel

last: Gutierrez

address: PO BOX 1095

department: Genetics

country: Spain

institute: University of Seville

data_processing:
libraries were run on Genome Analyzer (Illumina NovaSeq 6000).
paired-end reads of 150 nucleotide each were mapped against the N. crassa OR74A genome by using Star 2.7
quality was checked using FastQC
automatic preprocessing of the reads was carried out with AFTERQC 0.9.6
SeqMonk was used for visualization and quantification
Supplementary files format and content: raw counts, matrix text format

organism: Neurospora crassa

source_name: Sexual development tissue

growth_protocol: Induction of formation of protoperithecia were carried out by spreading a total of 2x104 conidia into nitrogen-poor Synthetic Crossing Medium (SCM) agar´s plates and then incubated at 22°C with light or in darkness, depending on the experiment, for 7 days to allow the formation of protoperithecia. Conidia from a strain of opposing mating type were collected and suspended in 2.5% Tween 20. Formation of protoperithecia in each strain was examined using a stereomicroscope between days 5 to 7 prior to fertilization. Crosses were performed by applying 2 ml of a conidia suspension (5x105 conidia/ml with 2.5% Tween 20) to the surface of the protoperithecium plates. After fertilization, sexual development occurred under the same culture conditions as protoperithecium development, and all the process was monitored using stereomicroscope.

extract_protocol:
Fungal material was harvested by scrapping the surface with a razor blade. Samples were collected before the crossing (2 and 1 day prior fertilization), right before crossing (day 0) and 1, 2, 4, and 6 days after fertilization. All tissues and perithecia were immediately frozen in liquid nitrogen and stored at -80°C.
Poly-A selection and cDNA libraries preparation for RNA were prepared according to the Illumina mRNA Sample Preparation Guide

treatment_protocol: For this experiment, strains of complementary mating type, ∆ve-1 mat A and wild type mat a were used.. Samples were collected before the crossing (2 and 1 day prior fertilization), right before crossing (day 0) and 1, 2, 4, and 6 days after fertilization.

tag: time point

value: 6 days after fertilization

value: Light


title: mutant zb10, V9 leaf, rep2

source_name: leaf

value: leaf


title: 18-6t4_S12

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
18-6t4_S12_L001

value: PBMCs


title: MCF7 cells, shRNF20-40, 1% O2 (biol rep 3)


title: mutant zb10, V9 leaf, rep3


title: MCF7 cells, shRNF20-40, 20% O2 (biol rep 1)


title: Dve1 Dark 6 days after fertilization replica 3

value: Dark


title: 18-6t2_S11

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
18-6t2_S11_L001

value: HOVON139/GIVE post-Tx


title: MCF7 cells, shRNF20-40, 20% O2 (biol rep 2)


title: mutant zb10, V9 leaf, rep1


title: Wild type Light 6 days after fertilization replica 3

value: Wild type


title: WT, V9 leaf, rep3


title: Wild type Dark 6 days after fertilization replica 3


title: 18-5PB_S25

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
18-5PB_S25_L001

value: End of induction treatment


title: MCF7 cells, shFACT, 1% O2 (biol rep 3)

value: FACT knockdown


title: MCF7 cells, shFACT, 1% O2 (biol rep 2)


title: WT, V9 leaf, rep2

value: WT


title: 17-t5_S10

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
17-t5_S10_L001


title: Dve1 Light 4 days after fertilization replica 3

value: 4 days after fertilization


title: WT, V9 leaf, rep1


title: 17-3t4_S5

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
17-3t4_S5_L001


title: mutant zb10, V4 leaf green section, rep3


title: Dve1 Dark 4 days after fertilization replica 3


title: MCF7 cells, shFACT, 20% O2 (biol rep 3)

value: breast cancer cells


title: 17-3t4_S24

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
17-3t4_S24_L001


title: MCF7 cells, shFACT, 20% O2 (biol rep 2)


title: Wild type Dark 4 days after fertilization replica 3


title: Wild type Light 4 days after fertilization replica 3


title: mutant zb10, V4 leaf green section, rep2


title: MCF7 cells, shFACT, 20% O2 (biol rep 1)


title: mutant zb10, V4 leaf white section, rep3


title: 1-6t4_S2

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
1-6t4_S2_L001

value: 12 months after randomization


title: Dve1 Dark 2 days after fertilization replica 3

value: 2 days after fertilization


title: 1-6t4_S4

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
1-6t4_S4_L001


title: MCF7 cells, shHIF-1α, 1% O2 (biol rep 2)

value: HIF-1alpha knockdown


title: MCF7 cells, shHIF-1α, 1% O2 (biol rep 3)


title: mutant zb10, V4 leaf white section, rep2


title: mutant zb10, V4 leaf green section, rep1


title: MCF7 cells, shFACT, 1% O2 (biol rep 1)


title: 1-6t2_S2

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
1-6t2_S2_L001

value: 6 months after randomization


title: mutant zb10, V4 leaf white section, rep1


title: MCF7 cells, shHIF-1α, 1% O2 (biol rep 1)


title: Wild type Light 2 days after fertilization replica 3


title: 16-6t2_S14

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
16-6t2_S14_L001


title: 16-3t4_S23

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
16-3t4_S23_L001

value: Venetoclax ramp-up


title: 16-t5_S9

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
16-t5_S9_L001


title: MCF7 cells, shHIF-1α, 20% O2 (biol rep 3)


title: Wild type Dark 2 days after fertilization replica 3


title: Dve1 Light 2 days after fertilization replica 3


title: 16-3t4_S12

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
16-3t4_S12_L001


title: WT, V4 leaf, rep2


title: MCF7 cells, shHIF-1α, 20% O2 (biol rep 2)


title: MCF7 cells, shHIF-1α, 20% O2 (biol rep 1)


title: 15-t7_S8

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
15-t7_S8_L001

value: 24 months after randomization


title: WT, V4 leaf, rep1


title: Wild type Light 1 day after fertilization replica 3

value: 1 day after fertilization

value: Light


title: Dve1 Dark 1 day after fertilization replica 3


title: 15-6t4_S22

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
15-6t4_S22_L001

value: PBMCs


title: WT, V4 leaf, rep3

value: leaf


title: Dve1 Light fertilization day replica 3

value: fertilization day


title: 13-t7_S7

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
13-t7_S7_L001

value: HOVON139/GIVE post-Tx


title: Sequencing data of leaf of heat-resistant line under heat stess condition, replicate 1, bulkRNAseq

city: HOUSTON

first: chuangye

last: Qi

state: Texas

address: One plaza

department: Huffington Center

institute: Baylor College of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt
trimmed reads mapped to reference genome by STAR.
Read count caculated by featurecounts
DEGs identified by DESeq2
Assembly: B73 V4
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: Leaf

extract_protocol:
RNA was harvested using RNeasy Plant Mini kit (Vazyme, Nanjing, China). 2 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina and index codes were added to attribute sequences to each sample
Libraries for mRNA-seq were constructed and sequenced by Novogene Bioinformatics Technology Co., Ltd (Beijing, China)

tag: inbred line

value: Leaf

value: 42℃ for 6h


title: Sequencing data of leaf of heat-resistant line under heat stress condition, replicate 2, bulkRNAseq


title: MCF7 cells, shNTC, 1% O2 (biol rep 2)

value: WT


title: Wild type Dark 1 day after fertilization replica 3

value: Wild type

value: Dark


title: Sequencing data of leaf of heat-resistant line under normal condition, replicate 2, bulkRNAseq

value: 32℃ for 6h


title: Dve1 Light 1 day after fertilization replica 3


title: Dve1 Dark fertilization day replica 3


title: MCF7 cells, shNTC, 20% O2 (biol rep 3)

value: breast cancer cells


title: 1-3t4_S10

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
1-3t4_S10_L001


title: 1-3t4_S8

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
1-3t4_S8_L001


title: Sequencing data of leaf of heat-resistant line under normal condition, replicate 1, bulkRNAseq


title: Wild type Light fertilization day replica 3


title: MCF7 cells, shNTC, 20% O2 (biol rep 2)


title: Sequencing data of leaf of heat-sensitive line under heat stress condition, replicate 2, bulkRNAseq


title: MCF7 cells, shNTC, 1% O2 (biol rep 3)


title: Wild type Dark fertilization day replica 3


title: Sequencing data of leaf of heat-sensitive line under heat stress condition, replicate 1, bulkRNAseq


