title: CD8-Ctrl_001

city: Melbourne

first: Luke

middle: C

last: Gandolfo

state: Victoria

address: 1G Royal Parade Parkville

department: Bioinformatics

country: Australia

institute: WEHI

description: Biological replicate 1

data_processing:
FASTQ files were output using standard Illumina protocols and software
Reads were aligned to the mouse genome by Rsubread 2.2.6
Read counts were summarized by Entrez Gene ID using featureCounts and Rsubread's built-in NCBI annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, Symbol, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: Skin

extract_protocol:
RNA was isolated from freshly sorted cells with the miRNeasy kit (Qiagen).
Total RNA was isolated from 2000-5000  sorted cells (Qiagen) and cDNA libraries were prepared using the SMARTer Stranded Total RNA-Seq kit for Pico Input (Takara)

tag: genotype/variation

value: CD8+ gBT-I

value: d14 HSV


title: CD8-Ctrl_002

status: Public on May 24 2022

type: SRA

description: Biological replicate 2

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: treatment


title: CD8-Ctrl_004

description: Biological replicate 4


title: CD8-Ctrl_003

description: Biological replicate 3


title: Group7_CD8cells_rep21

city: Oxford

first: Ashwin

last: Jainarayanan

address: Roosevelt Dr, Headington, Oxford OX3 7FY

department: KIR, NDORMS

country: United Kingdom

institute: University of Oxford

data_processing:
Batch corrections were performed using miRNAQC
Reads were aligned to the human genome reference (Human37) using sRNAtoolboxDB
Reads are mapped to microRNA reference libraries miRBase and MirGeneDB.
QC was done using miRNAQC
Expression matrix (Reads Per Millions) was also obtained using mirnaQC
Genome_build: Human37
Supplementary_files_format_and_content: Expression matrix (Reads Per Millions) of the identified miR per species, source file (raw) is listed on the heading row

organism: Homo sapiens

source_name: CD8 T cells

growth_protocol: T cells were activated with anti-CD3/CD28 beads for 72h, then expanded using IL-2 100 U/mL in the absence of beads

extract_protocol:
FACS sorted BSLB were lysed and RNA was purified using miRNA advance kit
microRNA libraries were prepared following NEBNext Small RNA kit (NEB) and the low yield protocol
Libraries were amplified (15 cycles) on a Tetrad (Bio-Rad) using in-house unique dual indexing primers and size selection was performed using Pippin Prep instrument (Sage Science) using the 3% Agarose, dye free gel with internal standards (size selection: 120 to 230bp).

treatment_protocol: Cells were split. One half was cultured in OptiMEM-I for isolation of EVs for no longer than 48h and the other half was cocultured with BSLBs to capture and isolate tSV

tag: tissue

value: PBMC

tag: cell type

value: CD8 T cells


title: Group7_CD8cells_rep24


title: Group7_CD8cells_rep23


title: Group7_CD8cells_rep20


title: CD4-Runx3_004

description: Biological replicate 4

value: CD4+ gDT-II


title: CD4-Runx3_003

description: Biological replicate 3


title: Group7_CD8cells_rep22


title: WTCHG_834294_233_1

source_name: CD4 S1

treatment_protocol: Cells were splt. One half was cultured in OptiMEM-I for isolation of EVs for no longer than 48h and the other half was cocultured with BSLBs to capture and isolate tSV

value: CD4 T cells


title: WTCHG_834291_233_1


title: WTCHG_836238_226_1

source_name: CD4 S0


title: WTCHG_836236_233_1


title: CD4-Runx3_002

description: Biological replicate 2


title: C9ORF72 mutation carrier female 26#6, chx treated

city: Worcester

first: Heleen

last: van 't Spijker

state: Massachusetts

address: 55 Lake Avenue North

country: USA

institute: University of Massachusetts Medical School

description:
iPSCs were treated with chx and with RNAse A+T (C9 line #26)
Processed data files:
all.rsem.gene.summary.counts.txt
all.rsem.gene.summary.tpm.txt
Name of column in processed data file: c9_26_chx

data_processing:
Library strategy: Ribo-Seq
Individual samples were first separated based on the 5nt barcode sequences and then adaptor sequences were removed using cutadapt.
Trimmed reads were quality filtered and mapped to human rRNA and tRNA references using Bowtie2.
Tophat2 was used to then map the remaining unmapped reads to a modified hg19 human genome containing the C9orf72 reporter sequence.
Due to our modified genome containing both endogenous C9orf72 and reporter C9orf72 reporter gene sequences, multimapped reads were included to retain reads mapping to sequences shared between these two genes (e.g., exon 1a, exon 2 and intronic sequences 5’ to the G4C2 repeat).
Genome_build: hg19 human transcriptome

