title: Luminal Breast Cancer Tumor [CM4]

description: Gene expression data from Luminal breast cancer

value: Formalin-fixed paraffin-embedded tissue sections

value: Mexican Patient

value: not available


title: PR8 immune P14 replicate B, GEX

status: Public on Dec 20 2024

type: SRA

city: Minneapolis

first: David

last: Masopust

state: MN

address: 2101 6th St SE

department: Microbiology and Immunology

country: USA

institute: University of Minnesota

description:
poly A RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

library_source: transcriptomic

data_processing:
RNA, ADT, and HTO libraires were sequenced with an Illumina NovaSeq 6000 S4 flow cell at the University of Minnesota’s Genomics Core. Reads were processed with 10X Genomics Cell Ranger v.7.0.0 with feature barcoding, where RNA reads were mapped to the mouse mm10–2.1.0 mouse reference and antibody reads mapped to known barcodes
Assembly: mm10-2.1.0
Supplementary files format and content: CellRanger output files
Library strategy: CITE-seq

molecule: polyA RNA

organism: Mus musculus

source_name: Blood, female reproductive tract, lung, medLN, salivary gland, and spleen

growth_protocol: 5 x 104 naïve CD45.1+ P14 TCR transgenic CD8 T cells, specific for the H-2Db-restricted LCMV gp33-41 epitope, were adoptively transferred to adult naïve female C57BL/6J mice followed by i.p. infection with 2x105 PFU LCMV Armstrong (Arm) or i.n. infection with 500 PFU PR8-gp33 1 day later. Memory mice immune to LCMV Armstrong (56 days post-infection) or PR8-gp33 (47 days post-infection) were sacrificed. Tissues were excised and digested, lymphocytes enriched, and P14 cells were purified using FACS.

extract_protocol:
After enzymatic and mechanical tissue diggestions, enriched lymphocyte cell suspensions were stained with Live/Dead dye (Ghost-Dye 510, Tonbo), fluorescent-conjugated antibodies (CD8b (RPA-T8), Thy1.1 (HIS51), CD45.1 (A20), Thy1.2 (30-H12)), and oligonucleotide-conjugated Biolegend TotalSeq-A antibodies (30 min at 4ºC ). P14 (Live, CD8a+, Thy1.1+ and CD45.1+) P14 T cells were sorted using a FACS Aria II (BD Biosciences).
We followed the 10X Genomics Chromium Single Cell 3’ v3 protocol to prepare RNA, antibody-derived-tag (ADT), and hashtag oligos (HTO) libraries.

treatment_protocol: After removing tissues, cells were released from the spleen, lymph nodes, and liver by mechanically disrupting them, followed by filtration through a 70-µm filter and washing in RPMI 1640 containing 5% fetal bovine serum (FBS). Spleen and Liver RBCs were lysed with ACK buffer and washed once. Blood RBCs were lysed with ACK buffer twice and and washed twice. Cells were enzymatically released from the lung, salivary gland, female reproductive tract (FRT), from the epithelial and lamina propria compartments of small intestine (SI). After enzymatic digestion, lymphocytes from single-cell suspensions of the lung and SI were enriched using a Percoll gradient.

tag: tissue

tag: cell type

value: CD8+ T cell

tag: library type

value: mRNA


title: 22Rv1 CPSF1 sh1 BR2

first: Scott

last: Dehm

address: Mayo Mail Code 806, 420 Delaware St SE

institute: Masonic Cancer Center, University of Minnesota

data_processing:
Fastq files containing 150 bp paired-end reads were aligned to the GRCh37 reference genome using HiSat2 (v. 2.1.0). Subread (v. 2.0.3) was used to quantify gene expression using the version 87 GRCh37 annotation from Ensembl. Count data were filtered to include only genes that had a cpm (counts per million) value greater than 2 cpm across all experimental conditions per cell line.
Assembly: GRCh37
Supplementary files format and content: Read counts as tab separated values

molecule: total RNA

organism: Homo sapiens

source_name: Cell Line

growth_protocol: LNCaP and 22Rv1 cells were maintained in RPMI 1640 media with 10% FBS, LNCaP95 cells were maintained in RPMI 1640 phenol red free media with 10% FBS

extract_protocol:
Total RNA was extracted from cells using the ReliaPrep RNA miniprep system (Promega).
RNA was submitted to the University of Minnesota Genomics Center for RNA-seq library synthesis using a TruSeq Stranded mRNA kit (Illumina) according to manufacturer’s instructions.

treatment_protocol: LNCaP, LNCaP95, 22Rv1 cells were transduced with lentivirus encoding shCTRL, shCPSF1-1, or shCPSF1-2, followed by two sequential rounds of selection with 2 μg/mL puromycin dihydrochloride for 22Rv1 and LNCaP and 1 μg/mL puromycin dihydrochloride  (Gibco, A11138-03). Infected cells were expanded and seeded in 6-well plates at 500,000 cells per well and grown for 72 h in normal RPMI 1640 + 10% FBS media for 22Rv1 and LNCaP and  RPMI 1640 phenol red free + 10% FBS for LNCaP95.

value: Cell Line

tag: cell line

value: Prostate Cancer

tag: treatment

value: shRNA targeting CPSF1 (1)


title: Luminal Breast Cancer Tumor [CM1]

type: RNA

city: Mexico City

first: Patricia

middle: Piña

last: Sánchez

state: CDMX

address: Cuauhtémoc Avenue

department: Medical Research Unit in Oncological Diseases

country: Mexico

institute: IMSS

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were analyzed with  the Transcriptome Analysis Console (TAC 4.0.1, Applied Biosystems) to identify differentially expressed genes between TNBC and luminal samples.  Quality control and normalization were performed using Robust Multichip Average (RMA).

label: biotin

source_name: Luminal Breast Cancer Tumor

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was obtained and purified from tissue sections embedded in paraffin and fixed with formalin with the RNeasy FFPE Kit (QIAGEN, 73504), following the manufacturer's instructions

tag: population

tag: age


title: BR-like dwarf rep 2 short-read

city: Toronto

first: Satyaki

last: Rajavasireddy

state: ON

address: 1265 Military Trail, Toronto,, SY246

department: Biological Sciences (Scarborough)

country: Canada

institute: University of Toronto

description: Library name: 1A_20_17

library_source: genomic

data_processing:
First 10 bp of each read as well as any adapters were removed with trimmomatic.
Trimmed reads were aligned to the Col-CEN v1.2 genome with BWA-MEM (bwa mem -R "@RG\tID:id\tSM:sample\tLB:lib" reference.fasta sample.R1.fastq sample.R2.fastq  | samblaster --excludeDups --addMateTags --maxSplitCount 2 --minNonOverlap 20)
SVs were identifed with LUMPY Express using a benchmarked pipeline described in Goktay et al. 2021.
SVs attributed to ChrC, ChrM, and the NOR on Chr2 were removed. SVs found within 2kb of an SV present in DMSO treated controls, or shared amongst four or more unrelated etoposide-treated lines were removed. Only deletions and duplications that were supported by split reads were retained in the final SV set.
Assembly: Col-CEN v1.2
Supplementary files format and content: vcf file contains information for each structural variant identified via lumpy express and which samples it was identified in.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Plants were grown in a Conviron growth chamber under long day conditions (16h 120 µmol fluorescent light) at 22C.

extract_protocol:
DNA was extracted from rosette leaf tissue using a CTAB protocol.
Up to 15 ng of genomic DNA was used as input for the Nextera DNA Flex Library Preparation Kit.

treatment_protocol: M1 plants were grown on 0.5X MS Media containing 160 µM of etoposide or DMSO for two weeks, after which they were transferred to soil. M1 plants were self-fertilized to yield M2 plants, which were self-fertilized to yield M3 plants.

value: leaf

value: etoposide

tag: generation


title: virescent rep 2 short-read

description: Library name: 13B_46_12


title: AID-cre tdTomato lymphocytes, AID+ MHV68-, 16 dpi WT 73.Bla MHV68, Rep. 3

city: Little Rock

first: Mark

last: Manzano

state: AR

address: 4301 W Markham St

department: Microbiology & Immunology

institute: University of Arkansas for Medical Sciences

description: Library name: WT-4-A

data_processing:
Raw sequence reads were checked for their quality using FastQC and then trimmed based on quality (PHRED >30). After trimming, reads less than 30 bp were discarded.
Trimmed sequence reads were mapped to reference genome mm10 with STAR aligner with default parameters.
The gene count tables were extracted from the alignment results using bedtool2 software.
The read counts were normalized using voom method.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include cpm for each smple.

source_name: draining lymph nodes

extract_protocol:
RNA was harvested using trizol.
Library was constructed by GeneWiz by the ultra-low input RNA seq protocol - using Illumina RNA prep with enrichment for full length transcripts.  Polyadenylated transcripts were reverse transcribed using SMART-Seq® v4 Ultra® Low Input RNA Kit (Clontech), followed by second-strand synthesis of full-length cDNA and amplification of the product. Illumina RNA prep with enrichment for full length transcripts.  Polyadenylated transcripts were reverse transcribed using SMART-Seq® v4 Ultra® Low Input RNA Kit (Clontech), followed by second-strand synthesis of full-length cDNA and amplification of the product. Illumina®-compatible sequencing libraries were constructed and then validated for sufficient concentration and appropriate fragment sizes. Samples were  sequenced on the Illumina HiSeq® 2500 with a 1x100 bp single-end configuration.

treatment_protocol: At 16 dpi, draining lymph nodes were isolated and homogenized. Staining for beta-lactamase activity was performed with CCF4-AM. Cells were sorted on a FACS Aria for AID+MHV68- or AID+MHV68+ populations from animals infected with either WT or M2.Stop 73.Bla MHV68.

value: draining lymph nodes

value: AID+ MHV68-

tag: genotype

value: AID-cre tdTomato

value: 16 dpi with WT 73.Bla MHV68


title: 22Rv1 CTRL sh BR2

value: CTRL shRNA


title: virescent rep 1 short-read

description: Library name: 13B_25_8


title: Luminal Breast Cancer Tumor [CM2]


title: 22Rv1 CPSF1 sh2 BR1

value: shRNA targeting CPSF1 (2)


title: AID-cre tdTomato lymphocytes, AID+ MHV68+, 16 dpi WT 73.Bla MHV68, Rep. 2

description: Library name: WT-3-AB

value: AID+ MHV68+


title: PR8 immune P14 replicate A, HTO

description:
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

library_source: other

molecule: protein

value: Blood, female reproductive tract, lung, medLN, salivary gland, and spleen

value: HTO

tag: hto


title: 22Rv1 CPSF1 sh1 BR1


title: PR8 immune P14 replicate A, ADT

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: ADT

tag: adt


title: AID-cre tdTomato lymphocytes, AID+ MHV68-, 16 dpi WT 73.Bla MHV68, Rep. 2

description: Library name: WT-3-A


title: PR8 immune P14 replicate A, GEX

value: CD8+ T cell


title: 22Rv1 CTRL sh BR3


title: 22Rv1 CTRL sh BR1


title: DMSO rep 1 short-read

description: Library name: 13_18

value: DMSO


title: AID-cre tdTomato lymphocytes, AID+ MHV68+, 16 dpi WT 73.Bla MHV68, Rep. 1

description: Library name: WT-2-AB


title: Armstrong immune P14 replicate B, HTO

source_name: Female reproductive tract, liver, lung, mesLN, small intestine epithelium (IEL), small intestine lamina propria (LP), and spleen


title: Armstrong immune P14 replicate B, ADT

value: Female reproductive tract, liver, lung, mesLN, small intestine epithelium (IEL), small intestine lamina propria (LP), and spleen