title: 13-3t4_S4

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
13-3t4_S4_L001


title: MCF7 cells, shNTC, 20% O2 (biol rep 1)


title: MCF7 cells, shNTC, 1% O2 (biol rep 1)


title: CUT&Tag_IgG_H1

city: Guangzhou

first: Liu

last: Yasong

address: Tianhe District Tianhe Road, No. 600

institute: Third Affiliated Hospital Of Sun Yat-Sen University

data_processing:
bcl2fast 2.19 software was used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through Fastp v0.21.0.In this step, clean data (clean reads) were obtained by removing adapter and low-quality reads.All the downstream analyses were based on the clean data with high quality.
Paired end reads were mapped to the GRCh38 genome using Bowtie2 v2.4.2, and extracted reads with MAPQ > 13. Then the PCR duplicates were removed using Picard v2.25.0.
Peaks were called using macs2 v2.2.7.1 with qvalue < 0.1.
The deeptools tool v3.5.1 was used to generate bigwig files from bam files.
Peaks were annotated by the function of annotatePeak of ChIPseeker v1.5.1.
Assembly: GRCh38
Supplementary files format and content: narrowpeak
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: Human embryonic stem cell line

growth_protocol: H1 ESC line was originally obtained from WiCell (Madison, USA), cultured in matrigel-coated plates in mTeSR medium and passaged following the standard protocol.

extract_protocol:
The cells were lysed  by gentle pipetting and placed on ice for 10 min. The cell nuclei remained intact by this treatment, and were collected by centrifuged for 5 min at 500 g at 4°C. The nucleus fraction were resuspended by 200 μl PBS, cross-linked by adding 2 μl of 10% Formaldehyde and incubated at room temperature for 2 min. The cross-link reaction was terminated by adding 5 μl of 25 mM glycine. The cross-linked cell nuclei were centrifuged for 5 min at 600 g at room temperature. The pellets were resuspended in 90 μl wash buffer. Then, 10 μl of Concanavalin A-coated magnetic beads were equilibrated at room temperature and added into each sample, incubation continued for 15 min. The unbound supernatant was removed and bead-bound cells were resuspended in a 1:50 dilution of FOXO1 primary antibody. Primary antibody incubation was performed on a rotating platform at 4°C overnight. Followed by incubation with a secondary antibody at room temperature for 1 h to increase the number of IgG molecules at each epitope bound by the primary antibody. Cell nuclei were washed and incubated with pA-Tn5 adapter complex at room temperature for 1 h and washed under stringent conditions following manufacturer’s instruction. Next, cell nuclei were resuspended in 50 μl Tagmentation buffer by addition of Mg2+ and incubated at 37°C for 1 h. To stop tagmentation, 1ul 10% SDS was added to 50 μl of sample, which was incubated overnight at 37 °C. To extract the genomic DNA, Tagment DNA Extract Beads were added to each tube. Samples were enriched by PCR amplification and a single solid-phase reversible immobilization (SPRI) magnetic bead cleanup step. For the negative control, we omitted the primary antibody, while the secondary antibody could randomly coat the chromatin at low efficiency without sequence bias. The purified DNA was used for library preparation.
library quality was assessed on the Agilent Bioanalyzer 2100 system, and pair-end sequencing was performed on an Illumina platform (Novogene, Beijing, China).

treatment_protocol: Briefly, H1  cells incubated at 37°C or 4°C were harvested, counted, split into 200,000 cells per group and centrifuged for 4 min at 500 g at 37°C or 4°C, respectively.

value: Human embryonic stem cell

tag: cut&tag antibody

tag: temperature

value: control


title: 13-3t4_S21

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
13-3t4_S21_L001

value: Venetoclax ramp-up


title: Dve1 Dark 1 day before fertilization replica 3

value: 1 day before fertilization


title: Dve1 Light 1 day before fertilization replica 3


title: CUT&Tag_FOXO1_H1_37C b

value: FOXO1 Antibody(Cell Signaling Technologies,2880)


title: Sequencing data of leaf of heat-sensitive line under normal condition, replicate 2, bulkRNAseq


title: 12-6t4_S17

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
12-6t4_S17_L001

value: 12 months after randomization


title: Wild type Dark 1 day before fertilization replica 3


title: 12-6t2_S6

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
12-6t2_S6_L001

value: PBMCs

value: 6 months after randomization


title: Sequencing data of leaf of heat-sensitive line under normal condition, replicate 1, bulkRNAseq


title: CUT&Tag_FOXO1_H1_4C b


title: Wild type Light 1 day before fertilization replica 3

value: Light


title: 12-5PB_S20

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
12-5PB_S20_L001

value: HOVON139/GIVE post-Tx

value: End of induction treatment


title: 13-6t4_S8

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
13-6t4_S8_L001


title: Dve1 Light 2 days before fertilization replica 3

value: 2 days before fertilization


title: 11-6t4_S18

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
11-6t4_S18_L001


title: POER4

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

description: 7-day-old PuC3H35-OE grow 7 d under 6% PEG6000 stress

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
The reference genomes and the annotation file were downloaded from  the Populus genome (version3.0,https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa ). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Genome_build: Populus trichocarpa v3.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa)

organism: Populus ussuriensis

source_name: Root

growth_protocol: Approximately 3 cm stem segments were excised from 4-week-old in vitro plants and cultured on half-strength Murashige and Skoog (1/2 MS) medium (Duchefa) containing 20 g/L sucrose. Media used in experiments were adjusted to pH 5.8 before adding 3 g l-1 Gelrite (Duchefa). MeJA were filter sterilized and added to the medium after autoclaving. Cultures were performed in 150 ml Erlenmeyer flasks with 50 ml medium and incubated under a 16 h light/8 h dark photoperiod at 25°C under illumination with cool white fluorescent lights at 45 µmol m−2 s−1.

extract_protocol:
Roots were removed, flash frozen on dry ice, and RNA was harvested using CTAB method. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In vitro P. ussuriensis plants were grown on 1/2 MS plates with 0.6% w/v agar and 2% w/v sucrose for 1 week and then  subsequently transfer to 1/2 MS medium with or without 6% PEG6000

value: PuC3H35-OE roots treated with 6% PEG6000

tag: age

value: 7 d after treated


title: Dve1 Dark 2 days before fertilization replica 3

value: Dark


title: CUT&Tag_FOXO1_H1_37C


title: POER3


title: POER1


title: human 4c 4h passage 62

description: human 4c 4h

data_processing:
Illumina Casava 2.19 software was used for basecalling.
Clean reads were obtained by removing adapter, and excluded reads containing ploy-N and low-quality from raw data.
Reads were aligned to the human genome (Ensembl GRCh38) with Hisat2
For quantification of gene expression, only the reads aligned to exons, and with the mapping quality score larger than 10 were counted using the featureCounts v2.0.1
Assembly: Ensembl GRCh38
Supplementary files format and content: tab-delimited text files include raw count values of genes for each Sample

molecule: polyA RNA

source_name: embryonic stem cell

extract_protocol:
Experiments were conducted by first replacing H1 culture medium with fresh Hibernate-A-based medium, allowing the cells to sit at room temperature for 30 min.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, and further processed for RNA-sequencing (Novogene, Beijing, China)

value: embryonic stem cell

value: cold


title: 11-6t2_S5

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
11-6t2_S5_L001


title: PWR3

description: 7-day-old WT grow 7 d under 6% PEG6000 stress

value: WT roots treated with 6% PEG6000


title: Wild type Light 2 days before fertilization replica 3

value: Wild type


title: 11-3t4A_S19

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
11-3t4A_S19_L001

value: Venetoclax ramp-up


title: PWR2


title: Wild type Dark 2 days before fertilization replica 3


title: human 4c 4h passage 47

description: human 4c 4h

treatment_protocol: Experiments were conducted by first replacing H1 culture medium with fresh Hibernate-A-based medium, allowing the cells to sit at room temperature for 30 min.