source_name: iPSCs

growth_protocol: iPSC lines from three C9ORF72 carriers and three healthy individuals were cultured on Matrigel and mTeSR1. Cortical neuron differentiation was performed as described (Almeida et al. 2013). HEK293T cells cultured in DMEM with 20%FBS and antibiotic-antimyotic were transfected with reporter plasmids using lipofectamine 2000.

extract_protocol:
RNA was extracted using TRIZol LS following the manufacturer’s protocol
Ribosome profiling libraries were prepared following published protocols (Heyer et al. 2015; Liu et al. 2018, 2019).

treatment_protocol: For harringtonine treatment, harringtonine was added to the medium for a final concentration of 2ug/mL and incubated at 37˚ for 5min. Cycloheximide was subsequently added to the media (100ug/mL) and the cells were then washed twice with ice-cold PBS containing cycloheximide (100ug/mL).For cycloheximide treatment alone, cycloheximide was added to the medium for a final concentration of 100ug/mL for a 1min incubation.

tag: individual

value: C9ORF72 mutation carrier female 26#6

value: iPSCs

value: chx and RNAse A+T


title: WTCHG_836237_226_1


title: WTCHG_836235_233_1


title: WTCHG_836236_226_1


title: WTCHG_834293_233_1


title: CD4-Runx3_001

description: Biological replicate 1


title: WTCHG_836235_226_1


title: Group7_CD8cells_rep18


title: Group7_CD8cells_rep17


title: WTCHG_834292_233_1


title: Group7_CD8cells_rep16


title: CD4-Ctrl_003

description: Biological replicate 3


title: WTCHG_834294_226_1


title: WTCHG_834293_226_1


title: Group7_CD8cells_rep15


title: CD4-Ctrl_002

description: Biological replicate 2


title: Group7_CD8cells_rep19


title: CD27 positive MAIT cells of Diabetic obese patient 2# [P2_CD27_pos_802D75]

city: Guangzhou

first: Jin

last: Wang

address: Zhongshan 2nd Road

country: China

institute: Sun yat-sen University

data_processing:
Raw reads trimmed with Cutadapt v0.5.0
RNA-seq reads were quantified and gene expression levels were calculated using Salmon  475 v0.13.1
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw counts and TPM values for each Sample

extract_protocol:
CD27 positive or negative MAIT cells were stained and sorted as CD27+ or CD27- CD3+ CD161+ TCR Va7.2+ on the BD FACSAria III cell sorter (BD Biosciencesa). RNA from 10,000 sorted cells was used to prepared RNA-seq library according to the single cell Smart-seq2 protocol.
RNA libraries were prepared for sequencing using Tn5 based DNA prepration Kit (TD503, Vazyme).

tag: subject status

value: diabetic obese patient

tag: cell types

value: CD27 positive MAIT cells


title: Group7_CD8cells_rep14


title: WTCHG_834292_226_1


title: CD4-Ctrl_001

description: Biological replicate 1


title: WTCHG_834291_226_1


title: JVFP-/-_AML_LSK

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Transcript alignment, counting, and inter-library normalization were performed using the Cell Ranger pipeline (10x Genomics, default settings, Version 2.1.1).
Using the Seurat R package for downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and cell

source_name: hemopoietic tissue

extract_protocol:
Sorted cells were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability.
The single cell suspension was loaded onto Chromium Chip B (10X Genomics PN 2000060) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of up to 10,000 cells proceeded using the Chromium Single Cell 3’ Reagent Kit v3 (10X Genomics PN 1000075) according to the manufacturer’s protocol.
scRNA-seq

value: Lin-c-Kit+ cells

value: hemopoietic tissue

tag: genotype


title: Group7_CD8cells_rep13


title: CD27 positive MAIT cells of Diabetic obese patient 1# [P1_CD27_pos_804D73]


title: CD4-Ctrl_004

description: Biological replicate 4


title: WTCHG_836238_234_1


title: WTCHG_836237_234_1


title: JVF_LSK


title: CD27 negative MAIT cells of Diabetic obese patient 3# [P3_CD27_neg_803D76]