title: LNCaP95 CPSF1 sh2 BR3

value: Cell Line

value: Prostate Cancer


title: line 12 rep 1 short-read

description: Library name: 12_11

value: leaf


title: AID-cre tdTomato lymphocytes, AID+ MHV68-, 16 dpi WT 73.Bla MHV68, Rep. 1

description: Library name: WT-2-A


title: LNCaP95 CPSF1 sh1 BR3

value: shRNA targeting CPSF1 (1)


title: line 10B rep 3 short-read

description: Library name: 10B_3

value: etoposide


title: Armstrong immune P14 replicate A, HTO


title: virescent relative without phenotype rep 1 short-read

description: Library name: 13B_18_47


title: Armstrong immune P14 replicate B, GEX

value: mRNA


title: LNCaP95 CTRL sh BR3


title: Smc3 in Wapl-ko_2_merged

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

data_processing:
Basecalling software: Illumina RTA
ChIP-seq reads were mapped uniquely with 0 to 2 errors against the Mus musculus mm9 genome assembly using  bowtie version 1.2.2.
Peaks were called using MACS v2.2.5 with default parameters for fold change, fixed extension sizes, and SPMR normalization (signal per mio. reads) for visualization purposes.
bedGraph files (*.bdg) have been built using MACS v2.2.5 with -B option and converted to bigWig format.
Heatmap matrizes and plots have been computed and plotted using Deeptools.
Assembly: mm9
Supplementary files format and content: bigWig files for ChIP-Seq signal distributions represent genomic distribution of the factors as described in the paper, they can be used for visualization in IGV and Juicebox browsers

source_name: mouse embryonic fibroblasts

growth_protocol: Primary MEFs (pMEFs) were generated from E13.5 embryos and cultured in full medium (DMEM supplemented with 10% FBS, 0.2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, and non-essential amino acids). Immortalized MEFs (iMEFs) were cultured in the same medium as pMEFs. Phoenix cells were cultured in DMEM supplemented with 10% FBS, 0.2 mM L-glutamine, 100 U/ml penicillin, and 100 µg/ml streptomycin.

extract_protocol:
One 24 cm² tray was used per ChIP experiment. Cells were crosslinked with 1/10th medium volume of crosslinking solution (11% formaldehyde, 100 mM NaCl, 0.5 mM EGTA, 50 mM Hepes, pH 8.0) at room temperature for 10 minutes and subsequently quenched with 125 mM glycine for 5 minutes. Cells were washed with PBS, collected by scraping, and centrifuged. Cell pellets were lysed in lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, pH 8.0, 1% SDS, protease inhibitors) on ice for 20 minutes. DNA was sonicated for 12 cycles (30 seconds on/off) using a Bioruptor. Five volumes of dilution buffer (20 mM Tris-HCl, pH 8.0, 2 mM EDTA, pH 8.0, 1% Triton X-100, 150 mM NaCl, 1 mM PMSF) were added to the lysate, followed by pre-clearing with 100 µl Affi-Prep Protein A beads at 4°C. Immunoprecipitation was performed with rabbit IgG or antibody overnight, followed by a 3-hour incubation with Affi-Prep Protein A beads. Beads were washed twice with Wash Buffer 1 (20 mM Tris-HCl, pH 8.0, 2 mM EDTA, pH 8.0, 1% Triton X-100, 150 mM NaCl, 0.1% SDS, 1 mM PMSF), twice with Wash Buffer 2 (20 mM Tris-HCl, pH 8.0, 2 mM EDTA, pH 8.0, 1% Triton X-100, 500 mM NaCl, 0.1% SDS, 1 mM PMSF), twice with Wash Buffer 3 (10 mM Tris-HCl, pH 8.0, 2 mM EDTA, pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% deoxycholate), and twice with TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0). The samples were eluted twice with 200 µl elution buffer (25 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.5% SDS) by shaking at 65°C for 20 minutes. The eluates were treated with RNase A at 37°C for 1 hour and proteinase K at 65°C overnight. Following the addition of 1 µl glycogen (20 mg/ml) and 1/10th volume sodium acetate (3 M, pH 5.2), DNA was extracted with phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated with ethanol. The DNA was resuspended in H₂O and submitted for library preparation and Illumina deep sequencing at the Campus Science Support Facility.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer's instructions. Briefly, ChIP DNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. The libraries were then amplified by PCR for 12 cycles, purified using AMPure XP beads (Beckman Coulter), and quantified by Qubit (Thermo Fisher). Library quality was assessed using an Agilent Bioanalyzer.

treatment_protocol: All experiments with MEFs were performed in quiescence. To achieve this, MEFs were grown to confluence, and then the full medium was replaced with resting medium. For the conditional deletion of floxed Phf2, Wapl, and Smc3 alleles, we used the inducible CreERT2 recombinase expressed from the Rosa26 locus (CreER). Cells were arrested in Opti-MEM (Invitrogen) supplemented with 2% charcoal-treated FBS, 100 U/ml penicillin, 100 µg/ml streptomycin, and 0.5 µM 4-hydroxytamoxifen (4-OHT, Sigma) for 7 days. For the conditional deletion of the floxed CTCF allele, MEFs were cultured for 4 hours in resting medium (DMEM supplemented with 2% FBS), 4 µg/ml polybrene, and Adeno-Cre virus (Penn Vector Core, 1 µl per 1 million cells). The medium was then replaced with resting medium for 7 days.

value: mouse embryonic fibroblasts

value: Wapl-ko

tag: antibody


title: Smc3 in w.t._4_merged


title: Armstrong immune P14 replicate A, ADT


title: LNCaP95 CPSF1 sh1 BR2


title: Smc3 in Phf2-ko_4_merged


title: line 10B rep 2 short-read

description: Library name: 10B_23


title: LNCaP95 CPSF1 sh2 BR2


title: Smc3 in Smc3-ko_12154_sorted


title: line 10B rep 1 short-read

description: Library name: 10B_12


title: Armstrong immune P14 replicate A, GEX


title: line 1 rep 1 short-read

description: Library name: 1_23


title: line 12 rep 2 short-read

description: Library name: 12_13


title: LNCaP95 CTRL sh BR2

value: CTRL shRNA


title: Mut_03

city: Shanghai

first: Yuwen

last: Cai

country: China

institute: Fudan University Shanghai Cancer Center

data_processing:
1, quality control of sequencing data: in this experiment, the two-end sequencing mode of illumina Novaseq6000 sequencing platform was used for high-throughput sequencing of multiple samples. According to the distribution characteristics of low quality scores of illumina sequencing data concentrated on the ends, the sequencing data was used by Skewer software (v0.2.2) to dynamically remove the 3 ′ end and low quality fragments, analyze the preprocessed data by FastQC software (v0.11.5), and the proportion of bases in Q20 and Q30 were counted.
2, reference genome alignment: for each sample, the STAR software (2.5.3a) aligned the preprocessed sequence with the reference genome (mm10). The principle of STAR software is to divide the entire sequence into multiple seed sequence alignment to the genome sequence, with continuous and non-continuous sequence alignment. The alignment results were analyzed using RSEQC (v2.6.4).
3, Transcript assembly and novel transcript prediction: the results of reads alignment to the reference genome were assembled using StringTie Software (v1.3.1c), classifying the new transcripts obtained by assembly, including the genes to which the transcript belongs, chromosome number, start & termination position, length, and number of exons.
4, quantification of gene expression levels: raw sequence counts of known genes were counted by StringTie Software for all of the samples, and the expression of known genes was calculated by Transcripts Per Million (TPM).
Assembly: mm10
Supplementary files format and content: The processed data was presented as Transcripts Per Million (TPM)

extract_protocol:
Cells were harvested and total RNA was extracted by using RNAmini kit ( Qiagen, Germany).
Step 1, mRNA enrichment: Eukaryotic mRNA was enriched with magnetic beads with Oligo (dT); Step 2, fragmented mRNA: randomly interrupt the mRNA into short fragments of about 200bp. Step 3, Strand-specific synthesis of cDNA: After reverse transcription of first-stranded cDNA with random primers, dTTP in dNTPs is replaced by dUTP during the synthesis of second-stranded cDNA. Step 4, Connect the sequencing connector: the double-stranded cDNA was purified using AMPure XP beads, flattened by the End Repair Mix ends, and added with the A tail and sequencing adaptor. Step 5, Two-stranded cDNA digestion: two-stranded cDNA was digested using USER enzyme to make the library contain only one-stranded cDNA. Step 6, PCR enrichment: the final cDNA library PCR was yielded by amplification of 15 cycles. Step 7, Library detection and quantification: libraries were quantified using qubit.


title: LNCaP95 CPSF1 sh2 BR1

value: shRNA targeting CPSF1 (2)


title: DMSO rep 9

description: Library name: C4_8_7

data_processing:
Adapters and low-quality ends were trimmed from reads with Trim Galore (parameters: --paired --retain_unpaired -q 25)
Transcript quantification was performed with Salmon; Araport 11 transcriptome used as reference and Col-CEN v1.2 genome as decoys
Five outliers were removed based upon PCAgrid function in R package rrcov and preliminary analyses
Differential expression analysis conducted with DESeq2. Genes that did not meet the threshold of having at least 10 counts in four or more samples were excluded. Each phenotype of interest was analyzed independently; DESeq2 design (~ treatment + phenotype) incorporated both treatment (etoposide or DMSO) and phenotype (present or absent).
Assembly: Araport 11 transcriptome
Supplementary files format and content: csv file of unnormalized counts for each sample
Supplementary files format and content: csv file of log2 fold changes and pvalues for all expressed genes; one file each for BR-like dwarf, short-internode dwarf, and virescent phenotypes

extract_protocol:
Leaf tissue was flash-frozen in liquid nitrogen. Frozen tissue was ground into a powder with a QIAGEN Tissuelyser II (30 beats/sec for 30 sec). RNA was extracted using a QIAGEN RNeasy Plant Mini Kit.
Libraries were constructed using poly(A) selection followed by the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).


title: PolII in Wapl-ko

value: PolII


title: Mut_02


title: PolII in wt_2_merged

value: wt


title: PolII in Smc3-ko


title: Mut_01


title: DMSO rep 7

description: Library name: C4_8_4


title: Phf2 in Wapl-ko_2_merged


title: LNCaP CPSF1 sh2 BR3

value: LNCaP


title: Phf2 in w.t._4_merged


title: DMSO rep 6

description: Library name: C23_34


title: LNCaP95 CTRL sh BR1


title: DMSO rep 5

description: Library name: C23_30


title: WT_02


title: LNCaP CTRL sh BR3


title: DMSO rep 4

description: Library name: C23_28


title: Phf2 in Phf2-ko


title: LNCaP CPSF1 sh1 BR3


title: LNCaP CPSF1 sh2 BR2


title: Input_A20_BAP1_KO_Clone1

city: Chicago

first: Lu

last: Wang

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: hg19,mm9
Supplementary files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: The SCLC cell lines NCI-H526 was obtained from ATCC, and were maintained with ATCC-formulated RPMI-1640 medium containing 10% FBS (Sigma).