title: PWR1


title: 10-t5_S2

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
10-t5_S2_L001


title: Dve1 Light 6 days after fertilization replica 2

value: 6 days after fertilization


title: OER5

description: 7-day-old PuC3H35-OE grow 7 d under control condition

value: nontreated PuC3H35-OE roots

value: 14-day old plants


title: human 4c 4h passage 46

description: human 4c 4h


title: OER2


title: human 4c 4h 37c 2h passage 62

description: human 4c 4h 37c 2h

value: reworm


title: CUT&Tag_FOXO1_H1_4C

value: Human embryonic stem cell

value: FOXO1 Antibody(Cell Signaling Technologies,2880)


title: OER1


title: 10-6t2_S4

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
10-6t2_S4_L001

value: PBMCs

value: HOVON139/GIVE post-Tx

value: 6 months after randomization


title: Dve1 Dark 6 days after fertilization replica 2


title: 10-5PB_S18

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
10-5PB_S18_L001

value: End of induction treatment


title: Wild type Dark 6 days after fertilization replica 2


title: Wild type Light 6 days after fertilization replica 2

value: Light


title: human 4c 4h passage 60

description: human 4c 4h


title: human 4c 4h 37c 2h passage 60

description: human 4c 4h 37c 2h


title: WR2

description: 7-day-old WT grow 7 d under control condition

value: nontreated WT roots


title: 070-5PB_S35

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
070-5PB_S35_L001


title: human 4c 4h 37c 2h passage 47

description: human 4c 4h 37c 2h

value: embryonic stem cell


title: Dve1 Dark 4 days after fertilization replica 2

value: 4 days after fertilization

value: Dark


title: WR3


title: Wild type Light 4 days after fertilization replica 2

value: Wild type


title: 10-6t4_S22

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
10-6t4_S22_L001

value: 12 months after randomization


title: human 4c 4h 37c 2h passage 46

description: human 4c 4h 37c 2h


title: human 37c passage 62

description: human 37c

value: control


title: Dve1 Light 4 days after fertilization replica 2


title: WR1


title: human 37c passage 47

description: human 37c


title: human 37c passage 60

description: human 37c


title: Dve1 Light 2 days after fertilization replica 2

value: 2 days after fertilization


title: Wild type Dark 4 days after fertilization replica 2


title: 068-6-4_S12

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
068-6-4_S12_L001


title: human 37c passage 46

description: human 37c


title: A549 shM16, AA starvation, input

city: nanjing

first: Zhang

last: Jun

state: jiangsu

address: longmiandadao

institute: China Pharmaceutical University

data_processing:
Cutadapt (v.2.8) was used to trim the adapters and low quality sequences with parameter (--match-readwildcards -a NNNNNNNNNNAGATCGGAAGAGCAC -q 20 -e 0.1 -O 3 -m 25 -M 35 -U 10 -A AGATCGGAAGAGCGT -A AGATCGGAAGAGCGTC -A AGATCGGAAGAGCGTCG -A AGATCGGAAGAGCGTCGT -A AGATCGGAAGAGCGTCGTG -A AGATCGGAAGAGCGTCGTGT).
Reads were aligned to rRNA and tRNA sequences so as to remove rRNA and tRNA reads using bowtie2 (v2.2.5) software. Then the clean reads were aligned to human genome (GRCh38) using STAR aligner (v2.7.5c) with parameter (-outFilterMultimapNmax 10 -alignEndsType EndToEnd -outFilterMismatchNmax 2 -outFilterScoreMinOverLread 0.3 -outFilterMatchNminOverLread 0.3 -outFilterIntronMotifs RemoveNoncanonicalUnannotated).
The mapped reads were quantified using featureCounts (v2.0.1) with -t exon parameter. The TPM (transcripts per kilobase million) was used for downstream analysis. Translation efficiency (TE) was calculated by (TPM of Ribo-seq)/(TPM of RNA-seq) and only genes with an RNA-seq TPM greater than 1 were used in the translation efficiency calculation. TE < 0.5 or > 2 were considered as translation-downregulated or translation-upregulated genes. Read coverage plot on each transcript were produced by RiboProfiler(v0.0.6).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts counts for each sample
Supplementary files format and content: tab-delimited text file includes TE (translation efficiency) for each sample
Library strategy: Ribo-seq

source_name: lung

growth_protocol: A549 lung cancer cells were cultured in DMEM (KeyGen Biotech, KGM12800N-500) supplemented with 10% FBS (Viva Cell, C04001-500) and 1% Penicillin-Streptomycin (Life,15140122) at 37℃ with 5% CO2.

extract_protocol:
Input RNA was extracted with TRIzol LS followed by chemical fragmentation. Ribo-seq samples were produced by RNase I digestion followed by RNA extraction using TRIzol LS.
40-60nt region for input and 30nt for ribo-seq were selected according to 15% polyacrylamide TBE-urea gel separation. Desired RNA species were excised and soaked overnight followed by ethanol precipitation. The purified RNA was dephosporylated and added with 3’adapter. The 5’ adapter was added after reverse transcription. Eventually, PCR amplification was proceeded using Phusion High-Fidelity DNA Polymerase.

treatment_protocol: A549 lung cancer cells were treated with complete medium or starvation medium for 2 h

value: lung

value: Non-Small Cell Lung Cancer

value: METTL16 knockdown

value: treated with CHX for 5min, amino acid starvation

tag: fraction

value: Total RNA


title: 068-6-2_S34

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
068-6-2_S34_L001

tag: tissue

value: PBMCs

value: HOVON139/GIVE post-Tx


title: Dve1 Dark 2 days after fertilization replica 2


title: A549 shM16, control, input

value: treated with CHX for 5min, normal culture


title: 070-6-2_S8

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
070-6-2_S8_L001

tag: sample type

value: 6 months after randomization


title: A549 shCtrl, AA starvation, input

description: ICAA

value: WT


title: 068-5PB_S21

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
068-5PB_S21_L001

tag: patient number

value: End of induction treatment


title: Wild type Light 2 days after fertilization replica 2

value: Light


title: QGP1_p13

city: Bern

first: Philipp

last: Kirchner

address: Murtenstrasse 31

department: Pathology

country: Switzerland

institute: University of Bern

data_processing:
Reads were demultiplexed and converted to FASTQ format using bcl2fastq v2.20.0.422
Cutadapt v2.5 was used to trim Illumina adapter sequences and mask 3’ homopolymers longer than 10 bp
Reads containing more than 20 masked bases or being shorter than 65 bp (tumoroid samples) or 50 bp (original tumor tissue) were removed
Trimmed reads were mapped against a custom list of ribosomal RNAs and repetitive RNA elements with bwa v0.7.17, discarding mapping reads. At each step, FastQC v0.11.7 was used to track read quality
Processed reads were mapped to the human genome (GRCh37, GENCODE annotation v37) with STAR v2.7.3a. Mapped reads were deduplicated based on the 8bp UMI located in the R2 using UMI-tools v0.5 with the default directional method. Deduplicated reads were assigned to GENCODE v37 genes in subread v2.0.1
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include raw featureCounts results for each Sample

growth_protocol: Two specimen types were used in this study (for original culutre method please refer to https://doi.org/10.1159/000507669):   1) Orginal tumor tissue from fresh frozen tumor specimen   2) Isolated primary PanNET cells were maintained in AdvDMEM + GF medium (DMEM-F12, 5% FBS, Hepes 10 mM, 1% L-glutamine (200 mM), 1% penicillin (100 U/mL), 1% streptomycin (0.1 mg/mL), 1% amphotericin B (0.25 mg/mL), 20 ng/mL EGF, 10 ng/mL bFGF , 100 ng/mL PlGF, 769 ng/mL IGF-1) and in 24-well Corning® Costar® ultra-low attachment  plates (3–5 × 10^5 cells/well) in a humidified cell incubator (21% O2, 5% CO2, 37°C). For drug screen cells were resuspended in fresh AdvDMEM + GF medium supplemented with 123 µg/mL growth-factor-reduced Matrigel® and plated in 96-well ULA plates (3–5 × 10^3 cells/well).