value: CD27 negative MAIT cells


title: JVFP-/-_MPN_LSK


title: Group7_CD8cells_rep12


title: WTCHG_836236_234_1


title: Group7_CD8cells_rep11


title: CD27 negative MAIT cells of Diabetic obese patient 1# [P1_CD27_neg_805D74]


title: Group7_CD8cells_rep10


title: CD27 negative MAIT cells of Diabetic obese patient 2# [P2_CD27_neg_801D75]


title: CD27 positive MAIT cells of Diabetic obese patient 3# [P3_CD27_pos_804D76]


title: WT_LSK

value: wild type


title: WTCHG_836235_234_1


title: Group7_CD8cells_rep9


title: TY1_kr_a

city: Tianjin

first: Xinyi

last: Cao

state: State...

address: Qi Xiangtai Road, HePing District, Tianjin, P.R. China

institute: Tianjin Medical University

library_source: genomic

data_processing:
Clean reads were aligned to the human reference genome (hg38) by bowtie2 (v2.3.5.1)
Reads mapped only once at locus were allowed for peak calling.
Bigwig files were derived from the output of deeptools v3.4.3
Annotation of peaks was performed using HOMER.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files were generated using deepTools v3.4.3

molecule: genomic DNA

source_name: human ADPKD cells

growth_protocol: WT 9-12 cells were cultured in Dulbecco’s Modified Eagle’s Medium/F-12 medium supplemented with 10% FBS and maintained at 37℃ incubator with 5% CO2.

extract_protocol:
WT 9-12 cells were cross-linked with 1% formaldehyde for 10 min at RT. Cross-linking was stopped by 150 mM glycine for 5 min at RT. Cells were washed with PBS twice and collected using ChIP cell lysis buffer (10 mM EDTA, 1% SDS and 50 mM Tris-HCl pH 8.0). Cells was fragmented by sonication (range 200-500 bp). Immunoprecipitation was performed using 2 μg TY1/PanKcr/H3K18cr antibody. After elution and reversal cross-linking, samples were treated with RNase A for 30 min at 37℃. DNA was purified and sequenced on the Illumina NovaSeq platform.
Libraries were prepared according to VAHTS Universal DNA Library Prep Kit for Illumina V3 Kit (Vazyme, # ND607-02).

treatment_protocol: WT 9-12 cells were stably expressing CDYL KR>A mutant with TY1 tag

value: Kidney

value: cystic cell

tag: chip antibody

value: anti-PanKcr (PTM Biolabs, PTM-501 )


title: WTCHG_834294_234_1


title: Group7_CD8cells_rep8


title: Group7_CD8cells_rep7


title: H3K18cr_kr_a


title: WTCHG_834293_234_1


title: Group7_CD8cells_rep6


title: Input_kr_a


title: co-culture iB γδ T cells 2

city: Heidelberg

first: Elisa

last: Donato

address: Im Neuenheimer Feld 280

department: Division of Stem Cells and Cancer

country: Germany

institute: Deutsches Krebsforschungszentrum  (DKFZ) - German Cancer Research Center

description:
RNA seq
normalized_counts cocolture.txt
S1605Nr11

data_processing:
RNA-seq:Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq
RNA-seq:Adapters were trimmed with Skewer (version 0.2.2).When performing paired-end sequencing, the first three nucleotides of the second sequencing read (Read 2) are derived from the Pico v2 SMART Adapter. Those three nucleotides have been trimmed.
RNA seq:Trimmed raw reads were aligned to the mouse reference genome (mm10) using STAR (version 2.5.2b) (Dobin et al. 2013)
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts

source_name: spleen

extract_protocol:
RNA-Seq:RNeasy Plus Micro Kit (Qiagen)
RNA-Seq: Libraries were prepared according to Takara's instructions accompanying the SMART Seq Stranded Total RNA-Seq Kit (Takara)

treatment_protocol: In vivo: mice were treated i.p. with two injections of 15 ng DTx per gram body weight separated by 48 hours. Mice were analyzed eight days after the first injection

value: immature B cells (B220+CD93+)

value: untreated, in vitro culture with Gamma delta T cells


title: co-culture iB γδ T cells 1

description:
RNA seq
normalized_counts cocolture.txt
S1605Nr10


title: H3K18cr_wt_oe

treatment_protocol: WT 9-12 cells were stably expressing CDYL with TY1 tag

value: CDYL overexpression


title: TY1_wt_oe

value: anti-H3K18cr (PTM Biolabs, PTM-517)