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit. For ATAC-seq, frozen cells were thawed and washed once with PBS and then resuspended in 500 uL of cold ATAC lysis buffer. The cell number was assessed by Cellometer Auto 2000 (Nexcelom Bioscience). 50K to 100K nuclei were then centrifuge (pre-chilled) at 500 g for 10 min. Supernatant was then removed and the nuclei were resuspended in 50 uL of tagmentated DNA by pipetting up and down six times. The reactions were incubated at 37 °C for 30 min in a thermomixer shaking at 1,000 rpm, and then cleaned up by the MiniElute reaction clean up kit (Qiagen).
ChIP-seq: ChIP-sequencing libraries were prepared using KAPA HyperPrep Kit (Kapa Biosystems) following manufacturer’s recommendation. In brief, 500ng of input DNA sheared by Covaris LE220 ultrasonicator or 10 ng of immunoprecipitated DNA was end-repaired and 3'-dA tailed. Adapter was then ligated to the DNA, and ligated product was PCR amplified and cleaned up using SPRIselect Reagent (Beckman Coulter). for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit
RNA-seq: Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with an longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used. Samples were pooled and sequencing on a HiSeq with a read length configuration of 150 PE.
ATAC-seq: Tagmentated DNA was amplified with barcode primers. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio® 5 System (Applied Biosystems, California, USA). Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® HiSeq (Illumina, California, USA) with a read length configuration of 150 PE for 50M PE reads (25M in each direction) per sample.

value: B cell lymphoma


title: LNCaP95 CPSF1 sh1 BR1


title: DMSO rep 2

description: Library name: C13_2


title: Input_A20_BAP1_KO_Clone2


title: LNCaP CPSF1 sh1 BR2


title: Phf2 in Smc3-ko_3_merged


title: WT_03


title: Phf2 in Ctcf-Wapl-ko_merged

value: Ctcf-Wapl-ko


title: DMSO rep 1

description: Library name: C13_15

value: DMSO


title: Phf2 in Ctcf-ko_merged

value: Ctcf-ko


title: DMSO rep 8

description: Library name: C4_8_6


title: LNCaP CTRL sh BR2

value: Cell Line


title: H3K9me3 in w.t.


title: H2AK119Ub_A20_BAP1_KO_Clone1


title: LNCaP CPSF1 sh2 BR1

value: Prostate Cancer


title: H3K9me3 in Wapl-ko


title: virescent realtive without phenotype rep 4

description: Library name: 13B_18_47

value: leaf


title: H2AK119Ub_A20_BAP1_KO_Clone2


title: virescent realtive without phenotype rep 3

description: Library name: 13B_18_24


title: LNCaP CPSF1 sh1 BR1

value: shRNA targeting CPSF1 (1)


title: DMSO rep 3

description: Library name: C13_5


title: virescent realtive without phenotype rep 2

description: Library name: 13B_18_21

value: etoposide


title: H2AK119Ub_A20_BAP1_WT

value: wild type


title: H3K27me3_A20_BAP1_KO_RB3


title: virescent realtive without phenotype rep 1

description: Library name: 13B_18_20


title: Input_A20_BAP1_WT


title: LNCaP CTRL sh BR1


title: 3_ThO_H1cJunKO+cJun_D25_CUTtag

city: Macau

first: Jiantao

last: Shi

address: niversity of Macau Avenida da Universidade Taipa, Macau, China

department: ICMS

institute: University of Macau

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
seq reads were aligned to the hg19 genome assembly using rsem with options --bowtie2 --bowtie2-sensitivity-level very_sensitive
expected_count were extract from the sample_name.genes.results and merged together to get a big table
ATACseq data was normalized by EDAseq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include count values for each Sample
Library strategy: CUT&TAG

source_name: Embryonic Stem Cells

growth_protocol: We mainly referred to the technical guidelines for Thalamus Organoids culture published by Xiang et al.(Xiang et al., 2019)Giandomenico, 2021).

extract_protocol:
50,000 cells were washed with 50 μl cold PBS and resuspended in 50 μl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% [vol/vol] IGEPAL CA-630). The suspension of nuclei was centrifuged for 10 min at 500g at 4℃, and then add 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase, and 22.5 μl nuclease-free H2O) from the Nextera DNA library Preparation Kit (96 samples) (FC-121-1031; Illumina);RNAseq:Total RNA was prepared with TRIzol (Invitrogen,15596026).1 μg total RNA was used for cDNA synthesis using HiScript®II Q RT SuperMix for qPCR (+gDNA wiper) (Vazyme,R223-01) according to the manufacturer’s instruction; CUT&Tag:3 ThOs were collected and digested by incubation at accutase at 37 ℃ for 0.5 hour and dispersed with pipette. Then 50,000 cells were used for the CUT&Tag experiment, and pA-Tn5 transposase was used to cut the genome and add a special adaptor sequence to build a library.
Run PCR to amplify the samples and incubated at 37°C for 30 min. Then the DNA was isolated using a MinElute Kit (QIAGEN). The ATAC-seq libraries were subjected to 12 cycles of amplification. Finally, the purified ATAC libraries were sequenced on the NextSeq 500 sequencing platform using a NextSeq 500 High Output Kit v2 (150 cycles) (FC-404-2002; Illumina) according to the manufacturer’s instructions.Purified RNA was analyzed to determine the RNA concentration and integrity;RNAseq;AHTS® Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme,NR603), VAHTS®RNA Adapters set3 for Illumina(Vazyme,N809) were used to make the libraries for sequencing according to the manufacturer’s instructions;CUT&Tag:The enrichment of target sites in the library was detected using qPCR. The c-Jun antibody(#9165; Cell Signaling Technology) was used to capture the binded proteins

treatment_protocol: ATAC-seq was performed as previously described (Buenrostro, Wu, Chang, & Greenleaf, 2015). Briefly, The 3 ThOs were collected and digested by incubation at accutase at 37 ℃ for 0.5 hour and dispersed with pipette;RNAseq:3pooled Organoids samples were incubated with TRIzol and lysed through pipetting on ice and next extracted according to the manufacturer's instructions. Purified RNA was analyzed to determine the RNA concentration and integrity. rganoid;c-Jun CUT&Tag data was generated by the Hyperactive Universal CUT&Tag Assay Kit (Vazyme) according to the manufacturer’s instructions.

value: Embryonic Stem Cells

value: WT

value: neural differentiation and thalamus organoids induction


title: H3K27me3_A20_BAP1_KO_DMSO


title: H3K9me3 in Phf2-ko

value: mouse embryonic fibroblasts


title: H3K4me3 in Phf2-ko


title: H2AK119Ub_A20_BAP1_KO_RB3


title: 1_ThO_H1WT_D25_CUTtag


title: H3K4me3 in Wapl-ko

value: Wapl-ko


title: virescent rep 6

description: Library name: 13B_46_31


title: WT_01


title: H2AK119Ub_A20_BAP1_KO_DMSO


title: virescent rep 4

description: Library name: 13B_46_16


title: H3K4me3 in w.t.


title: virescent rep 5

description: Library name: 13B_46_23


title: 12_ThO-12_H1cJunKO+cJun_D30_RNAseq_rp2

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
seq reads were aligned to the hg19 genome assembly using rsem with options --bowtie2 --bowtie2-sensitivity-level very_sensitive
expected_count were extract from the sample_name.genes.results and merged together to get a big table
ATACseq data was normalized by EDAseq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include count values for each Sample

value: c-Jun Knockout


title: 11_ThO-11_H1cJunKO+cJun_D30_RNAseq_rp1


title: cl13gp33pos69pos.3

description: CD69+ H-2Db/gp33 tetramer+ CD8+  50 days after LCMV Cl13 infection of CD4+ T cell depleted mice

data_processing:
Cutadapt was used to remove the first three nucleotides of the sequencing read which were derive from the Clontech template-switching oligo. Initial quality control analysis of RNA sequencing (FASTQ) data for each sample was performed using the FastQC software (version 0.11.5).
Trimmomatic (version 0.33) was used to trim FASTQ data.
UCSC version mm10 (GRCm38, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)) was used as the mouse reference genome. HISAT2 (version 2.0.2-beta) was used to map single-end reads.
Insertion size metrics were calculated for each sample using Picard software (version 1.126) (http://picard.sourceforge.net.).  Mapping statistics are summarized in Table S4. Samtools (version 1.3_BCFTools_HTSLib) was used to sort and index the bam files.
Gene abundance estimates were generated using the Rsubread featureCounts program.
Assembly: UCSC version mm10 (GRCm38, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)).
Supplementary files format and content: Gene abundance estimates  generated with the Rsubread featureCounts program are provided as a tab-deliminited file.

source_name: secondary lymphoid organs

growth_protocol: 5 x 104 naïve CD45.1+ P14 TCR transgenic CD8 T cells, specific for the H-2Db-restricted LCMV gp33-41 epitope, were transferred to adult naïve female C57BL/6J mice, which were then infected i.p. with 2x105 PFU LCMV Armstrong (Arm), one day later. At day 4 after infection some mice were sacrificed and CD69+ P14 cells were isolated by fluorescence-activated cell sorting (FACS) of splenocytes. To generate bystander activated P14 cells, LCMV Armstrong memory mice (>30 days after infection) were infected with Vesicular stomatitis virus (VSV). Two days later, CD69+ bystander activated P14 cells were isolated by FACS of splenocytes from VSV infected mice. LCMV Armstrong memory mice (>30 days after infection) were sacrificed and FACS was used to isolate CD69+ FRT (female reproductive tract), CD69+ SI-IEL (small intestine intraepithelial lymphocytes), CD69+ SI-LP (small intestine lamina propria), and CD69+ and CD69- SPL (spleen) and LN (pooled lymph nodes) P14 cells. To establish chronic infection, C57BL/6J mice received 200 µg of anti-CD4 antibody one day prior to i.v. infection with 2 x 106 PFU LCMV Cl13 followed by anti-CD4 antibody treatment the next day. Endogenous gp33 tetramer+ CD8 T cells were isolated by FACS of splenocytes from chronically infected mice.

extract_protocol:
FACS sorted cells were homogenized using QIAshredder columns (QIAGEN) and RNA was extracted using an RNeasy micro kit (QIAGEN) per the manufacturer’s instructions.
Sequencing libraries were prepared using the Clontech SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit.

treatment_protocol: After removing tissues, cells were released from the spleen and lymph nodes by mechanically disrupting them, followed by filtration through a 70-µm filter and washing in RPMI 1640 containing 5% fetal bovine serum (FBS). Spleen RBCs were lysed with ACK buffer and washed once. Cells were enzymatically released from the female reproductive tract (FRT) and from the epithelial and lamina propria compartments of small intestine (SI). After enzymatic digestion, lymphocytes from single-cell suspensions of the SI were enriched using a Percoll gradient.