extract_protocol:
Total RNA was extracted from fresh frozen tumor tissue or cultured cells using Single Cell RNA Purification Kit (Norgen Biotek, #51800)
Sequencing libraries were prepared from RNA using the SMARTer Stranded Total RNA-Seq Kit v3 for picogram input material (Takara, #634488)
Libraries were sequenced as paired-end 101 bp (tumoroid samples) or paired-end 81 bp (original tumor tissues) reads on a NovaSeq 6000 (Illumina) platform at ~30M reads/sample

treatment_protocol: Patient-derived tumoroids were treated with DMSO-control (0.16%), 11.52uM Temozolomide (#S1237), 0.53uM cisplatin (#4333164) for 7 days (168h) in 3-D culture

value: pancreatic NEN cell culture model

value: untreated

tag: batch

value: 2 (original tumor)


title: NT3_p35

tag: cell line


title: 070-3-4_S22

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
070-3-4_S22_L001

tag: timepoint

value: Venetoclax ramp-up


title: A549 shM16, AA starvation, ribo-seq

tag: cell type

tag: genotype

value: Ribosome-protected RNA


title: 064-6-2_S33

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
064-6-2_S33_L001


title: Wild type Dark 2 days after fertilization replica 2

value: 2 days after fertilization

value: Wild type

tag: treatment

value: Dark


title: C9502m_fresh_frozen_tumor

source_name: CUP liver metastasis

value: CUP liver metastasis

value: tumor tissue


title: Brain Organoid/Cell Culture/Mouse lineage tracing

city: Vienna

first: Simon

middle: Emanuel

last: Haendeler

address: Dr. Bohr Gasse 9

department: Max Perutz Labs

country: Austria

institute: University of Vienna

data_processing:
Demultiplexing by extraction of sample barcode in b2 tag concatenated with bc tag and allowing for one missmatch when comparing to known sample barcodes
LID error correction by UMI-tools algorithm
Removal of LIDs that occure in multiple samples with threshold 0.95
Filtering of LIDs with low read count
Supplementary files format and content: lineage size of every lineage in sample as csv
Library strategy: Lineage tracing with genomic barcoding

organism:
Homo sapiens
Mus musculus

source_name: Brain Organoid/Stem Cell Culture/Mouse Brain

growth_protocol: Two retroviral libraries based on pRSF retrovirus expressing TagBFP were used for lineage tracing. hESC cells and mice were infected. For whole organoid lineage tracing single stem cell suspensions were prepared, sorted for TagBFP and plated in Essential 8 media supplemented with RevitaCell to recover for 1-2 days before the organoid protocol was initiated.

extract_protocol:
Genomic DNA was extracted by phenol/chloroform extraction.
After 12 freeze/thaw cycles only the viral barcode inserts were amplified by using lineage tracing genomic DNA primers, which also introduced sequencing adaptors

treatment_protocol: In experiments that included puromycin treatment, media was supplemented with 0.3 mg/ml Puromycin from day 11 on.

value: hESC


title: A549 shM16, control, ribo-seq

value: lung

value: Non-Small Cell Lung Cancer

value: METTL16 knockdown


title: 064-5PB_S20

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
064-5PB_S20_L001

value: PBMCs

value: HOVON139/GIVE post-Tx


title: C8802p_fresh_frozen_tumor

source_name: stomach primarius

value: stomach primarius


title: A549 shCtrl, AA starvation, ribo-seq

description: rCAA

value: WT

value: treated with CHX for 5min, amino acid starvation


title: 054-6-2_S7

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
054-6-2_S7_L001

value: 6 months after randomization


title: C8101m_fresh_frozen_tumor

value: untreated

value: 2 (original tumor)


title: MM1144, untreated, p52 ChIP, biorep2

city: Singapore

first: Yinghui

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

data_processing:
Reads aligned to hg38 using bwa mem and filtered for duplicates, poor quality and blacklisted regions
Coverage across 20 bp windows quantified by BAMscale
Peaks called by MACS2
Assembly: hg38
Supplementary files format and content: bigWig, fragment coverage across 20 bp windows
Supplementary files format and content: narrowPeak, MACS2 peak calls

source_name: Haematopoietic and Lymphoid

growth_protocol: Cells were cultured in RPMI 1640 media with 2.05 mM L-Glutamine (SH30027.01; Hyclone).

extract_protocol:
Cells were fixed in 1% formaldehyde for 12 minutes, swelled in 0.5% SDS buffer then lysed in 0.5% SDS + 5% Triton buffer (2:1). Genomic DNA was sheared to 100-500bp by sonication.
ChIP libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

treatment_protocol: Cells were transduced with TLCV2-containing virus and selected with 0.5 µg/ml puromycin for 72H. Transduced cells were subjected to 1 µg/ml Doxycycline to induce Cas9 expression before GFP sorting.

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

tag: Sex

value: Female

tag: chip antibody

value: NFKB2 antibody (A300-BL7039; Bethyl Laboratories)


title: Dve1 Light 1 day after fertilization replica 2

tag: time point

value: 1 day after fertilization

tag: strain

value: Light


title: 054-5PB_S32

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
054-5PB_S32_L001

value: End of induction treatment


title: 054-3-4_S19

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
054-3-4_S19_L001

value: Venetoclax ramp-up


title: Wild type Light 1 day after fertilization replica 2

value: Wild type


title: C5501m_fresh_frozen_tumor

source_name: CUP ovary metastasis

value: CUP ovary metastasis

value: tumor tissue


title: 064-6-4_S11

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
064-6-4_S11_L001

source_name: PBMCs

value: PBMCs

value: HOVON139/GIVE post-Tx

value: 12 months after randomization


title: KMS11, untreated, H3K4me1 ChIP, biorep2

value: WT


title: MM1144, untreated, p52 ChIP, biorep1

value: untreated


title: Wild type Dark 1 day after fertilization replica 2

value: Dark


title: C3301m_fresh_frozen_tumor

source_name: colon liver metastasis

value: colon liver metastasis

value: 2 (original tumor)


title: Dve1 Light fertilization day replica 2

value: fertilization day


title: C0701m_fresh_frozen_tumor

source_name: pancreas liver metastasis

value: pancreas liver metastasis


title: 048-6-2_S18

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
048-6-2_S18_L001

value: 6 months after randomization


title: 048-6-4_S10

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
048-6-4_S10_L001


title: KMS11, untreated, H3K4me1 ChIP, biorep1

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

value: Female


title: aP490m_fresh_frozen_tumor

source_name: pancreas lymphnode metastasis

value: pancreas lymphnode metastasis


title: KMS11, untreated, H3K27me3 ChIP, biorep2


title: 048-5PB_S21

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
048-5PB_S21_L001

value: End of induction treatment


title: Dve1 Dark 1 day after fertilization replica 2

value: 1 day after fertilization


title: KMS11, untreated, H3K27me3 ChIP, biorep1


title: 039-6-2_S6

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
039-6-2_S6_L001

value: PBMCs


title: MM1144, untreated, H3K27ac ChIP, biorep2

value: H3K27ac antibody (07-360; Merck)


title: QGP1_p5_Temozolomide

value: pancreatic NEN cell culture model

value: Temozolomide (11.52uM)

value: 1 (tumoroid samples)


title: Wild type Dark fertilization day replica 2

value: Wild type

value: Dark


title: 039-5PB_S17

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
039-5PB_S17_L001

value: HOVON139/GIVE post-Tx


title: Dve1 Light 1 day before fertilization replica 2

value: 1 day before fertilization

value: Light


title: QGP1_p5_DMSO

value: DMSO-control (0.16percent)


title: Dve1 Dark 1 day before fertilization replica 2


title: MM1144, untreated, H3K27ac ChIP, biorep1

value: Haematopoietic and Lymphoid

value: WT

value: untreated


title: QGP1_p5_Cisplatin

value: Cisplatin (0.53uM)


title: 039-3-4_S20

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
039-3-4_S20_L001

value: Venetoclax ramp-up


title: 038-6-4_S9

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
038-6-4_S9_L001

value: 12 months after randomization


title: NT3_p44_Temozolomide


title: HUVEC_VEGF-18h_scRNA-seq

city: Kumamoto

first: Shunsuke

last: Kamei

address: 2-2-1 Honjo

institute: Kumamoto University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: HUVEC

growth_protocol: HUVEC cells were maintained in EGM-2 medium supplemented with 5% (v/v) fetal bovine serum in 5% CO2 at 37°C.

extract_protocol:
Freshly collected HUVECs were washed with PBS twice and the cells were dissociated by Accumax. The isolated cells were resuspended in PBS.
Library was performed according to the manufacter’s instructions (Chromium NextGEM Single Cell 3' Kit v3.1, 10x Genomics).

treatment_protocol: HUVEC cells ware starved in EBM-2 basal medium with 0.5% (v/v) fetal bovine serum for 10h, treated with 20 ng/mL human recombinant VEGF-A165 for 0h or 18h.