title: co-culture iB γδ T cells 3

description:
RNA seq
normalized_counts cocolture.txt
S1605Nr12


title: Group7_CD8cells_rep5

value: PBMC

value: CD8 T cells


title: Group7_CD8cells_rep4


title: iB cells alone 2

description:
RNA seq
normalized_counts cocolture.txt
S1605Nr5

value: untreated, in vitro culture immature B cell


title: Input_wt_oe


title: WTCHG_836237_227_1

value: CD4 T cells


title: WTCHG_836238_227_1


title: WTCHG_836236_227_1


title: WTCHG_834292_234_1


title: iB cells Tcrd-H2B d8 3

description:
RNA seq
normalize_counts_RNAseq2.txt
S2313Nr13

value: DTx, eight days


title: WTCHG_834291_234_1


title: iB cells Tcrd-H2B d8 2

description:
RNA seq
normalize_counts_RNAseq2.txt
S2313Nr12


title: WTCHG_836235_227_1


title: Group7_CD8cells_rep2


title: TY1_ctrl

value: anti-TY1 (Sigma, SAB4800032)

value: control


title: iB cells alone 1

description:
RNA seq,
normalized_counts cocolture.txt
S1605Nr4


title: iB cells Tcrd-H2B d8 1

description:
RNA seq
normalize_counts_RNAseq2.txt
S2313Nr11


title: PanKcr_ctrl


title: Group7_CD4cells_rep24

source_name: CD4 T cells


title: WTCHG_834294_227_1


title: WTCHG_834293_227_1


title: Group7_CD8cells_rep3


title: iB cells Tcrd-GDL d8 4

description:
RNA seq
normalize_counts_RNAseq2.txt
S2313Nr6

value: Tcrd-GDL


title: Group7_CD4cells_rep23


title: iB cells Tcrd-GDL d8 5

description:
RNA seq
normalize_counts_RNAseq2.txt
S2313Nr7


title: WTCHG_834292_227_1


title: Group7_CD4cells_rep22


title: CDYL_wt_oe_2_RNA

data_processing:
Low quality reads was filtered using internal software Trim Galore
Clean reads were mapped to reference using HISAT2. Only unique mapped reads were used in further analysis.
DEGs (differential expressed genes) between samples were generated by DESeq2
Bigwig files were derived from the output of deeptools v3.4.3
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values for each sample.
Supplementary_files_format_and_content: Bigwig files were generated using deepTools v3.4.3

extract_protocol:
Total RNA isolation was performed using TRIzol (Invitrogen). Total RNAs from cultured cells were subjected to Oligo dT selection and adaptor ligation.
Construction of RNA-seq library was completed by BGI company (Shenzhen,China).