value: secondary lymphoid organs

value: P14 CD8 T cell

value: female

value: C57BL/6 mouse strain

value: >30 days post infection LCMV-Cl13


title: cl13gp33pos69pos.2


title: virescent rep 3

description: Library name: 13B_25_31


title: 10_ThO-10_H1cJunKO_D30_RNAseq_rp2


title: CIITA_A20_BAP1_WT

value: B cell lymphoma


title: cl13gp33pos69pos.1


title: CIITA_A20_BAP1_KO


title: virescent rep 2

description: Library name: 13B_25_26


title: SpleenTRM.5

description: CD8+ CD45.1+ P14 from Spleen (SPL) TRM (CD62L- CD69+)

source_name: spleen

value: spleen

value: >30 days post infection LCMV-Armstrong


title: 9_ThO-9_H1cJunKO_D30_RNAseq_rp1


title: IRF1_A20_BAP1_KO


title: IRF1_A20_BAP1_WT


title: variegated line, green, variegated progeny rep 3

description: Library name: 5A_58_34

value: leaf


title: 8_ThO-8_H1WT_D30_RNAseq_rp2


title: virescent rep 1

description: Library name: 13B_25_23

value: etoposide


title: SpleenTRM.3


title: H2AK119Ub_A20_BAP1_KO_Clone1_Rep2


title: SpleenTEM.4

description: CD8+ CD45.1+ P14 from pooled secondary lymphoid organs ( CD62L- CD69-)


title: H2AK119Ub_A20_BAP1_KO_Clone2_Rep2


title: variegated line, green, variegated progeny rep 2

description: Library name: 5A_58_31


title: SpleenTEM.3


title: 7_ThO-7_H1WT_D30_RNAseq_rp1


title: 5_ThO-5_H1cJunKO+cJun_D25_RNAseq_rp1


title: variegated line, green, no variegated progeny rep 10

description: Library name: 5A_58_33


title: UTX_A20_BAP1_KO


title: SpleenTEM.1


title: variegated line, white

description: Library name: 5A_58_20


title: variegated line, green, variegated progeny rep 1

description: Library name: 5A_58_18


title: 3_ThO-3_H1cJunKO_D25_RNAseq_rp1


title: SLObys69pos.4

description: CD8+ CD45.1+CD69+ memory P14 48 hours after bystander VSV infection

value: >30 days post infection LCMV-Armstrong and 2 days post infection VSV


title: 2_ThO-2_H1WT_D25_RNAseq_rp2

value: Embryonic Stem Cells


title: UTX_A20_BAP1_WT

value: wild type


title: H3K27me3_A20_BAP1_KO


title: SpleenTRM.4


title: SLObys69pos.3


title: 1_ThO-1_H1WT_D25_RNAseq_rp1

value: WT

value: neural differentiation and thalamus organoids induction


title: SLObys69pos.1


title: SLOTRM.6

description: CD8+ CD45.1+ P14 from pooled lymph nodes (LN) TRM (CD62L- CD69+)


title: 9_ThO_H1cJunKO+cJun_D30_ATACseq


title: variegated line, green, no variegated progeny rep 6

description: Library name: 5A_3_2


title: 8_ThO_H1cJunKO_D30_ATACseq


title: variegated line, green, no variegated progeny rep 7

description: Library name: 5A_3_29


title: 4_ThO-4_H1cJunKO_D25_RNAseq_rp2


title: variegated line, green, no variegated progeny rep 5

description: Library name: 5A_3_18


title: H2AK119Ub_A20_BAP1_WT_Rep2


title: H3K27me3_A20_BAP1_WT


title: SLOTRM.4


title: 7_ThO_H1WT_D30_ATACseq


title: H2AUb_BAP1_WT_Rep1


title: BAP1_LLC

source_name: LLC

value: LLC

value: Lewis lung carcinoma


title: H2AUb_BAP1_KO_Rep1


title: variegated line, green, no variegated progeny rep 9

description: Library name: 5A_58_13


title: 6_ThO_H1cJunKO+cJun_D25_ATACseq

value: c-Jun Knockout


title: BAP1_A20


title: 5_ThO_H1cJunKO_D25_ATACseq


title: variegated line, green, no variegated progeny rep 3

description: Library name: 5A_2_3


title: NaiveCD8.2

description: CD8+ CD45.1+CD44- P14

value: secondary lymphoid organs

value: P14 CD8 T cell

value: naïve mice


title: ATAC_A20_BAP1_KO_Clone2


title: 6_ThO-6_H1cJunKO+cJun_D25_RNAseq_rp2


title: variegated line, green, no variegated progeny rep 2

description: Library name: 5A_2_24


title: 4_ThO_H1WT_D25_ATACseq


title: variegated line, green, no variegated progeny rep 1

description: Library name: 5A_2_17


title: SLOTRM.5

value: female

value: C57BL/6 mouse strain


title: NaiveCD8.1

description: CD8+ CD45.1+CD44- P14


title: 3_ThO_H1cJunKO+cJun_D20_ATACseq


title: ATAC_A20_BAP1_KO_Clone1

value: B cell lymphoma


title: 2_ThO_H1cJunKO_D20_ATACseq


title: variegated line, green, no variegated progeny rep 4

description: Library name: 5A_2_4


title: ATAC_A20_BAP1_WT


title: A20_BAP1_KO_GSK_Rep2


title: BR-like dwarf relative without phenotype rep 4

description: Library name: 1A_4_22


title: BR-like dwarf relative without phenotype rep 3

description: Library name: 1A_4_17


title: BR-like dwarf relative without phenotype rep 2

description: Library name: 1A_4_16


title: LP69posTRM.1

description: CD8+ CD45.1+ P14 from small intestine lamina propria (LP) Tissue Resident Memory Cells (CD62L- CD69+)

source_name: small intestine lamina propria lymphocytes

value: >30 days post infection LCMV-Armstrong


title: A20_KO_DMSO_Rep2

value: DMSO


title: LP69posTRM.2

value: small intestine lamina propria lymphocytes


title: NaiveCD8.3

description: CD8+ CD45.1+CD44- P14


title: LNTCM.3

description: CD8+ CD45.1+ P14 from pooled secondary lymphoid organs ( CD62L+ CD69-)


title: variegated line, green, no variegated progeny rep 8

description: Library name: 5A_3_8

value: leaf

value: etoposide


title: R203AKD5

city: Boston

first: Tomonori

last: Oka

state: MA

department: CBRC

institute: Massachusetts general hospital

data_processing:
The sequencing reads were mapped to the human genome (hg19) using STAR (v2.5)
Transcript assembly and quantification were conducted using StringTie and Ballgown. DEGs were analyzed through limma using count values for the analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited text files containing read counts

source_name: actinic keratosis (skin)

extract_protocol:
Lysis buffer
The libraries were prepared by Novogene (Sacramento, CA) using the NEBNext Ultra RNA Library Prep kit. The sequencing was conducted by Novogene, employing the Illumina NovaSeq 6000 System.

value: actinic keratosis (skin)

tag: day

value: vaseline plus 5-FU 4 day treatment


title: A20_BAP1_KO_GSK_Rep1


title: BR-like dwarf rep 6

description: Library name: 1A_20_8


title: BR-like dwarf relative without phenotype rep 1

description: Library name: 1A_4_11


title: LP69posTRM.3


title: R216AKD0


title: BR-like dwarf rep 5

description: Library name: 1A_20_6


title: LNTCM.1


title: LCMVD4.3

description: CD8+ CD45.1+CD69+ P14 4 days after infection with LCMV Armstrong

value: >4 days post infection LCMV-Armstrong


title: A20_WT_DMSO_Rep2

value: wild type


title: A20_WT_DMSO_Rep1


title: 1_ThO_H1WT_D20_ATACseq

value: Embryonic Stem Cells

value: WT

value: neural differentiation and thalamus organoids induction


title: LNTCM.2

value: secondary lymphoid organs

value: P14 CD8 T cell


title: R203AKD0


title: R190AKD0


title: R216AKD5


title: LCMVD4.1

value: female


title: BR-like dwarf rep 2

description: Library name: 1A_14_25


title: IEL69posTRM.2

description: CD8+ CD45.1+ P14 from the small intestine epithelium Tissue Resident Memory Cells (CD62L- CD69+)

source_name: small intestine intraepithelial lymphocytes

value: C57BL/6 mouse strain


title: R190AKD5


title: IEL69posTRM.3

value: small intestine intraepithelial lymphocytes


title: R202AKD5

value: calcipotriol plus 5-FU 4 day treatment


title: BR-like dwarf rep 1

description: Library name: 1A_14_15


title: A20_BAP1_KO_RB5uM_Rep2

value: B cell lymphoma

value: RB5 5µM


title: A20_KO_DMSO_Rep1

value: DMSO


title: IEL69posTRM.1

value: >30 days post infection LCMV-Armstrong


title: R196AKD5

value: actinic keratosis (skin)


title: A20_BAP1_KO_RB5uM_Rep1


title: R194AKD5


title: A20_BAP1_KO_DMSO_Rep2


title: LCMVD4.2


title: short-internode dwarf realtive without phenotype rep 3

description: Library name: 34C_9_23

value: leaf

value: etoposide


title: A20_BAP1_KO_DMSO_Rep1


title: BR-like dwarf rep 3

description: Library name: 1A_14_5


title: FRT69posTRM.4

description: CD8+ CD45.1+ P14 from the female reproductive tract (FRT) Tissue Resident Memory Cells (CD62L- CD69+)

source_name: female reproductive tract

value: female reproductive tract


title: short-internode dwarf realtive without phenotype rep 2

description: Library name: 34C_9_12


title: BR-like dwarf rep 4

description: Library name: 1A_20_5


title: R196AKD0


title: A20_BAP1_WT_DMSO_Rep2

value: wild type


title: FRT69posTRM.3


title: A20_BAP1_KO_RB10uM_Rep2

value: RB5 10µM


title: short-internode dwarf realtive without phenotype rep 4

description: Library name: 34C_9_3


title: A20_BAP1_WT_DMSO_Rep1


title: short-internode dwarf realtive without phenotype rep 1

description: Library name: 34C_9_11


title: 22Rv1 CPSF1 sh2 BR2

value: Cell Line

value: Prostate Cancer

value: shRNA targeting CPSF1 (2)


title: S49__BPCMML__PT_1007T6__BM_blast

city: Manchester

first: Kiran

last: Batta

address: The University of Manchester

country: United Kingdom

institute: University of Manchester

data_processing:
FASTQ files were quality assessed and aligned via STAR (v2.5.1b) to human GENCODE reference transcriptome (v42; GRCh38.p13/hg38) and samples (S2) filtered for low fraction of uniquely mapped reads. Reads quantification was performed using Salmon (v1.4.0) in alignment-based mode and gene-level abundances (TPM and raw counts) estimated with TxImport (v1.30.0). DEseq2 was used to perform differential gene expression analysis and calculate VST (variance stabilizing transformation) normalized read values for each gene (Love et al., 2014).
Assembly: GENCODE (v42; GRCh38.p13/hg38)
Supplementary files format and content: Processed files were saved in CSV (comma separated values) format. The "Tximport_raw_countmat.csv" file includes gene-level quantified reads obtained from TxImport following transcript-level quantification with Salmon (tximport function with type="salmon", tx2gene=tx2gene, txIn = TRUE, txOut = FALSE and countsFromAbundance = 'no'). The "Tximport_TPM_mat.csv" file contains gene-level abundance derived as per the "Tximport_raw_countmat.csv" file. The "DeSeq2_vst_normalised_countmat.csv" file are counts imported in DESeq2 (DESeqDataSetFromTximport function), filtered to remove non-informative/duplicated genes, and subsequently normalized (vst function).

source_name: Bone marrow

extract_protocol:
Total RNA was extracted from primary sorted cells using the RNeasy Plus Micro Kit (74034, Qiagen), as per manufacturer instruction. RNA quality was quantified via Qubit and analyzed using the Agilent Bioanalyzer.
Libraries were generated using the NEB Next Ultra II (pA) RNA (E7770, New England Biolabs) kit following a 10ng input workflow.
Libraries (1x101bp) were sequenced using the NovaSeq 6000 sequencing system (Illumina), installed with SP type flow cells, aiming for 45 million reads per sample.

value: Bone marrow

value: Blast (Live/SSC-Alo/CD45dim)

tag: disease state

value: Blast phase chronic myelomonocytic leukemia


title: short-internode dwarf rep 6

description: Library name: 34C_7_7


title: FRT69posTRM.2

value: P14 CD8 T cell

value: female

value: C57BL/6 mouse strain


title: R202AKD0

value: calcipotriol plus 5-FU 4 day treatment


title: S48__Control__Donor_1157T1__BM_HSPC

value: Hematopoietic stem and progenitor cells - HSPCs (Live/CD34positive)

value: Healthy control


title: S47__BPCMML__PT_1217T4__BM_blast


title: short-internode dwarf rep 3

description: Library name: 34C_6_36

value: leaf


title: short-internode dwarf rep 4

description: Library name: 34C_7_22

value: etoposide


title: A20_BAP1_KO_IRF1_Rep1

value: B cell lymphoma

value: infected with GFP_IRF1


title: short-internode dwarf rep 5

description: Library name: 34C_7_50


title: A20_BAP1_KO_IRF1_Rep2


title: S45__BPCMML__PT_930T3__PB_blast

source_name: Peripheral blood

value: Peripheral blood


title: A20_BAP1_KO_GFP_Rep2

value: infected with GFP


title: A20_BAP1_KO_GFP_Rep1


title: R194AKD0

value: actinic keratosis (skin)


title: short-internode dwarf rep 2

description: Library name: 34C_6_24


title: short-internode dwarf rep 1

description: Library name: 34C_6_21


title: S44__Control__Donor_1207T1__BM_HSPC


title: A20_BAP1_KO_Clone 2_Rep2


title: Ida012

city: Memphis

first: Alessandra

last: d'Azzo

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description: Gene expression data from Hippocampus