value: HUVEC

value: Vascular endothelial cell

value: wild type

value: human recombiant VEGF-A

tag: time


title: Wild type Light 1 day before fertilization replica 2

source_name: Sexual development tissue


title: NT3_p44_DMSO

value: pancreatic NEN cell culture model

value: 1 (tumoroid samples)


title: HUVEC_VEGF-0h_scRNA-seq

description: 10x Genomics


title: Dve1 Light 2 days before fertilization replica 2

value: 2 days before fertilization


title: Dve1 Dark fertilization day replica 2

value: fertilization day

value: Dark


title: LP1, p52KD, H3K27ac ChIP, biorep3

data_processing:
Reads aligned to hg38 using bowtie2 and filtered for duplicates, poor quality and blacklisted regions
Coverage across 20 bp windows quantified by BAMscale
Peaks called by MACS2
Assembly: hg38
Supplementary files format and content: bigWig, fragment coverage across 20 bp windows
Supplementary files format and content: narrowPeak, MACS2 peak calls

value: Plasma Cell Myeloma

value: Female

value: H3K27ac antibody (07-360; Merck)


title: Wild type Dark 1 day before fertilization replica 2

value: 1 day before fertilization

value: Wild type


title: NT3_p44_Cisplatin

value: Cisplatin (0.53uM)


title: 038-5PB_S19

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
038-5PB_S19_L001

data_processing:
Raw FASTQ files were uploaded to the ARResT/Interrogate immunoprofiler for annotation and initial exploratory analysis. The full productive IGH repertoire for each sample was downloaded in .csv format and processed in R (R Core Team, 2020) during further analysis.
Assembly: GRCh38
Supplementary files format and content: Tab delimited tekst file containing: sample,QC.status,scenario,rearrangements,raw.count,w.junction.count,w.junction.percent,artefacts.count,artefacts.percent,usable.count,usable.percent,w.most.pop.cln.s..count,w.most.pop.cln.s..percent,uniq.usable.seq.count,clonotypes.count,diversity..norm.ed..count,effective.species.count,R1.Q.mean.stdev.count,R2.Q.mean.stdev.count,joined.normally.count,joined.normally.percent,joined.loosely.count,joined.loosely.percent,total.joined.count,total.joined.percent,saved.from.unjoined.count,saved.from.unjoined.percent,low.quality..ee.nt...0.01..count,low.quality..ee.nt...0.01..percent,short...50nt..count,short...50nt..percent,annotated.count,annotated.percent,w.TR.receptor.count,w.TR.receptor.percent,w.B.chain.count,w.B.chain.percent,w.VJ.Vb..Db..Jb.count,w.VJ.Vb..Db..Jb.percent,w.VJ.Vb..Db..Jb.cln

value: PBMCs

value: HOVON139/GIVE post-Tx

value: End of induction treatment


title: Wild type Light fertilization day replica 2

value: Light


title: aP321m_fresh_frozen_tumor

value: pancreas liver metastasis

value: tumor tissue

value: untreated

value: 2 (original tumor)


title: 032-6-4_S24

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
032-6-4_S24_L001

value: 12 months after randomization


title: Dve1 Dark 2 days before fertilization replica 2

value: 2 days before fertilization


title: LP1, p52KD, H3K27ac ChIP, biorep2

value: Haematopoietic and Lymphoid

value: WT


title: 032-6-2_S15

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
032-6-2_S15_L001

value: 6 months after randomization


title: C9502m_tumoroid_Temozolomide

value: CUP liver metastasis

value: primary cells isolated from tumor tissue

value: Temozolomide (11.52uM)

value: 1 (tumoroid samples)


title: LP1, p52KD, H3K27ac ChIP, biorep1

value: Plasma Cell Myeloma

value: Female

value: H3K27ac antibody (07-360; Merck)


title: Wild type Light 2 days before fertilization replica 2

value: Wild type

value: Light


title: C9502m_tumoroid_DMSO

value: DMSO-control (0.16percent)


title: LP1, control, H3K27ac ChIP, biorep3

value: control


title: Wild type Dark 2 days before fertilization replica 2

value: Dark


title: 038-6-2_S16

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
038-6-2_S16_L001

value: PBMCs

value: HOVON139/GIVE post-Tx


title: LP1, control, H3K27ac ChIP, biorep2

value: Haematopoietic and Lymphoid


title: C8802p_tumoroid_Temozolomide

value: stomach primarius


title: C9502m_tumoroid_Cisplatin

value: Cisplatin (0.53uM)


title: LP1, control, H3K27ac ChIP, biorep1

value: WT


title: Dve1 Dark 6 days after fertilization replica 1

value: 6 days after fertilization


title: Dve1 Light 6 days after fertilization replica 1


title: 031-5PB_S14

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
031-5PB_S14_L001

value: End of induction treatment


title: C8802p_tumoroid_Cisplatin

value: primary cells isolated from tumor tissue

value: 1 (tumoroid samples)


title: 031-3-4_S17

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
031-3-4_S17_L001

value: Venetoclax ramp-up


title: C8101m_tumoroid_Temozolomide

value: CUP liver metastasis

value: Temozolomide (11.52uM)


title: 024-6-2_S16

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
024-6-2_S16_L001

value: 6 months after randomization


title: Wild type Dark 6 days after fertilization replica 1

value: Wild type


title: KMS11, control, input ChIP, biorep1

value: Plasma Cell Myeloma

value: Female

value: control

value: no antibody


title: C8802p_tumoroid_DMSO

value: DMSO-control (0.16percent)


title: 032-5PB_S18

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
032-5PB_S18_L001

value: PBMCs

value: HOVON139/GIVE post-Tx


title: C8101m_tumoroid_DMSO


title: 024-6-4_S31

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
024-6-4_S31_L001

value: 12 months after randomization


title: KMS11, p52KD, H3K27ac ChIP, biorep2

value: Haematopoietic and Lymphoid

value: WT

value: H3K27ac antibody (07-360; Merck)


title: Wild type Light 6 days after fertilization replica 1

value: 6 days after fertilization

value: Light


title: 014-6-2_S22

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
014-6-2_S22_L001


title: Dve1 Light 4 days after fertilization replica 1

value: 4 days after fertilization


title: Dve1 Dark 4 days after fertilization replica 1

value: Dark


title: C8101m_tumoroid_Cisplatin

value: CUP liver metastasis

value: primary cells isolated from tumor tissue

value: Cisplatin (0.53uM)

value: 1 (tumoroid samples)


title: KMS11, p52KD, H3K27ac ChIP, biorep1

value: Plasma Cell Myeloma

value: Female


title: KMS11, control, H3K27ac ChIP, biorep3

value: control


title: 014-5PB_S30

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
014-5PB_S30_L001

value: PBMCs

value: End of induction treatment


title: 031-6-4_S23

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
031-6-4_S23_L001

value: HOVON139/GIVE post-Tx

value: 12 months after randomization


title: C5501m_tumoroid_DMSO

value: CUP ovary metastasis

value: DMSO-control (0.16percent)


title: 014-3-4_S15

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
014-3-4_S15_L001

value: Venetoclax ramp-up


title: KMS11, control, H3K27ac ChIP, biorep2

value: Haematopoietic and Lymphoid

value: WT

value: H3K27ac antibody (07-360; Merck)


title: C3301m_tumoroid_Temozolomide

value: colon liver metastasis

value: Temozolomide (11.52uM)


title: KMS11, p52KD, H3K27ac ChIP, biorep3


title: KMS11, control, H3K27ac ChIP, biorep1


title: Dve1 Light 2 days after fertilization replica 1

value: 2 days after fertilization

value: Light


title: Vector_2

city: Nanjing

first: Lufeng

last: Zheng

state: Jiangsu

address: Tongjia Xiang 24

department: School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: breast cancer cells

growth_protocol: Cells were cultured in DMEM medium (Gibco, Grand Island, NY, USA) at 37 °C under a humidified atmosphere with 5% CO2, and supplemented with 10% FBS (Gibco), 80 U/ml penicillin, and 0.08 mg/ml streptomycin.