tag: cell line


title: iB cells Tcrd-GDL d8 2

description:
RNA seq
normalize_counts_RNAseq1.txt
S1197Nr8


title: CDYL_wt_oe_1_RNA


title: iB cells Tcrd-GDL d8 3

description:
RNA seq
normalize_counts_RNAseq1.txt
S1197Nr9


title: Group7_CD8cells_rep1


title: WTCHG_834291_227_1


title: Group7_CD4cells_rep21


title: Group7_CD4cells_rep20


title: CDYL_ctrl_2_RNA


title: CDYL_ctrl_1_RNA


title: H3K18cr_ctrl


title: WTCHG_836238_220_1


title: WTCHG_836237_220_1


title: Group7_CD4cells_rep19


title: iB cells Tcrd-GDL ctl 8

description:
RNA seq
normalize_counts_RNAseq2.txt
S2313Nr5

value: untreated


title: WTCHG_836236_220_1


title: Group7_CD4cells_rep18


title: Input_ctrl


title: iB cells Tcrd-GDL ctl 7

description:
RNA seq
normalize_counts_RNAseq2.txt
S2313Nr4


title: WTCHG_836235_220_1


title: iB cells Tcrd-GDL ctl 6

description:
RNA seq
normalize_counts_RNAseq2.txt
S2313Nr3


title: WTCHG_834294_220_1


title: iB cells Tcrd-GDL d8 1

description:
RNA seq
normalize_counts_RNAseq1.txt
S1197Nr7


title: iB cells Tcrd-GDL ctl 5

description:
RNA seq
normalize_counts_RNAseq2.txt
S2313Nr2


title: Group7_CD4cells_rep16


title: WTCHG_834293_220_1


title: Group7_CD4cells_rep15


title: iB cells Tcrd-GDL ctl 4

description:
RNA seq
normalize_counts_RNAseq2.txt
S2313Nr1


title: WTCHG_834292_220_1


title: Group7_CD4cells_rep14


title: iB cells Tcrd-GDL ctl 2

description:
RNA seq
normalize_counts_RNAseq1.txt
S1197Nr11


title: Group7_CD4cells_rep13


title: 11__LolaFdez_RNA_Seq_Small_S11_L001_R1_001

source_name: CD8 EV


title: Group7_CD4cells_rep12


title: iB cells Tcrd-GDL ctl 1

description:
RNA seq
normalize_counts_RNAseq1.txt
S1197Nr10


title: WTCHG_834291_220_1


title: Group7_CD4cells_rep17


title: 8__LolaFdez_RNA_Seq_Small_S8_L001_R1_001


title: Group7_CD4cells_rep11


title: MA10_ATACseq

city: Saint Louis

first: Charles

middle: K

last: Kaufman

state: MO

address: 660 S Euclid Ave

department: Oncology

institute: Washington University in St. Louis

description: Melanoma cells

data_processing:
Demultiplex and trim reads with Cutadapt
Align reads to GRCz10/danRer11 using BWA-MEM
Remove duplicate reads with GATK
Index and filter for high quality reads with SAMtools and bamtools
Identify peaks with MACS2 callpeak function
Genome_build: danRer11
Supplementary_files_format_and_content: bigwig and narrowPeak files generated

organism: Danio rerio

source_name: Sorted melanoma tumor

extract_protocol:
FACS for fluorescent tag: mCherry for melanocytes (MC) and GFP for melanoma cells (MA)
Up to 50,000 cells were tagmented with an Illumina Nextera kit and purified with a Qiagen MinElute Purification Kit. DNA was amplified with a 9x cycling protocol combined with bead purification of proper sized fragments.

value: Melanoma

tag: run #


title: MA11_ATACseq

description: Melanoma cells


title: Group7_CD4cells_rep9


title: Group7_CD4cells_rep10


title: iB cells Tcrd-GDL ctl 3

description:
RNA seq
normalize_counts_RNAseq1.txt
S1197Nr12


title: MA9_ATACseq

description: Melanoma cells


title: Group7_CD4cells_rep8


title: 5__LolaFdez_RNA_Seq_Small_S5_L001_R1_001

source_name: CD8 S1


title: 7__LolaFdez_RNA_Seq_Small_S7_L001_R1_001

source_name: CD4 EV


title: 9__LolaFdez_RNA_Seq_Small_S9_L001_R1_001


title: 3__LolaFdez_RNA_Seq_Small_S3_L001_R1_001


title: 2__LolaFdez_RNA_Seq_Small_S2_L001_R1_001


title: Group7_CD4cells_rep7


title: MA8_ATACseq

description: Melanoma cells


title: MA7_ATACseq

description: Melanoma cells


title: Group7_CD4cells_rep6


title: MA6_ATACseq

description: Melanoma cells


title: 6__LolaFdez_RNA_Seq_Small_S6_L001_R1_001


title: 1__LolaFdez_RNA_Seq_Small_S1_L001_R1_001


title: iB cells alone 3

description:
RNA seq
normalized_counts cocolture.txt
S1605Nr6


title: MA5_ATACseq

description: Melanoma cells


title: 15__LolaFdez_RNA_Seq_Small_S15_L001_R1_001


title: MA4_ATACseq

description: Melanoma cells


title: Group7_CD4cells_rep5


title: Group7_CD4cells_rep4


title: Group7_CD4cells_rep3


title: MC_Homo_ATACseq

description: Homozygous Melanocytes

source_name: Sorted skin

value: Skin melanocytes


title: Group7_CD4cells_rep2


title: 14__LolaFdez_RNA_Seq_Small_S14_L001_R1_001


title: MC_Het6_ATACseq

description: Heterozygous Melanocytes


title: IPF 6

city: Los Angeles

first: DIANHUA

last: JIANG

state: CA

address: 8700 BEVERLY BLVD

institute: CEDARS SINAI

description:
IPF-6
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp

data_processing:
Raw scRNA-seq data was aligned to human genome GRCh38 with Cell Ranger (10x Genomics). Downstream quality control, normalization and visualization were done with Seurat package. For quality control, the output expression matrix from Cell Ranger was done based on number of genes detected in each cell, number of transcripts detected in each cell and percentage of mitochondrial genes. The expression matrix was then normalized and visualized with UMAP.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv