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: RMA

label: Biotin

source_name: Flash-frozen hippocampus dissected from whole brain of post-natal mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were housed in a fully AAALAC (Assessment and Accreditation of Laboratory Animal Care)-accredited animal facility with controlled temperature (22°C), humidity, and lighting (alternating 12-h light/dark cycles). Food and water were provided ad libitum.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mice were sacrificed then brains were dissected and hippocampi were manually selected under the dissecting scope. Hippocampi were flash-frozen in liquid nitrogen then lysed in the Trizol solution.

value: Brain; Hippocampus

tag: gender

value: 5 month

value: Neu1 deficient


title: Ida011

description: Gene expression data from Hippocampus

value: male


title: Ida009

description: Gene expression data from Hippocampus

value: Wild-type


title: Ida010

description: Gene expression data from Hippocampus


title: A20_BAP1_KO_Clone 2_Rep1


title: S43__BPCMML__PT_136T1__BM_blast

value: Bone marrow

value: Blast (Live/SSC-Alo/CD45dim)

value: Blast phase chronic myelomonocytic leukemia


title: Ida007

description: Gene expression data from Hippocampus


title: S46__BPCMML__PT_1159T3__PB_blast


title: CF subject CFB1018, exposed to IL-17+TNFa

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

description: Library name: 24

data_processing:
Raw fastq files were pseudoaligned to human genome assembly GRCh38.p12 using kallisto software version 0.45.0
Assembly: Raw fastq files were pseudoaligned to human genome assembly GRCh38.p12 using kallisto software version 0.45.0
Supplementary files format and content: GRCh38.p12
Supplementary files format and content: Tab-separated text file containing length, estimated counts, and transcripts per million (TPM) for each gene isoform

source_name: airway epithelial cells

extract_protocol:
RNA was extracted using Qiagen RNeasy Lipid Tissue Mini Kit # 74804.
mRNA libraries were prepared using Illumina TruSeq stranded mRNA sample preparation kit (Illumina #RS-122-2101).

value: airway epithelial cells

tag: donor

tag: batch

tag: disease

value: CF


title: CF subject CFB0918, exposed to IL-17+TNFa

description: Library name: 23

tag: tissue


title: S42__BPCMML__PT_919T1__BM_blast

tag: cell type


title: CF subject CFB0818, exposed to IL-17+TNFa

description: Library name: 22


title: A20_BAP1_WT_Rep2

tag: cell line

value: wild type


title: S40__BPCMML__PT_620T1__BM_blast


title: A20_BAP1_WT_Rep1

tag: treatment


title: S41__BPCMML__PT_713T5__BM_blast


title: A20_BAP1_KO_Clone 1_Rep2


title: S39__BPCMML__PT_1049T8__BM_blast


title: CF subject CFB0618, exposed to IL-17+TNFa

description: Library name: 20


title: CF subject CFB0718, exposed to IL-17+TNFa

description: Library name: 21


title: embWPC ALBSF 04

city: San Juan de Alicante

first: Guillermina

last: López-Bendito

state: Alicante

address: Av Ramon y Cajal s/n, Campus de San Juan

department: Instituto Neurociencias CSIC-UMH

country: Spain

institute: Universidad Miguel Hernández (UMH)

data_processing:
Quality control of the raw data was performed with FastQC (v.0.11.9)
RNA-seq reads were mapped to the Mouse genome (GRCm39/mm10 Ensembl release 104, May 2021) using STAR (v2.7.9a) (Dobin et al., 2013) and SAM/BAM files were further processed using SAMtools v1.15 (Li et al., 2009).
Aligned reads were counted and assigned to genes using Ensembl release 104 gene annotation and FeatureCounts, Subread (v2.0.1) (Liao et al., 2014).
Normalization of read counts and differential expression analyses were performed using DESeq2 (v1.32) (Love et al. 2014), Bioconductor (v3.15) in the R statistical computing and graphics platform (v4.2.2 "Innocent and Trusting").
Assembly: GRCm39/mm10 Ensembl release 104
Supplementary files format and content: Tab-delimited text files include Gene Counts values for each Sample.

source_name: ALBSF-VPM (Thalamus)

extract_protocol:
To collect tissue from the PMBSF and ALBSF territories, ctrl and embWPC P0 pups were euthanized via decapitation, and their brains were dissected out under RNase-free conditions to prevent RNA degradation. The brains (five brains were pooled for each sample) were collected in ice-cold KREBS solution and sliced into 300 μm sections using a vibratome. The PMBSF and ALBSF territories were rapidly microdissected under a stereo microscope. The bulk tissue was immediately transferred to lysis buffer of the RNeasy® Micro Kit (Qiagen, 74004) for total RNA extraction, following the manufacturer’s instructions. RNA quality was measured for all samples using an Agilent Bioanalyzer 2100 system, and only samples with RNA Integrity Number (RIN) > 8 were used for library construction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Then the quantified libraries were  pooled and sequenced for 150pb paired-read and performed on an Illumina Novaseq6000 platform using 2x150 sequencing to read depth of > 40 million reads per sample at Novogene Co. Ltd.  genomics core facility (Cambridge, UK).

value: ALBSF-VPM (Thalamus)

value: Bulk Tissue

tag: Stage

value: Postnatal day 0

value: embWPC


title: embWPC ALBSF 03


title: CF subject CFB1018, control

description: Library name: 18

value: control


title: S37__BPCMML__PT_965T1__PB_blast

value: Peripheral blood


title: CF subject CFB0518, exposed to IL-17+TNFa

description: Library name: 19


title: Ida006

description: Gene expression data from Hippocampus

value: Brain; Hippocampus

value: female

tag: age

value: 1 month


title: Ida002

description: Gene expression data from Hippocampus

value: male


title: Ida003

description: Gene expression data from Hippocampus

value: Wild-type


title: Ida005

description: Gene expression data from Hippocampus

value: Neu1 deficient


title: Ida008

description: Gene expression data from Hippocampus

value: 5 month


title: Ida001

description: Gene expression data from Hippocampus


title: embWPC ALBSF 02


title: S38__BPCMML__PT_776T4__PB_blast

value: Blast (Live/SSC-Alo/CD45dim)

value: Blast phase chronic myelomonocytic leukemia


title: S36__BPCMML__PT_343T1__BM_blast

value: Bone marrow


title: CF subject CFB0918, control

description: Library name: 17

value: airway epithelial cells

value: CF


title: embWPC ALBSF 01

value: ALBSF-VPM (Thalamus)

value: Bulk Tissue


title: CF subject CFB0818, control

description: Library name: 16


title: S34__BPCMML__PT_671T1__PB_blast


title: CF subject CFB0618, control

description: Library name: 14


title: RNA-Seq_human_melanoma_WM9_69

city: Deggendorf

first: Melanie

last: Kappelmann-Fenzl

address: Dieter-Görlitz Platz 1

department: Applied Computer Science

country: Germany

institute: Deggendorf Institute of Technology

description: Library name: RNA_WM9_69

data_processing:
quality check using FastQC
Paired-end reads were aligned to the human reference genome sequence (hg38) using the STAR alignment software (v 2.5.2a).
Counts for RNA-Seq reads were calculated using the feature-counts software (v 1.4.6-p5)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes counts normalized to library size by DESeq2 for each Sample

source_name: melanoma cell line derived from metastatic site

growth_protocol: Human melanoma cell lines Sbcl-2, WM3211, WM1366, WM793, WM1158, and WM9 (a generous gift from Dr. M. Herlyn, Wistar Institute, Philadelphia, USA) derived from RGP (Sbcl-2), VGP (WM3211, WM1366, WM793), and melanoma MET (WM1158, WM9) were maintained in a culture medium consisting of MCDB153 (Sigma-Aldrich, Steinheim, Germany) with 20% Leibovitz’s L-15 (PAA Laboratories, Coelbe, Germany), 2% FCS, 1.68 mM CaCl2 (Sigma), and 5 µg/ml insulin (Sigma-Aldrich, Steinheim, Germany) at 37 °C and 5% CO2. NHEM were derived from neonatal foreskin (NHEMs, PromoCell, Heidelberg, Germany) and were cultured in melanocyte growth media M2 at 37 °C and 5% CO2.

extract_protocol:
The total RNA samples were isolated using Total RNA kit I (Omega Bio-Tek, Inc., Norcross, GA, USA) according to manufacturer’s instructions. All of the RNA samples were examined for integrity and purity by the TapeStation 4200 (Agilent).
Library preparation was performed with three biological replicates using the TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat Kit according to the manufactor´s instructions (Illumina Inc., San Diego, CA, USA). The resulting libraries were checked for size (200-500 bp) by TapeStation 4200 (Agilent) using the High-Sensitivity DNA Kit (Agilent) and concentration by the Qubit 4 Fluorometer (Thermo Fischer).

treatment_protocol: no treatment

value: metastasis


title: Ctrl PMBSF 04

source_name: PMBSF-VPM (Thalamus)

value: PMBSF-VPM (Thalamus)

value: Postnatal day 0

value: Control


title: RNA-Seq_human_melanoma_WM793_73

description: Library name: RNA_WM793_73

source_name: melanoma cell line derived from primary cunaneous melanoma

value: primary Tumor (VGP)


title: RNA-Seq_human_melanoma_WM1366_72

description: Library name: RNA_WM1366_72

value: melanoma cell line derived from primary cunaneous melanoma


title: Ctrl PMBSF 03


title: Ctrl PMBSF 02


title: RNA-Seq_human_melanoma_WM9_75

description: Library name: RNA_WM9_75

value: melanoma cell line derived from metastatic site


title: CF subject CFB0718, control

description: Library name: 15

value: control


title: S33__BPCMML__PT_171T1__PB_blast

value: Peripheral blood


title: A20_BAP1_KO_RB10uM_Rep1

value: B cell lymphoma

value: RB5 10µM


title: CF subject CFB0518, control

description: Library name: 13


title: RNA-Seq_human_melanoma_WM1366_66

description: Library name: RNA_WM1366_66


title: S35__Control__Donor_1162T1__BM_HSPC

value: Hematopoietic stem and progenitor cells - HSPCs (Live/CD34positive)

value: Healthy control


title: S32__BPCMML__PT_1061T1__BM_blast

value: Bone marrow

value: Blast (Live/SSC-Alo/CD45dim)

value: Blast phase chronic myelomonocytic leukemia


title: Ctrl PMBSF 01

value: Bulk Tissue


title: non-CF subject B1118, exposed to IL-17+TNFa

description: Library name: 12

value: airway epithelial cells

value: non-CF


title: RNA-Seq_human_melanoma_WM793_67

description: Library name: RNA_WM793_67


title: RNA-Seq_human_melanoma_WM1158_68

description: Library name: RNA_WM1158_68

source_name: melanoma cell line derived from metastatic site: Lymph node

value: melanoma cell line derived from metastatic site:Lymph node

value: metastasis


title: S31__BPCMML__PT_745T2__BM_blast


title: A20_BAP1_KO_Clone 1_Rep1


title: non-CF subject B1018, exposed to IL-17+TNFa

description: Library name: 11


title: Ctrl ALBSF 03

value: ALBSF-VPM (Thalamus)