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

treatment_protocol: MCF-7 cells were infected with miR-9 overexpression lentivirus and the control lenvirus. Cells with stable-infectin were screened using puromycin, and subjected to  deep sequencing, in triplicate, using  Illumina NovaSeq 6000.


title: LP1, untreated, p52 ChIP, biorep3

value: Plasma Cell Myeloma

value: untreated

value: NFKB2 antibody (A300-BL7039; Bethyl Laboratories)


title: Vector_1


title: Dve1 Dark 2 days after fertilization replica 1

value: Dark


title: C3301m_tumoroid_Cisplatin

value: primary cells isolated from tumor tissue

value: Cisplatin (0.53uM)

value: 1 (tumoroid samples)


title: LP1, untreated, p52 ChIP, biorep2

value: Female


title: Wild type Light 2 days after fertilization replica 1

value: Wild type


title: MiR_9_2


title: C0701m_tumoroid_Temozolomide

value: pancreas liver metastasis


title: C0701m_tumoroid_Cisplatin


title: LP1, untreated, p52 ChIP, biorep1

value: Haematopoietic and Lymphoid


title: KMS11, untreated, p52 ChIP, biorep4

value: WT


title: C0701m_tumoroid_DMSO

value: DMSO-control (0.16percent)


title: Wild type Dark 2 days after fertilization replica 1


title: MiR_9_1


title: JJN3, untreated, p52 ChIP, biorep3


title: Wild type Light 4 days after fertilization replica 1

value: 4 days after fertilization


title: YES2-2

city: Beijing

first: Qingyu

last: Luo

address: Panjiayuannanli No.17#, Chaoyang District

department: State Key Laboratory of Molecular Oncology

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Clean reads were obtained after the removal of reads containing adapter and ploy-N and having low quality.
HISAT2 was used to align the clean reads to the reference genome.
Differential expression was assessed using DESeq by using read counts as input.
Genome_build: hg18
Supplementary_files_format_and_content: Text file for counts and RPKM values of each gene

source_name: ESCC cells

extract_protocol:
TRIzol extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human ESCC cell lines

value: Parental


title: Dve1 Dark 1 day after fertilization replica 1

value: 1 day after fertilization


title: YES2-1


title: aP490m_tumoroid_Temozolomide

value: pancreas lymphnode metastasis

value: Temozolomide (11.52uM)


title: Wild type Dark 4 days after fertilization replica 1


title: JJN3, untreated, p52 ChIP, biorep2

value: Plasma Cell Myeloma

value: untreated

value: NFKB2 antibody (A300-BL7039; Bethyl Laboratories)


title: YES2_DDP-2

value: Resistant


title: C3301m_tumoroid_DMSO

value: colon liver metastasis

value: primary cells isolated from tumor tissue

value: 1 (tumoroid samples)


title: Wild type Light 1 day after fertilization replica 1

value: Wild type

value: Light


title: aP490m_tumoroid_DMSO


title: Wild type Dark 1 day after fertilization replica 1

value: Dark


title: JJN3, untreated, p52 ChIP, biorep1

value: Haematopoietic and Lymphoid

value: WT

value: Female


title: aP490m_tumoroid_Cisplatin

value: Cisplatin (0.53uM)


title: Dve1 Light 1 day after fertilization replica 1

value: 1 day after fertilization


title: LP1, untreated, input ChIP, biorep1

value: no antibody


title: 450-2

value: Human ESCC cell lines

value: Parental


title: Dve1 Light fertilization day replica 1

value: fertilization day


title: aP321m_tumoroid_Temozolomide

value: pancreas liver metastasis

value: Temozolomide (11.52uM)


title: Dve1 Dark fertilization day replica 1


title: JJN3, untreated, input ChIP, biorep1

value: Plasma Cell Myeloma

value: untreated


title: 450-1


title: Wild type Light fertilization day replica 1


title: Wild type Dark fertilization day replica 1


title: LP1, untreated, H3K27ac ChIP, biorep2

value: H3K27ac antibody (07-360; Merck)


title: aP321m_tumoroid_Cisplatin

value: primary cells isolated from tumor tissue

value: 1 (tumoroid samples)


title: 450_DDP-2

value: Resistant


title: 450_DDP-1


title: aP321m_tumoroid_DMSO

value: DMSO-control (0.16percent)


title: ATAC_H1_37C_rep1

data_processing:
bcl2fast 2.19 software was used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through Fastp v0.21.0. In this step, clean data (clean reads) were obtained by removing adapter and low-quality reads.All the downstream analyses were based on the clean data with high quality.
Paired end reads were mapped to the GRCh38 genome using Bowtie2 v2.4.2, and extracted reads with MAPQ > 13. Then the blacklist of genome and MT chromsome were removed from data, and  the PCR duplicates were removed using Picard v2.25.0.
Peaks were called using macs2 v2.2.7.1 with qvalue < 0.05.
The deeptools tool v3.5.1 was used to generate bigwig files from bam files.
Peaks were annotated by the function of annotatePeak of ChIPseeker v1.5.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: narrowpeak
Supplementary_files_format_and_content: bigwig

source_name: Human embryonic stem cell line

extract_protocol:
The suspension of H1 cell nuclei was then centrifuged for 5 min at 500g at 4 °C, followed by the addition of 40 μl Tn5 transposase reaction mix (20 μl 2x TD buffer, 0.4 μl 1% Digitonin, 0.4 μl 10% Tween 20, 4 μl 3×PBS, 13.2 μl nuclease-free H2O and 2 μl Transposome).
The transposition reaction was incubated at 37°C for 30 min.Equimolar Adapter1 and Adapter 2 were added after transposition. PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated (Novogene, Beijing, China).

treatment_protocol: In brief, a total of 50,000 H1 cells incubated at 37°C or 4°C were washed twice with 50 μl of PBS at 37°C or 4°C, respectively. The cells were resuspended in 50 μl lysis buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.5% NP40, pH7.4).

tag: celltype

value: Human embryonic stem cell

tag: temperature


title: JJN3, untreated, H3K27ac ChIP, biorep3

value: Haematopoietic and Lymphoid

value: WT

value: Female


title: LP1, untreated, H3K27ac ChIP, biorep3


title: LP1, untreated, H3K27ac ChIP, biorep1


title: Dve1 Dark 1 day before fertilization replica 1

value: 1 day before fertilization

value: Dark


title: ATAC_H1_4C_rep2


title: YES2_DDP-1

value: Human ESCC cell lines


title: Dve1 Light 1 day before fertilization replica 1

value: Light


title: JJN3, untreated, H3K27ac ChIP, biorep2


title: Wild type Light 1 day before fertilization replica 1

value: Wild type


title: ATAC_H1_4C_rep1


title: JJN3, untreated, H3K27ac ChIP, biorep1


title: Wild type Dark 1 day before fertilization replica 1


title: PDAC-4 PJ-Ex

type: RNA

city: Kurume

first: Takahiko

last: Sakaue

state: Fukuoka

address: 67 Asahi-machi

institute: Kurume University School of Medicine

hyb_protocol: biotin labeled miRNA was hybridized to ThermoFisher GeneChip miRNA 4.0 array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The data were processed with median polish summarization and quantile normalization by ThermoFisher Transcriptome Analysis Console Software.

label: biotin

source_name: pancreatic cancer, pancreatic juice, exosome

label_protocol: 130ng of total RNAs were labeled  using the FlashTag™ Biotin HSR RNA Labeling Kit (ThermoFisher), following the manufacturer’s instructions (User manual of the FlashTag™ Biotin HSR RNA Labeling Kit, ThermoFisher)

extract_protocol: Total RNAs including miRNAs were isolated and purified from cells using miRNeasy Mini Kit  (Qiagen)　according to the manufacturer's instructions.