source_name: Lung Lin–EpCAM+ cells

extract_protocol: mRNAs from sorted single cells were reverse transcribed and amplified as previously described. Library preparation and sequencing were performed as described previously. Sequencing libraries for cDNA from single cells were prepared as per the Single Cell 3′ v2 Reagent Kits User Guide (10x Genomics, Pleasanton, CA, USA). Cellular suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell Gel Bead-In-EMulsions (GEMs). GEM-reverse transcription (RT) was performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA, USA). GEMs were collected and the cDNA was amplified and purified with SPRIselect Reagent Kit (Beckman Coulter, Brea, CA, USA). Indexed sequencing libraries were constructed using Chromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems, Roche Holding AG, Basel, Switzerland). Sequencing libraries were loaded on a NextSeq500 (Illumina, San Diego, CA, USA) with a custom sequencing setting (26bp for Read 1 and 98bp for Read 2) to obtain a sequencing depth of ~200K reads per cell.

tag: diagnosis

value: IPF

value: Lung Lin-EpCAM+ cells

tag: assay

value: scRNA-sequencing


title: 18__LolaFdez_RNA_Seq_Small_S18_L001_R1_001


title: MC_Het4_ATACseq

description: Heterozygous Melanocytes


title: 23__LolaFdez_RNA_Seq_Small_S23_L001_R1_001


title: PanKcr_wt_oe

value: Kidney

value: cystic cell


title: 20__LolaFdez_RNA_Seq_Small_S20_L001_R1_001


title: IPF 5

description:
IPF-5
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: MA3C_RNAseq

description: Melanoma cells

data_processing:
Assess read quality with FastQC
Align to GRCz11/danRer11 using STAR
Quantify transcriptome using RSEM
Normalize reads with DESeq2
Genome_build: danRer11
Supplementary_files_format_and_content: tab-delimited text files with CPM values for each sample
Supplementary_files_format_and_content: tab-delimited text files with RPKM values for each sample
Supplementary_files_format_and_content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells, as well as

extract_protocol:
FACS for fluorescent tag: mCherry for melanocytes (MC) and GFP for melanoma cells (MA), then use Machery Nagel kit to extract total RNA
cDNA generated using Clontech SMARTer cDNA amplification kit


title: 19__LolaFdez_RNA_Seq_Small_S19_L001_R1_001


title: MA3B_RNAseq

description: Melanoma cells


title: IPF 3

description:
IPF-3
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: MC_Het5_ATACseq

description: Heterozygous Melanocytes


title: MA3A_RNAseq

description: Melanoma cells


title: 17__LolaFdez_RNA_Seq_Small_S17_L001_R1_001


title: 30H

type: genomic

city: Memphis

first: Jason

last: Chiang

state: Tennessee

address: 262 Danny Thomas Pl

department: Pathology

institute: St. Jude Children's Research Hospital

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Raw signal intensities from IDAT files were normalized using the functional normalization method implemented in minfi (v.1.26.0). Poor quality (P > 0.01) and failed probes were removed from the downstream analysis. The probes targeting the X and Y chromosomes, containing single-nucleotide polymorphism, and not mapping uniquely to the human reference genome (hg19) were also filtered out.
Identification of differentially methylated probes and regions were performed using limma (v3.48.0) and bumphunter.
Genes within differentially methylated regions were queried against MSigDB v7.4.

label: Cy3 and Cy5

source_name: Brain

label_protocol: Standard Illumina Protocol

extract_protocol: Microdissection of high-grade and low-grade areas was accomplished by laying unstained sections upon a printout of a marked H&E-section and scraping the area of interest with sterile razor blades or 30-gauge needles under a stereomicroscope with 40× magnification. Genomic DNA was prepared from the microdissected sections following the instructions of a QIAamp DNA FFPE Tissue Kit.

value: brain

tag: tumor stage

value: tumor


title: IPF 4

description:
IPF-4
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: IPF 2

description:
IPF-2
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: lin-52 3A rep4

city: Houghton

first: Paul

middle: Donald

last: Goetsch

state: MI

address: 1400 Townsend Drive

department: Biological Sciences

institute: Michigan Technological University

data_processing:
Sequence reads were trimmed using fastp.
Transcriptome was mapped to version WBcel235 using STAR.
Reads counts per transcript were obtained using HTSeq.
Differentially expressed genes were assessed using DESeq2.
Assembly: WBcel235
Supplementary files format and content: *_htseq.txt: Tab-delimited text files include reads counts for genes in each replicate as determined by htseq-count.