value: Postnatal day 0

value: Control


title: non-CF subject B0918, exposed to IL-17+TNFa

description: Library name: 10


title: RNA-Seq_human_melanoma_WM1158_74

description: Library name: RNA_WM1158_74


title: S30__BPCMML__PT_55T1__BM_blast


title: RNA-Seq_human_melanoma_WM3211_71

description: Library name: RNA_WM3211_71


title: Ctrl ALBSF 02


title: non-CF subject B0618, exposed to IL-17+TNFa

description: Library name: 8


title: RNA-Seq_human_melanoma_Sbcl2_70

description: Library name: RNA_Sbcl2_70

value: melanoma cell line derived from primary cunaneous melanoma

value: primary tumor (RGP)


title: RNA-Seq_human_melanoma_WM3211_65

description: Library name: RNA_WM3211_65


title: Ctrl ALBSF 01


title: S29__BPCMML__PT_872T1__PB_blast

value: Peripheral blood


title: non-CF subject B0818, exposed to IL-17+TNFa

description: Library name: 9


title: S27__BPCMML__PT_660T1__PB_blast


title: non-CF subject B0518, exposed to IL-17+TNFa

description: Library name: 7


title: RNA-Seq_human_melanoma_Sbcl2_64

description: Library name: RNA_Sbcl2_64


title: Ctrl ALBSF 04


title: treated, replicate 2, scRNAseq

city: Buffalo

first: Spencer

last: Rosario

address: Elm & Carlton Sts

institute: Roswell Park Comprehensive Cancer Center

description:
TX2
10x Sequencing

library_source: transcriptomic single cell

data_processing:
Genome alignment, filtering, demultiplexing, barcoding, and unique molecular identifier counting were performed using Cell Ranger v7.1.
Assembly: mm10
Supplementary files format and content: 3 files necessary for Seurat: 1) barcodes.tsv.gz, 2) features.tsv.gz, 3) matrix.mtx.gz

source_name: tumor

growth_protocol: 100,000 MOC-2 HNSCC cells were subcutaneously injected onto the hind quarters/back of each mouse and allowed to become palpable (approximately 50-100 mm3) before treatment.

extract_protocol:
Single cell suspensions were generated from six MOC-2 tumor-bearing male mice at 24 hours after intratumoral drug or vehicle treatment as described. Cells were stained with Zombie UV Viability Dye (BioLegend, San Diego, CA) andlive cells were isolated by FACS sorting on an Aria II running FACSDiva (BD Biosciences).Each tumor sample was hash tagged withChromium Next GEM Single Cell 3ʹv3.1 Cell Multiplexing Oligo (10x Genomics, Pleasanton, CA), counted, and pooled in equal ratio prior to scRNA-seq. Indexed sequencing libraries were constructed using the Chromium Single-Cell 3′ Library Kit (Parse Biosciences, Seattle, WA) by the Baylor College of Medicine Single Cell Genomics Core and subsequently sequenced using NovaSeq X Plus PE150 by the Novogene Corporation (Sacramento, CA).
Indexed sequencing libraries were constructed using the Chromium Single-Cell 3_ Library Kit (Parse Biosciences, Seattle, WA) by the Baylor College of Medicine Single Cell Genomics Core.
Standard Novoseq library preps were utilized

treatment_protocol: All reagents were dissolved in either DMSO or sterile water based on solubility requirements and included Copper(II) diethyldithiocarbamate at 85 mg/50 ml (VWR, Radnor, PA), 2-C1-IB-MECA at 20 mg/50 ml (Millipore, Burlington, MA), 2'3'-c-di-AM(PS)2 )Rp,Rp) at 715 ng/50 ul , 5’ppp-dsRNA/Lyovec at 375 ng/50 ml (Invivogen, San Diego, CA), R848 at 15 mg/50 ml (Invivogen), galunisertib at 30 mg/50 ml (Selleckchem, Houston, TX), epcadostat at 5 mg/50 ml (Selleckchem), Nw-Hydroxy-nor-L-arginine at 6 mg/50 ml (Sigma-Aldrich, St. Louis, MO), L-NMMA at 100 ng/50 ml (Abcam, Boston, MA), clodronate at 80 mg/50 ml (Abcam), and 4-1BB ligand at 1 mg/50 ml (NovusBio). Combinatorial treatments were reconstituted as a 10x stock, combined as necessary, and diluted to a 1x concentration with the appropriate diluent. Treatments were intratumorally injected with a 28 gauge needle as a 50 ml bolus.

value: tumor

value: HNSCC

value: experimental agent


title: S25__BPCMML__PT_823T1__PB_blast


title: RNA-Seq_human_melanoma_NHEM_77

description: Library name: RNA_NHEM_77

source_name: juvenil foreskin

value: juvenil foreskin

value: NHEM

value: normal


title: treated, replicate 1, scRNAseq

description:
TX1
10x Sequencing


title: S24__BPCMML__PT_697T1__PB_blast

value: Blast (Live/SSC-Alo/CD45dim)

value: Blast phase chronic myelomonocytic leukemia


title: non-CF subject B1018, control

description: Library name: 5

value: airway epithelial cells

value: non-CF

value: control


title: RNA-Seq_human_melanoma_NHEM_76

description: Library name: RNA_NHEM_76


title: vehicle, replicate 3, scRNAseq

description:
DMSO3
10x Sequencing

value: vehicle


title: S23__BPCMML__PT_495T1__BM_blast

value: Bone marrow


title: non-CF subject B0918, control

description: Library name: 4


title: S28__Control__Donor_1170T1__BM_HSPC

value: Hematopoietic stem and progenitor cells - HSPCs (Live/CD34positive)

value: Healthy control


title: vehicle, replicate 2, scRNAseq

description:
DMSO2
10x Sequencing


title: non-CF subject B0818, control

description: Library name: 3


title: treated, replicate 3, scRNAseq

description:
TX3
10x Sequencing


title: vehicle, replicate 1, scRNAseq

description:
DMSO1
10x Sequencing


title: S22__Control__Donor_1138T1__BM_HSPC


title: U87MG_ASO-1570_Replicate 3

city: Farmington

first: Marina

last: Yurieva

state: Connecticut

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

data_processing:
Read QC with fastqc and multiqc
Trimming with trimmomatic
Genome alignment with STAR
Transcriptome assembly with stringtie
Splicing analysis and quantification with rMATS
Assembly: GRCh38/hg38
Supplementary files format and content: Table of PSI values from rMATS
Supplementary files format and content: Table of gene counts

source_name: glioblastoma

growth_protocol: MDA-MB231 and U87MG cells were transfected with indicated ASOs. RNA was extracted 48h later and subjected to library prep

extract_protocol:
Libraries were prepared using the RNA-seq stranded mRNA kit from Illumina and sequenced as 151 PE reads on a HiSeq 2000
Stranded, paired-end, RNA-seq

treatment_protocol: 200nM ASOs were transfected using lipofectamine 3000

value: glioblastoma

value: adherent glioblastoma


title: U87MG_ASO-CTL_Replicate 3

value: ASO-CTL 200nM


title: non-CF subject B0518, control

description: Library name: 1


title: S20__Control__Donor_929T1__BM_HSPC


title: S26__BPCMML__PT_888T1__PB_blast

value: Peripheral blood


title: U87MG_ASO-1570_Replicate 1


title: non-CF subject B0618, control

description: Library name: 2


title: U87MG_ASO-1570_Replicate 2


title: Naïve_day35_mouse5

first: Emma

last: Layton

address: Dover street

data_processing:
cutadapt was used to remove adaptors, filter for quality, and for reads of 18-26 nucleotides in length
reads were mapped to tRNA using bowtie1 with 0 mismatches and discarded from further analysis
remaining reads were mapped to rRNA using bowtie1 with 0 mismatches and discarded form further analysis
remaining reads were mapped to the mouse genome (mm10) using bowtie1 with 1 mismatch
featurecounts was used to quanity reads mapped to miRNA loci using an mmu.gff3 annotation file from miRbase
Assembly: mm10
Supplementary files format and content: Excel file of raw counts for all samples (output from featurecounts) and normalised counts for all samples calculated with DESeq2

source_name: Faecal sample

extract_protocol:
Faecal samples were stored at 4˚C prior to extraction of total RNA using the mirVana kit.
500ng total RNA per sample was used as input for library building with the NEBnext small RNA library preparation kit. SR adaptors and RT primers were undiluted. Amplification was performed with 12 PCR cycles. Size selection was performed using the Novex 6% TBE gel.
small RNA sequencing

value: Faecal sample

tag: days post-treatment

value: Day 35


title: S19__BPCMML__PT_812T4__BM_blast


title: S21__BPCMML__PT_963T2__PB_blast


title: S18__BPCMML__PT_316T1__PB_blast


title: Naïve_day35_mouse4

tag: genotype


title: MC38 tumors, GB2-treated-1

city: xi'an

first: Wei

last: Gaofei

state: Shaanxi

address: beilin

institute: Northwestern Polytechnical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: MC38 tumors subscutaneously inoculated in C57BL/6 mice

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.


title: U87MG_ASO-CTL_Replicate 2


title: U87MG_ASO-CTL_Replicate 1


title: MC38 tumors, PBS-treated-3

value: MC38 tumors subscutaneously inoculated in C57BL/6 mice

value: PBS


title: Naïve_day35_mouse3


title: MDA-MB231_ASO-1570_Replicate 3

source_name: breast carcinoma

value: breast carcinoma

value: adherent breast cancer


title: S17__BPCMML__PT_543T4__BM_blast

value: Blast (Live/SSC-Alo/CD45dim)

value: Blast phase chronic myelomonocytic leukemia


title: MC38 tumors, GB2-treated-3


title: MC38 tumors, PBS-treated-2


title: Naïve_day35_mouse2


title: S16__BPCMML__PT_756T2__BM_blast


title: MDA-MB231_ASO-1570_Replicate 2


title: Naïve_day35_mouse1


title: S15__BPCMML__PT_246T1__BM_blast


title: MC38 tumors, PBS-treated-1


title: Naïve_day21_mouse5

value: Day 21


title: MC38 tumors, GB2-treated-2


title: MDA-MB231_ASO-1570_Replicate 1


title: RAW264.7 cells, GB2-treated-2


title: S14__BPCMML__PT_822T2__BM_blast


title: RAW264.7 cells, GB2-treated-3


title: MDA-MB231_ASO-CTL_Replicate 3


title: S13__BPCMML__PT_1122T7__BM_blast


title: MDA-MB231_ASO-CTL_Replicate 2


title: RAW264.7 cells, GB2-treated-1


title: MDA-MB231_ASO-CTL_Replicate 1


title: S11__BPCMML__PT_293T2__BM_blast


title: RAW264.7 cells, untreated-3

value: untreated


title: Naïve_day21_mouse3


title: Naïve_day21_mouse2


title: S12__BPCMML__PT_416T11__BM_blast

value: Bone marrow


title: S10__BPCMML__PT_783T3__BM_blast


title: non-CF subject B1118, control

description: Library name: 6

value: airway epithelial cells

value: non-CF

value: control


title: Naïve_day21_mouse1

value: Healthy control


title: Luminal YFP-, PRcr, Duct, Rep2

city: Parkville

first: Yunshun

last: Chen

state: VIC

address: 1G Royal Parade

department: ACRF Cancer Biology and Stem Cells

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Libraries were sequenced on an Illumina Nextseq 500
Reads were aligned to the mouse genome mm10 by the align function of the Rsubread software tool version 2.2.2.
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq annotation.
Read counts from the two separate runs of the same sample were aggragated together to form the final gene count for that sample.
Assembly: mm10
Supplementary files format and content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: mammary duct

extract_protocol:
Total RNA was extracted using Qiagen's miRNeasy kit and DNase treated.
A minimum of 10 ng of total RNA was used to construct libraries following Ilumina's recommended protocol for TruSeq RNA Library Prep Kit v2.