value: pancreatic juice

tag: gender

value: male

tag: age

tag: Stage

value: Stage 2B


title: ATAC_H1_37C_rep2


title: PDAC-3 PJ-Ex

tag: tissue

value: Stage 4


title: Dve1 Light 2 days before fertilization replica 1

value: 2 days before fertilization


title: KMS11, p52KD, RNAseq, biorep3

data_processing:
counts across GENCODE v35 features by featureCounts
Assembly: hg38
Supplementary files format and content: tsv, counts generated by featureCounts

extract_protocol:
phenol-chloroform extraction followed by DNAse treatment and rRNA depletion
NEBNext® UltraTM II Directional RNA Library Prep Kit

value: Plasma Cell Myeloma


title: Dve1 Dark 2 days before fertilization replica 1

data_processing:
libraries were run on Genome Analyzer (Illumina NovaSeq 6000).
paired-end reads of 150 nucleotide each were mapped against the N. crassa OR74A genome by using Star 2.7
quality was checked using FastQC
automatic preprocessing of the reads was carried out with AFTERQC 0.9.6
SeqMonk was used for visualization and quantification
Supplementary files format and content: raw counts, matrix text format


title: KMS11, p52KD, RNAseq, biorep2


title: PDAC-1 PJ-Ex

value: female


title: JN_M3

city: Philadelphia

first: Patrick

last: Grohar

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

description: RNA

data_processing:
RNA sequencing reads were aligned to hg38 using STAR (v2.7.0f)
The index was prepared using default parameters except for ‐‐sjdbGTFfile, where the Gencode v23 annotations were used
Default parameters were used for alignment with the following modifications: ‐‐readFilesCommand zcat ‐‐outReadsUnmapped Fastx ‐‐quantMode GeneCounts ‐‐outSAMtype BAM SortedByCoordinate.
Gene‐level transcript quantification was performed using STAR's built‐in quantification algorithm
After filtering for low abundance transcripts differential expression analysis was carried out using DESeq2 (v1.28.1)
Significant genes were determined using a cutoff of adjusted p < 0.01
GSEA was performed with the fgsea (1.14.0) package
Kegg pathway enrichment analysis was performed with the clusterProfiler (v3.16.1) package
A hypergeometric test was used to calculate overlap significance of differentially expressed gene sets.
Genome_build: hg38
Supplementary_files_format_and_content: FGC2198_featureCounts.txt. TXT file of raw gene counts for washout samples.
Supplementary_files_format_and_content: STAR_raw_counts_with_ext_gene_lurb.txt. TXT file of raw gene counts for continuous samples.

source_name: JN-DSRCT-1 cells

growth_protocol: Cells were grown at 37_C with 5% CO2. RPMI1640 was supplemented with 10% FBS, 2 mmol/L L-glutamine, and 100 U/mL and 100 mg/mL penicillin and streptomycin, respectively.

extract_protocol:
RNA was extracted using the Qiagen RNEasy Mini kit.
Libraries prepared with Illumina's stranded poly-A selection kit

treatment_protocol: Continuous samples had media aspirated and replaced with 5nM lurbinectedin. Washout samples were treated with 25nM lurbinectedin for 1 hr followed by replacement with drug free medium

value: JN-DSRCT-1 cells

value: media

value: 16 hours washout


title: JN_M2

description: RNA


title: MIA PaCa Ex

source_name: pancreatic cancer cell line, exosome

value: MIA PaCa-2


title: KMS11, control, RNAseq, biorep3

value: Haematopoietic and Lymphoid

value: WT

value: Female

value: control


title: Wild type Dark 2 days before fertilization replica 1

value: Dark


title: Wild type Light 2 days before fertilization replica 1

value: Wild type

value: Light


title: JN_S16_2

description: RNA

value: solvent


title: JN_M1

description: RNA


title: KMS11, p52KD, RNAseq, biorep1


title: BxPC3 Ex


title: JN_S16_1

description: RNA


title: JN_S16_3

description: RNA


title: KMS11, control, RNAseq, biorep2


title: PANC-1 Ex


title: Amplicon seq from tumor 2

city: Stony Brook

first: Richard

last: Lin

address: 1 Circle Road

institute: Stony Brook University

description: sgRNAswereamplifiedbyPCR,followedbylibrarypreandsequencing

data_processing:
The sequencing data was processed for sgRNA  representation. The 8bp barcodes were first demultiplexed from the sequencing reads, followed by adapter trimming. The remaining spacer sequences were aligned to the designed sgRNA library by bowtie, with tolerance of a single nucleotide mismatch. The number of mapped sequences were imported into R/RStudio to quantify the total number of reads. Besides, the computational tool MAGeCK (model-based analysis of genome-wide CRISPR-Cas9 knockout) was used to confirm the identified mapping counts.
Assembly: mm38
Supplementary files format and content: All.count.txt
Library strategy: amplicon seq

source_name: The pancreatic tumor tissue was extracted from mice at week 13 post implantation

growth_protocol: αKO cells were cultured in complete DMEM media (Gibco, Thermo Fisher Scientific) with 10% FBS (Corning 35-015-CV) and 1% P/S (penicillin/streptomycin: Gibco 15140-122), incubated at 37 °C with 5% CO2.

extract_protocol:
Qiagen DNeasy Blood & Tissue Kit (#13323) was used to extract DNA according to the manufacturer's protocol. The concentration of DNA was determined by NanoDrop ND 1000.
amplicon seq library was prepared by 2-step PCR amplifying the sgRNA region

treatment_protocol: aKO cells were transfected with GeCKOv2 library A  (3 sgRNA targeting each gene of the whole mice genome), resulting in 1 gene KO per each cell. The mixed cell pool was then implated to the pancreas of B6 mice for screening purpose.

value: pancreatic tumor

value: week 13 post implantation

value: aKO transfected with GeCKOv2 (lentiv2) mouse library

value: pancreatic cancer cells

value: transfected with lentiCRISPRv2, and then implanted into the pancreas of B6 mice for screening


title: PDAC-2 PJ-Ex

value: pancreatic juice

value: female

value: Stage 4


title: CP-4 PJ-Ex

source_name: chronic pancreatitis, pancreatic juice, exosome

value: male


title: Amplicon seq from tumor 1

source_name: The pancreatic tumor tissue was extracted from mice at week 7 post implantation

value: week 7 post implantation


title: JN_L16_3

description: RNA

value: JN-DSRCT-1 cells

value: lurbinectedin

value: 16 hours washout


title: KMS11, control, RNAseq, biorep1

source_name: Haematopoietic and Lymphoid

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

value: WT

value: Female

value: control


title: CP-2 PJ-Ex


title: KMS11, p52KD, H3K27ac HiChIP, biorep1

data_processing:
Contact matrix across 2500 bp windows generated by cooler
Significant interactions called by FitHiChIP in L+M mode with 2500 bp bin size, lower/upper distance thresholds of 10KB/2MB and coverage bias regression.
Assembly: hg38
Supplementary files format and content: cool, contact matrix generated by cooler
Supplementary files format and content: bedpe, significant interactions called by FitHiChIP
Library strategy: HiChIP Mnase

extract_protocol:
10 million frozen cells per biological replicate were processed following the standard Dovetail HiChIP MNase Kit (Dovetail Genomics)
HiChIP libraries were prepared using the Dovetail HiChIP MNase Kit (Dovetail Genomics).

treatment_protocol: Cells were transduced with TLCV2-containing virus and selected with 0.5 µg/ml puromycin for 72H. Transduced cells were subjected to 1 µg/ml Doxycycline to induce Cas9 expression before GFP sorting. Cells were frozen in LN2.

value: Acetyl-Histone H3 (Lys27) (D5E4) XP® Rabbit mAb (#8173; Cell Signaling Technology)


title: JN_L16_2

description: RNA


title: KMS11, control, H3K27ac HiChIP, biorep1


title: CP-1 PJ-Ex


title: JN_L16_1

description: RNA


title: KMS11, p52KD, ATAC-seq, biorep3

data_processing:
Coverage across 20 bp windows quantified by BAMscale
Peaks called by MACS2
Assembly: hg38
Supplementary files format and content: bigWig, fragment coverage across 20 bp windows
Supplementary files format and content: narrowPeak, MACS2 peak calls

extract_protocol:
The cells were resuspended cold ATAC-Resuspension Buffer containing 0.1% NP40, 0.1% Tween20, and 0.01% Digitonin and incubated on ice for 3 min. The cells were then washed in RBS containing 0.1% Tween-20 at 500 g at 4 °C before subjecting the nuclei to the transposase reaction for 30 min at 37 °C. Termination of the reaction and DNA purification was performed using Zymo DNA clean and Concentrator kit.
The purified DNA was amplified with NEBNext High-Fidelity 2x PCR Master Mix then purified and size selected twice with AMPure beads. Nextera Tn5 Transposase is employed for tagmentation.


title: ONECUT3-OE, rep2

city: Hangzhou

first: Hongyan

last: Tong

state: Zhejiang

address: No. 79 Qingchun Rd., Shangcheng District, Hangzhou, Zhejiang, China

department: Department of Hematology

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-90/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M20/gencode.vM20.annotation.gtf.gz
Differential expression analysis of two conditions was performed using the DESeq2 R package (1.26.0).
Assembly: GRCm38
Supplementary files format and content: File includes Count and  FPKM values for each sample

source_name: TP53 KO mouse

growth_protocol: The primary MEF cells were cultured in DMEM containing 10% fetal bovine serum (FBS), 1% Penicillin/Streptomycin, 1x Sodium Pyruvate (Gibco, USA), 1x MEM Non-Essential Amino Acids Solution (Gibco, USA) and 1x GlutaMAX Supplement (Gibco, USA). And the cells were passaged when the cell confluency reached about 80%-90%. Primary MEF were used for maximum of five passages.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen).
NEBNext Ultra II Directional RNA Library Prep Kit was used for library preparation.