organism: Caenorhabditis elegans

source_name: late embryo

growth_protocol: Synchronized lin-52(WT) or lin-52(3A) L1s were grown in standard S-basal media liquid culture for 72 hours at 20°C and fed HB101 bacteria. Adult worms were treated with standard bleaching solution to collect embryos, and embryos were incubated at 20°C for up to 3.5 hours then frozen in TRIzol reagent (ThermoFisher) using liquid nitrogen.

extract_protocol:
Total RNA was extracted after three freeze/thaw cycles following TRIzol manufacturer instructions and purified by isopropanol precipitation.
A total of 1 µg of RNA was used for RNA-seq library preparation. Poly(A) transcripts were enriched using the NEBNext Poly(A) mRNA Magentic Isolation Module and prepped for sequencing using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Samples were multiplexed using the NEBNext Multiplex Oligos for Illumina Dual Index Primers Set. Libraries were sequenced on an Illumina HiSeq X system by Novogene Corporation Inc. (Davis, CA) to acquire 150-bp paired-end reads.

tag: strain/genotype

tag: developmental stage

value: late embryo

value: whole body


title: IPF 1

description:
IPF-1
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: 33L


title: Group7_CD4cells_rep1

value: PBMC

value: CD4 T cells


title: MA1_RNAseq

description: Melanoma cells


title: 26H


title: MA2_RNAseq

description: Melanoma cells


title: lin-52 3A rep3


title: 1F_nkx2-2_rep3

city: Oklahoma

first: David

middle: J

last: Forsthoefel

state: OK

address: 825 NE 13th St

department: Genes and Human Disease Research Program

institute: Oklahoma Medical Research Foundation

data_processing:
Read quality was assessed with FastQC (v0.11.5) before and after trimming with BBDuk (v36.99) for paired end reads: k=13 ktrim=r mink=11 qtrim=rl trimq=10 minlength=35 tbo tpe.
Reads were mapped to the dd_Smed_v6 transcriptome restricted to 28,069 unique transcripts as in (Forsthoefel et al., eLife, 2020) using Bowtie2 (v2.3.1) for paired end reads, with "-a" multi-mapping and "--local" soft-clipping allowed.
Read summarization was conducted with the "featureCounts" utility in the Subread package (v1.6.3) (Liao et al., Nuc. Acids Res., 2019), using a custom ".SAF" file and options "-p -M -O -F SAF" to include multi-mapping and multi-overlapping reads.
Genome_build: Dresden S. mediterranea transcriptome dd_Smed_v6 (http://planmine.mpi-cbg.de/) (Brandl et al., Nuc. Acids Res., 2016)
Supplementary_files_format_and_content: Processed data are in a tab-delimited .txt file, wich includes geneID, transcript length, log2 Fold Changes, logCPM,and FDR-adjusted P value.

organism: Schmidtea mediterranea

source_name: Whole animal

growth_protocol: Asexual Schmidtea mediterranea (clonal line CIW4) were maintained in 0.5 g/L Instant Ocean salts with 0.0167 g/L sodium bicarbonate dissolved in Type I water, and fed with beef liver paste. For all experiments, planarians were starved seven days prior to fixation.

extract_protocol:
Total RNA was extracted from 6-10 uninjured planarians per biological replicate using Trizol as described (Forsthoefel et al., eLife, 2020).
mRNA was enriched from 1 µg total RNA/sample using oligo-dT homopolymer beads, and libraries were generated using the Illumina Truseq Stranded mRNA Library Prep Kit according to the manufacturer's protocol. Final libraries were assayed on the Agilent TapeStation for appropriate size and quantity. Libraries were pooled in equimolar amounts as ascertained by fluorometric analysis, then final pools were absolutely quantified using qPCR on a Roche LightCycler 480 with Kapa Biosystems Illumina Library Quantification Reagents.

treatment_protocol: Planarians were fed once with 1 µg dsRNA mixed with 1 µl blue food coloring, 8 µl water, and 40 µl 2:1 liver:water homogenate, then starved seven days prior to RNA extraction.