value: mammary duct

tag: cell population

value: luminal YFP–

tag: model


title: RAW264.7 cells, untreated-1


title: Infected_day35_mouse7

value: Faecal sample

value: Infected with low dose Trichuris muris


title: S09__BPCMML__PT_837T5__BM_blast


title: Luminal YFP-, PRcr, TEB, Rep2

source_name: mammary TEB

value: mammary TEB


title: Luminal YFP-, PRcr, TEB, Rep1


title: Infected_day35_mouse6

value: Day 35


title: Naïve_day21_mouse4


title: RAW264.7 cells, untreated-2


title: S08__Control__Donor_1126T1__BM_HSPC

source_name: Bone marrow

value: Hematopoietic stem and progenitor cells - HSPCs (Live/CD34positive)


title: Luminal YFP-, PRcr, Duct, Rep1


title: Infected_day35_mouse5


title: Luminal GFP-, Elf5, TEB, Rep2

value: luminal GFP–


title: Infected_day35_mouse4


title: Luminal GFP-, Elf5, Duct, Rep2


title: S06__BPCMML__PT_544T1__PB_blast

source_name: Peripheral blood

value: Peripheral blood

value: Blast (Live/SSC-Alo/CD45dim)


title: Infected_day35_mouse3


title: S05__BPCMML__PT_993T5__BM_blast

value: Blast phase chronic myelomonocytic leukemia


title: S03__BPCMML__PT_821T3__BM_blast


title: Infected_day35_mouse2


title: Infected_day35_mouse1


title: Luminal GFP-, Elf5, Duct, Rep1


title: S04__BPCMML__PT_1068T2__BM_blast


title: Luminal GFP-, Elf5, TEB, Rep1


title: Luminal YFP+, PRcr, TEB, Rep2

value: luminal YFP+


title: Infected_day21_mouse7

value: Day 21


title: S02__BPCMML__PT_279T1__PB_blast


title: Luminal YFP+, PRcr, Duct, Rep2


title: Luminal YFP+, PRcr, TEB, Rep1


title: Infected_day21_mouse6


title: P7

city: Suita

first: Satoshi

last: Masuyama

state: Osaka

address: 2-2, Yamada-oka

department: Nephrology

country: Japan

institute: Osaka university

data_processing:
Basecalls were performed using bcl2fastq for Novaseq output.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.35 (TRAILING:20 MINLEN:32 SLIDINGWINDOW:10:20  )
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2 v2.1.0
Read counts for each sample were obtained using FeatureCounts v1.4.6
Normalization and significance testing were done using the Bioconductor package, edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: splenocyte

growth_protocol: Naive CD4 T cells from splenocyte were polarized to Th17 in IMDM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA   Library Prep Kit following manufacturer's protocols.

treatment_protocol: 10nM pemafibrate in the presence of 10% FBS until day 2. Cells were then fed with IMDM supplemented with 10% FBS for 2 days.

value: splenocyte

value: primary

value: T cells

value: WT

value: pemafibrate


title: S07__BPCMML__PT_303T4__BM_blast

value: Bone marrow


title: HCT116 cells, siUPF1, NMDi, biol rep 4

city: Sheffield

first: Jack

last: Riley

address: Firth Court, Western Bank

department: School of Biosciences

institute: The University of Sheffield

data_processing:
RNAseq reads were aligned to hg38 using STAR aligner.
Transcript counts were quantified against our custom TCGA transcriptome assembly using Salmon.
Assembly: hg38
Supplementary files format and content: Tar archived file (.tar.gz) containing salmon quantification file (.sf) alongside corresponding metadata.

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% fetal bovine serum at 37 degrees celsius and 5% CO2.

extract_protocol:
RNA was extracted 72 hours after initial siRNA transfection using TRI Reagent (Sigma-Aldrich) as per manufacturers instructions.
mRNA was enriched by PolyA capture. Libraries were produced using standard Illumina protocols

treatment_protocol: siRNA were transfected at 30nM using Lipofectamine RNAiMAX (Invitrogen). A second-hit was performed in the same manner 48 hours later.

value: colorectal carcinoma cells

value: siUPF1 + NMDI14


title: P8


title: S01__BPCMML__PT_689T1__PB_blast


title: Luminal YFP+, PRcr, Duct, Rep1

value: mammary duct


title: Infected_day21_mouse4

value: Faecal sample

value: Infected with low dose Trichuris muris


title: P3


title: Infected_day21_mouse3


title: Luminal GFP+, Elf5, TEB, Rep2

value: mammary TEB

value: luminal GFP+


title: Ida004

description: Gene expression data from Hippocampus

source_name: Flash-frozen hippocampus dissected from whole brain of post-natal mouse

value: Brain; Hippocampus

value: male

value: 1 month

value: Neu1 deficient


title: HCT116 cells, siUPF1, NMDi, biol rep 3


title: Luminal GFP+, Elf5, Duct, Rep2


title: Infected_day21_mouse5

value: Day 21


title: V4

value: splenocyte

value: primary

value: vehicle


title: HCT116 cells, siUPF1, NMDi, biol rep 2


title: V7

value: T cells

value: WT


title: Infected_day21_mouse2


title: V3


title: Infected_day21_mouse1


title: Luminal GFP+, Elf5, TEB, Rep1


title: HCT116 cells, siUPF1, NMDi, biol rep 1

value: colorectal carcinoma cells


title: HCT116 cells, siUPF1, DMSO, biol rep 4

value: siUPF1 + DMSO


title: Luminal GFP+, Elf5, Duct, Rep1

value: mammary duct


title: Infected_day0_mouse7

value: Faecal sample

value: Healthy control (prior to infection)

value: Day 0


title: Basal, PRcr, TEB, Rep2

value: mammary TEB

value: basal


title: HCT116 cells, siUPF1, DMSO, biol rep 3


title: Ws, replicate3, ScRNA-seq

city: Wuxi

first: Mingkun

last: Luo

state: Jiangsu

address: No. 9, Shanshui East Road, Binhu District, Wuxi City, Jiangsu Province, China

institute: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences

description:
Library name: sample6
Gexscope

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information.
Assembly: GCF_018340385.1
Supplementary files format and content: Matrix file

organism: Cyprinus carpio 'koi'

source_name: skin

extract_protocol:
Different components were macrodissected and stored at 4 ℃ GEXSCOPETM Tissue Preservation Solution. Then, we washed samples for 3 times with Hanks Balanced Salt Solution (HBSS) and minced them into 1–2 mm-thick pieces, 2 ml GEXSCOPETM Tissue Dissociation Solution (Singleron Biotechnologies) was added to each sample and allowed for digestion at 37 ℃ for 15 minutes to dissociate the tissue into single cells. Then, we filtrate the samples using 40-μm sterile strainers, followed by centrifuging at 1,000 rpm for 5 minutes. After the centrifugation, the precipitation was resuspended in 1 ml phosphate-buffered saline (PBS; HyClone, Marlborough, United States). Subsequently, 2 ml GEXSCOPETM Red Blood Cell Lysis Buﬀer (Singleron Biotechnologies) was added into the cell suspension and incubated at 25°C for 10 minutes to remove red blood cells. After that, the mixture was centrifuged at 500 × g for 5 minutes, followed by re-suspending the precipitation with PBS.
We used GEXSCOPETM Single Cell RNA Library Kit Tissue (Singleron Biotechnologies) to barcode single cells, capture mRNA from isolated single cells, and generate cDNA libraries for scRNA-seq. Then, individual libraries were diluted to 4 ng/μl, and pooled for sequencing on illumina NovaSeq 6000 platform  with 150 bp paired-end reads.

value: skin


title: Ws, replicate2, ScRNA-seq

description:
Library name: sample5
Gexscope


title: Infected_day0_mouse6


title: Basal, PRcr, Duct, Rep2


title: HCT116 cells, siUPF1, DMSO, biol rep 2


title: Ws, replicate1, ScRNA-seq

description:
Library name: sample4
Gexscope


title: Infected_day0_mouse5


title: Rs, replicate3, ScRNA-seq

description:
Library name: sample3
Gexscope


title: Basal, PRcr, TEB, Rep1


title: HCT116 cells, siDsRed, NMDi, biol rep 4

value: siDsRed + NMDI14


title: HCT116 cells, siUPF1, DMSO, biol rep 1


title: Basal, PRcr, Duct, Rep1


title: Rs, replicate2, ScRNA-seq

description:
Library name: sample2
Gexscope


title: HCT116 cells, siDsRed, NMDi, biol rep 3


title: Infected_day0_mouse4


title: Basal, Elf5, TEB, Rep2


title: Rs, replicate1, ScRNA-seq

description:
Library name: sample1
Gexscope


title: Infected_day0_mouse2


title: Basal, Elf5, Duct, Rep2


title: Basal, Elf5, TEB, Rep1


title: HCT116 cells, siDsRed, NMDi, biol rep 2


title: Infected_day0_mouse1


title: Alr1700-3xFLAG, rep2

city: Freiburg im Breisgau

first: Manuel

last: Brenes-Álvarez

address: Schänzlestraße 1

department: Genetics and Experimental Bioinformatics

institute: University of Freiburg

description: CLIP-seq

data_processing:
Quality control was performed using FASTQC
Reads were aligned to Nostoc genome using bowtie2 (alignment in mode --very-sensitive-local)
Peak calling was carried out by PEAKachu (https://github.com/tbischler/PEAKachu)
Assembly: ASM970v1
Supplementary files format and content: A table for the peak calling output is provided (peak_table.xlsx). Columns include the replicon, position and strand of the detected peaks. In addition, for each peak it is also shown the log2foldchange of the comparison between the targetome of PatR-3xFLAG and the background (WT), adjusted p-value and the number of reads counted in each peak per biological replicate.

organism: Nostoc sp. PCC 7120 = FACHB-418

source_name: Nostoc sp. PCC 7120

growth_protocol: Nostoc sp. PCC 7120 WT and Alr1700-3xFLAG strain were grown photoautotrophically with constant shaking under standard conditions (30 ºC and 50 µE illumination) in liquid BG11 medium. Filaments were collected by centrifugation at 3,270 x g for 5 min at room temperature, washed and then resuspended in BG110 (medium without a combined nitrogen source) to induce heterocyst differentiation for 24h.