treatment_protocol: For control group, no Doxycycline was added, while MEF cells were treated with 100 ng/ml Doxycycline to induce ONECUT3 overexpression.

value: embryo

value: mouse embryonic fibroblast

value: Doxycycline


title: Co-culture replicate 3

city: Madison

first: Thibaut

last: Rosay

state: Wisconsin

department: MMI

institute: UW Madison

data_processing:
reads were trimmed, decontaminated and quality-filtered using BBmap software suite
Reads were mapped to the E. coli O157:H7 strain EDL933 genome using Bowtie2
Raw counts were generated using the featureCounts package and were then normalized for sequencing depth and gene length
Raw counts were used as input for the differential expression analysis using edgeR
Assembly: NZ_CP008957.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include the differential expression analysis using edgeR

organism: Escherichia coli

growth_protocol: Bacteria were grown 6h in DMEM low glucose in anaerobic conditions

extract_protocol:
TruSeq Stranded Total RNA LT Sample Prep Kit, 2ug of total DNAse treated RNA were used to prepare cDNA
Illumina ScriptSeq  #BB1224

treatment_protocol: cocultures are in a 1/1 ratio

value: co-culture with E. feacalis


title: JN_S12_3

description: RNA

value: solvent

value: 12 hours washout


title: Co-culture replicate 2


title: Control, rep2

value: no Doxycycline


title: control replicate 2


title: JN_S12_1

description: RNA


title: control replicate 1


title: Control, rep3


title: JN_S12_2

description: RNA


title: KMS11, control, ATAC-seq, biorep3


title: ONECUT3-OE, rep3


title: Control, rep1


title: JN_L12_3

description: RNA


title: KMS11, p52KD, ATAC-seq, biorep2


title: KMS11, control, ATAC-seq, biorep2


title: KMS11, control, ATAC-seq, biorep1


title: Co-culture replicate 1


title: KMS11, p52KD, ATAC-seq, biorep1


title: JN_L12_2

description: RNA


title: SP mRNA-Seq DbhVLM-mCherry replicate 4

city: Hefei

first: Liang

last: Wang

state: Anhui

address: 96 Jinzhai Road

institute: University of Science and Technology of China

data_processing:
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR v2.6.1a with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using featureCounts function from Rsubread (v2.0.1) and rpkm function of edgeR (v3.28.1). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: spleen CD45+ cells

growth_protocol: Mice were bred and maintained under a controlled temperature (22-25ºC) with a 12 h-light/12 h-dark cycle (light on from 7 am to 7 pm), and ad libitum access to water and a standard chow diet.

extract_protocol:
Total RNA of CD45+ cells was extracted using a Takara MiniBest Universal RNA Extraction kit (code no. 9767) according to the manufacturer’s instructions. Poly(A) mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB,E7490L).
poly(A) mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB,E7490L).First-strand cDNA was synthesized with the SuperScript II Reverse Transcriptase (Invitrogen,18064014) and Second Strand cDNA was synthesized using Second Strand cDNA Synthesis Kit (Invitrogen,A48570). Libraries were subsequently constructed with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB,E7645L).

treatment_protocol: AAV-DIO-hM3Dq-mCherry or the same volume of AAV-DIO-mCherry was bilaterally injected into the VLM of Dbh-Cre mice. CD45+ cells were obtained from the spleen and bone marrow 4 hour after CNO injections.

value: spleen CD45+ cells

value: DbhVLM-mCherry

tag: growth phase

value: 12 week

value: CNO injections


title: G2_1

city: Houston

first: Jiexi

state: TX

address: 1881 East Road

institute: The University of Texas MD Anderson Cancer Center

data_processing:
The NextSeq RTA (version 2.4.11.0) was used for base calling
bcl2fastq (version 2.20.0) was used to convert the .bcl files into .fastq files
Fastq files were aligned to the mouse reference genome (mm10) using HISAT2 (version 2.1.0) and assembled using StringTie (version 2.1.1)
R (version 3.5.2) and R package DESeq2 (version 1.32.0) was used for data normalization.
Assembly: mm10
Supplementary files format and content: DESeq2 raw counts

source_name: 157 G2 Apcmin

extract_protocol:
RNA was isolated using the RNeasy Kit (Qiagen)
Libraries were generated using BGI services.

tag: cell line

value: 157 G2 Apcmin

value: mouse adenoma colonoid line

value: Apcnull/LSL-mTERT-homo


title: SP mRNA-Seq DbhVLM-mCherry replicate 3


title: ONECUT3-OE, rep1


title: NuMA_control_rep2

first: Wenxue

last: Zhao

address: Yiheyuan Road

institute: Peking University

data_processing:
The raw sequences were cleaned using TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped to human reference genome hg19 by STAR (v2.7.1a) with default parameter. All mapped bam files were converted to bigwig using bedtools (v2.24.0) (Quinlan, 2014). for visualization in IGV. High quality mapped reads were quantified using htseq -count (v0.11.3) (Anders et al., 2015). Differentially expressed genes were analyzed by DEseq2 (Love et al., 2014).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: colon cancer

extract_protocol:
Total RNA was extracted from cultured wildtype and NuMA-depleted HCT116 cells with 10,000,000 cells in each sample.
RNA sequencing libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina® (NEB England BioLabs). RNA-seq paired-end reads were sequenced on the Illumina NovaSeq 6000 platform.

value: colon cancer

value: human colon cancer cell line

value: wild type


title: G0_2

source_name: 179 G0 Apcmin

value: 179 G0 Apcmin

value: Apcnull/LSL-mTERT-het


title: SP mRNA-Seq DbhVLM-mCherry replicate 2


title: control replicate 3

value: WT

value: control


title: NuMA_control_rep1


title: JN_S6_3

description: RNA

value: JN-DSRCT-1 cells

value: solvent

value: 6 hours washout


title: SP mRNA-Seq DbhVLM-mCherry replicate 1

value: spleen CD45+ cells


title: G0_1

source_name: 75 G0 Apcmin

value: 75 G0 Apcmin


title: NuMA_depleted_rep2

value: NuMA depletion


title: JN_S6_2

description: RNA


title: SP mRNA-Seq DbhVLM-hM3Dq replicate 8

value: 12 week

value: CNO injections


title: JN_S6_1

description: RNA


title: NuMA_depleted_rep1


title: SP mRNA-Seq DbhVLM-hM3Dq replicate 7


title: G2_2

source_name: 236 G2 Apcmin

value: 236 G2 Apcmin

value: mouse adenoma colonoid line


title: 145: E4bp4-LKO mice, 20 weeks NASH diet

city: Ann Arbor

first: Sujuan

state: MI

address: 2800 Plymouth Road

department: Molecular & Integrative Physiology

institute: University of Michigan

data_processing:
RNA-seq
Sequencing data Filtering: remove the reads mapped to rRNA and get raw data, and then processed and removed the sequencing reads which containing low-quality, adaptor-polluted and high content of unknown base (N) reads
Genome Mapping: mapped clean reads to reference genome using HISAT2
Gene Expression Analysis
Assembly: HISAT2(http://daehwankimlab.github.io/hisat2/)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Liver

growth_protocol: All mice are housed on a 12 hours:12 hours light/dark cycle at 25℃ with free access to water and regular chow (26.8% kcal from protein, 16.6% kcal from fat, and 56.4% kcal from starch).

extract_protocol:
RNA was harvested using Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit).
1)mRNA enrichment: Oligo dT Selection or rRNA depletion;2)RNA fragment and reverse transcription:Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer;3)End repair, add A tailing and adaptor ligation:The  synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments;4)PCR amplification:The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer;5)Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: Two-month old WT mice and E4bp4 liver specific knockout (E4bp4-LKO) mice to NASH diet for 20 weeks.

value: Liver

value: NASH diet, 20 weeks


title: SP mRNA-Seq DbhVLM-hM3Dq replicate 6


title: 144: E4bp4-LKO mice, 20 weeks NASH diet