extract_protocol:
Proteins from the eluted RNA-protein complexes were digested in 400 µL proteinase K buffer (50 mM Tris-HCL, pH 6, 5 mM EDTA and 0.5%SDS) with 400 µg of proteinase K for 30 min at 37 °C. Another 400 µL of proteinase K buffer + 9M urea was added for an additional incubation of 30 min at 37 °C. RNA fragments were isolated using  phenol-chloroform and chloroform extractions. RNA was later treated with 2U of TURBO DNAse (Life Technologies) to eliminate DNA traces, followed by RNA cleanup using RNA Clean & Concentrator columns (Zymo Research).
Synthesis of cDNA was facilitated by SMARTScribe reverse transcriptase (TaKaRa), which adds the loop adapter at the 3’-end in the first-strand synthesis step and the SMART oligo at the 5’-end in the subsequent template switching and extension step. Annealing of the loop adapter to RNA was achieved by incubating both at 72°C for 3 min and 42°C for 2 min. All components were added to this mixture according to the manufacturer's instructions, including the SMART oligo, 100 U SMARTScribe reverse transcriptase (TaKaRa), and 40 U of Ribolock RNase inhibitor (Life Technologies), and the reaction was incubated at 42°C for 90 min and 70°C for 10 min, followed by cooling to 12°C. After cDNA synthesis, the samples were excised from 3% Nusieve agarose gels and purified with the NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel), using NTC buffer to solubilize the gel slices. The cDNA was amplified in 22 PCR cycles with Phusion high-fidelity DNA polymerase (New England BioLabs) using Illumina 8-nt index primers for both sides, and PCR samples were purified using the Agencourt AMPure XP system (Beckman Coulter) according to the manufacturer’s instructions. All individual amplified cDNA libraries were pooled in equimolar ratios and size selected between 100 - 320 bp using the Pippin Prep system (Sage System) according to the manufacturer’s instructions and subsequently purified using the Agencourt AMPure XP system (Beckman Coulter).

treatment_protocol: WT and cells of Alr1700-3xFLAG strain were irradiated with UV light (1.6 mJ/cm2) to crosslink the proteins to their interacting RNA. After harvesting, cells were resuspended in NT-P buffer (50 mM NaH2PO4, 300 mM NaCl, 0.05% Tween, pH 8.0) supplemented with protease Inhibitor (cOmplete EDTA-free, Roche). Cells were mechanically lysed in a pre-chilled Precellys homogenizer (Bertin Technologies) using 9 cycles of 10 s shaking at 6,000 rpm followed by a pause of 5 s.  Glass beads were removed by centrifugation at 1,500 x g for 2 min. Next, membranes were pelleted by centrifugation at 21,000 x g for 30 min at 4 ºC. 2 mL of clarified lysate was incubated with 80 µL of anti-FLAG M2 magnetic beads (Sigma) prewashed 5 times in NT-P buffer. From this point on, all the washing steps were performed with 2 mL of buffer. The samples were incubated at 4 °C while gently rotating for 1 h. Beads were washed three times with high-salt NT-P buffer (50 mM NaH2PO4, 1 M NaCl, 0.05% Tween20, pH 8.0) and twice with cold NT-P buffer. Elution of the RNA-protein complexes were carried out by resuspending the beads in 50 µL of TBS buffer (50 mM Tris-HCl, 150 mM NaCl, pH 7.5) supplemented with 0.5 µg/µL FLAG peptide (Sigma) and 2 µL Ribolock RNase inhibitor (life Technologies) at 4 °C for 15 min, while gently shaking at 900 rpm.

value: Nostoc sp. PCC 7120

tag: chip antibody

value: Anti-FLAG M2 (Sigma, M8823)

value: UV-crosslinked sample


title: Alr1700-3xFLAG, rep3

description: CLIP-seq


title: G4_rep2

city: New York

first: Jianlong

last: Wang

state: NY

department: Department of Medicine

institute: Columbia University Irving Medical Center

description: Double negative population of ESCs, sheIF4A2 infected

data_processing:
Alignment was done by Bowtie2 (v2.3.4.3).
Sorting was done by name using Samtools (v1.9)
Count was done by Htseq (v0.11.2)
Normalization was done by using edgeR (v3.26.8)
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with normalized expression levels for every gene and every sample

source_name: Embryonic stem cells

growth_protocol: Feeder-free mouse embryonic stem cells (mESCs) were cultured on 0.1% gelatin-coated plates under standard conditions: DMEM supplemented with 15% fetal calf serum (FBS), 1000 units/mL recombinant leukemia inhibitory factor (LIF), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM MEM non-essential amino acids (NEAA), 1% nucleoside mix (100X stock, Sigma), and 50 U/mL Penicillin/Streptomycin).

extract_protocol:
Total RNAs were extracted using Trizol according to the manufacturer's instructions.
Total RNAs were taken for the preparation of PolyA RNA-seq libraries and the massively parallel sequencing was perfomred with the Illumina HiSeq platform.  Paired-end 150 bp-length reads were produced.

treatment_protocol: The 2C reporter mESCs were infected with shNT or sheIF4A2. After the drug selection, the double positive and double negative subpopulations were sorted and processed with the total RNA extraction.

tag: cell types

value: mESC J1

tag: strain

tag: subpopulation


title: HCT116 cells, siDsRed, DMSO, biol rep 4

value: siDsRed + DMSO


title: G3_rep2

description: Double positive population of ESCs, sheIF4A2 infected


title: Basal, Elf5, Duct, Rep1


title: WT, rep3

description: CLIP-seq


title: CD14- PR-cre/YFP+, ML, Rep3

data_processing:
Libraries were sequenced on an Illumina Nextseq 500
Reads were aligned to the mouse genome mm10 by the align function of the Rsubread software tool version 1.29.6.
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq annotation.
Read counts from the two separate runs of the same sample were aggragated together to form the final gene count for that sample.
Assembly: mm10
Supplementary files format and content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: Mammary gland

extract_protocol:
Total RNA was extracted using Qiagen's miRNeasy kit and DNase treated.
A minimum of 50 ng of total RNA was used to construct libraries following Ilumina's recommended protocol for TruSeq RNA Library Prep Kit v2.

value: Mammary gland

value: luminal

value: CD14- PR-cre/YFP+, ML


title: G4_rep1


title: HCT116 cells, siDsRed, DMSO, biol rep 3

value: colorectal carcinoma cells


title: Infected_day0_mouse3


title: G3_rep1


title: HCT116 cells, siDsRed, DMSO, biol rep 2


title: HCT116 cells, siDsRed, DMSO, biol rep 1


title: CD14+ PR-cre/YFP+, HR+ LP, Rep3

value: CD14+ PR-cre/YFP+, HR+ LP


title: HCT116 cells, 20uM CHIR99021, biol rep 3

extract_protocol:
RNA was extracted using Total RNA Purification Plus Kit (Norgen Biotek) as per manufacturers instructions.
mRNA was enriched by PolyA capture. Libraries were produced using standard Illumina protocols

treatment_protocol: Media was changed to RPMI-1640 media supplemented with either 0uM or 20uM CHIR99021 for 24 hours.


title: CD14- PR-cre/YFP+, ML, Rep1


title: HCT116 cells, siDsRed, NMDi, biol rep 1


title: oxWGBS-Seq of Human Cs+ HCC T4

city: Nanning

first: Junxian

address: 71, Hedi Road, Qingxiu District

department: Department of Clinical Laboratory

institute: Guangxi Medical University Cancer Hospital

description: Library name: oxWGBS_Cs+_T_4

data_processing:
We used the Trim Galore  to remove sequencing adapters and low-quality data from the sequencing reads.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: HCC tumor tissue

extract_protocol:
After quality control, lambda DNA was added as a bisulfite conversion efficiency control. Genomic DNA was fragmented to 200-400 bp using a Covaris M220 Focused-ultrasonicator (Covaris, USA). The fragmented DNA was then end-repaired, 3' adenylated, and ligated with methylation-modified sequencing adapters.
5hmC was oxidized to 5fC, followed by bisulfite treatment using the EZ DNA Methylation Gold Kit (Zymo Research). Unmethylated C and oxidized 5fC were converted to U (T after PCR amplification), while methylated C remained unchanged. PCR amplification was performed to generate the final oxWGBS library.

value: HCC tumor tissue


title: WT, rep1

description: CLIP-seq

value: WT


title: G2_rep2

description: Double negative population of ESCs, shNT infected

value: shNT


title: G1_rep2

description: Double positive population of ESCs, shNT infected


title: CD14+ PR-cre/YFP+, HR+ LP, Rep2


title: G2_rep1


title: HCT116 cells, 20uM CHIR99021, biol rep 2


title: oxWGBS-Seq of Human Cs+ HCC T3

description: Library name: oxWGBS_Cs+_T_3


title: Alr1700-3xFLAG, rep1

description: CLIP-seq


title: WT, rep2

description: CLIP-seq


title: HCT116 cells, 20uM CHIR99021, biol rep 1


title: G1_rep1


title: HCT116 cells, 20uM CHIR99021, biol rep 4


title: CD14+ PR-cre/YFP-, HR- LP, Rep2

value: CD14+ PR-cre/YFP-, HR- LP


title: p35S:MIR396, 5DAC, Replicate 4

city: Rosario

first: Julia

middle: Lidia

last: Baulies

state: Santa Fe

address: Ocampo y Esmeralda s/n

country: Argentina

institute: Instituto de Biología Molecular y Celular de Rosario

description:
JB16
10x Genomics

data_processing:
Yielded reads were pseudo-aligned to the Arabidopsis genome (TAIR10) using the kallisto bustools software.
Seurat matrices were constructed with the Seurat R package.
Assembly: TAIR10
Supplementary files format and content: Seurat object

source_name: Root tips

growth_protocol: Sterilized seeds were sown in Petri dishes containing solid medium (Murashige and Skoog salts, 1% sucrose, 0.5g/L MES, 0.8% w/v agar, pH = 5,7) and stratified at 4°C in the dark for at least one day. The plates were placed vertically under continuous light at 22°C.

extract_protocol:
Approximately 1000 roots per sample (wild type and p35S:MIR396, uncut controls and 5 days after cut) were collected per quadruplicate for protoplasting. The seeds were sown on nylon mesh, roots were cut at approximately 1cm from the tip, and placed in digesting solution (20mM MES, 400mM mannitol, 20mM KCl, 1.5% cellulase, 0.4% macerozyme, 10mM CaCl2) covered from the light. To enrich the samples with meristematic tissue, the roots were incubated for 20 minutes until the transition zone (between the proliferation and elongation zones) was digested and the tips were released, which was confirmed under microscope. Then, the excess tissue was filtered out using a 1 mm-pore mesh. Digestion continued for 90 minutes and, after filtering the solution twice with a 40µm pore cell strainer, cells were centrifuged down for two minutes at 300rcf and 4°C, washed with washing buffer (enzyme-free digestion solution) and centrifuged again with the same conditions. Buffer was discarded, leaving a small amount at the bottom to resuspend protoplasts, which were then counted in a Neubauer chamber under a light field microscope, and diluted to a concentration of 1000cells/µl.
12000 cells per replicate were sorted on a 10x Chromium platform and libraries were prepared using a 3’ Gene Expression v3.1 kit, following the provider’s instructions.

treatment_protocol: Control samples were collected ad 3 days old without treatment. For 5DAC samples, 3-day-old seedlings were cut with surgical microblades under a stereoscopic microscope, on agar plates with a nylon mesh of 100µm pore and 70µm fiber. Pores and fibers were used as reference for cut positions. Te samples were collected 5 days after cutting (8 days old).

tag: ecotype

value: Root tips

value: 8 days old (cut at 3 days old)

value: 5 days after cut


title: oxWGBS-Seq of Human Cs+ HCC T2

description: Library name: oxWGBS_Cs+_T_2


title: p35S:MIR396, Control, Replicate 4

description:
JB15
10x Genomics

value: 3 days old

value: Control


title: CD14+ PR-cre/YFP-, HR- LP, Rep1


title: HCT116 cells, 0uM CHIR99021, biol rep 3

value: 0uM CHIR99021 (DMSO)


title: CD14+ PR-cre/YFP-, HR- LP, Rep3


title: oxWGBS-Seq of Human Cs+ HCC P3

description: Library name: oxWGBS_Cs+_P_3

source_name: HCC adjacent tissue

value: HCC adjacent tissue


title: oxWGBS-Seq of Human Cs+ HCC P2

description: Library name: oxWGBS_Cs+_P_2