value: clonal line CIW4

value: live uninjured whole planarians

value: starved 7 days

tag: RNAi


title: Healthy donor 6

description:
Normal-6
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp

value: Healthy


title: MC_Het3_RNAseq

description: Heterozygous Melanocytes


title: 1F_nkx2-2_rep2

tag: strain


title: 27L


title: 1F_nkx2-2_rep1


title: MC_Het2_RNAseq

description: Heterozygous Melanocytes


title: 33H


title: lin-52 3A rep2


title: 21__LolaFdez_RNA_Seq_Small_S21_L001_R1_001


title: Healthy donor 4

description:
Normal-4
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: Healthy donor 5

description:
Normal-5
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: 26L


title: MC_Het1_RNAseq

description: Heterozygous Melanocytes


title: 25H


title: lin-52 WT rep4


title: 22H


title: 27H


title: Healthy donor 3

description:
Normal-3
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: 23H


title: MC_WT3_RNAseq

description: Wild type Melanocytes


title: 22L


title: 1F_ctrl_rep2

value: egfp(RNAi) (control)


title: 30L


title: lin-52 WT rep3


title: MC_WT2_RNAseq

description: Wild type Melanocytes

value: Skin melanocytes


title: 24L


title: Healthy donor 1

description:
Normal-1
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: 1F_ctrl_rep1


title: MC_WT1_RNAseq

description: Wild type Melanocytes


title: 20L


title: lin-52 WT rep2


title: 25L


title: 20H


title: lin-52 3A rep1


title: 12L


title: lin-52 WT rep1


title: 24H


title: 11L


title: Healthy donor 2

description:
Normal-2
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: 12H


title: 11H


title: 23L


title: Rag1-/-CCR10+/EGFP skin_GFP-ILC_rep2

status: Public on May 23 2022

type: RNA

city: HELOTES

first: Ming

last: Xu

state: TX

address: 9754 Magic Cedar

department: MIMG

institute: UTHSCSA

hyb_protocol: Following fragmentation and Terminal Labeling, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST 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: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: tissue isolation and digestion

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

growth_protocol: Rag-/- CCR10 +/EGFP and CCR10 +/EGFP B6 mice were housed at 25C and 50% humidity.

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

treatment_protocol: GFP+ and GFP- ILCs were sorted from the skin of indicated mice based on CD45.2+CD3-Lin- markers by MoFlow Sorter and directly sorted into Trizol solution on ice.

tag: gender

value: Female

tag: exclusion markers

value: CD3 CD5 CD11b B220 Anti-7-4 Anti-Gr-1 Anti-Ter-126

value: skin


title: Rag1-/-CCR10+/EGFP skin_GFP+ILC_rep1

value: CD3 CD5 CD11b B220 Anti-7-4 Anti-Gr-1 Anti-Ter-123

tag: cell type

tag: tissue


title: CCR10+/EGFP skin_GFP-ILC_rep1

value: CD3 CD5 CD11b B220 Anti-7-4 Anti-Gr-1 Anti-Ter-121


title: Rag1-/-CCR10+/EGFP skin_GFP-ILC_rep3

value: CD3 CD5 CD11b B220 Anti-7-4 Anti-Gr-1 Anti-Ter-127


title: NHBE CH223191 + HDM [NHBE_25]

city: Munich

first: Ulrich

middle: M

last: Zissler

address: Biedersteiner Str. 29

department: Center of Allergy & Environment (ZAUM)

institute: Technical University of Munich & Helmholtz Center Munich

description: NHBE CH223191 + HDM

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and 20 bit Tiff.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Agilent.SingleColor.28004 microarray, Software GeneSpring 14.5; Threshold: 1.0, Logbase: 2; Normalization: Quantile; Baseline Transformation: None; Filtered on Expression (20.0-100.0); Filtered on Flags (Detected, Not Detected); T test unpaired , P<=:0.05, FC>=1.5

source_name: NHBE

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Agilent Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, GER). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: NHBEs were grown to a confluency of 80% and rested for 12h before stimulation.

extract_protocol: NHBEs were directly transferred into RNAcell protect reagent (Qiagen) and stored at -80°C until RNA extraction. Total RNA was extracted using RNeasy Mini Kit (Cat.-No. 74104, Qiagen, Hilden, Germany) with on-column DNase digestion (Cat.-No. 79254, DNase-Free DNase Set, Qiagen) for avoiding DNA contaminations (Zissler UM, 2016 Mucosal Immunology). RNA quantification was performed by ultraviolet–visible spectrophotometry (Nanodrop Technologies, Wilmington, DE, USA), for assessment of the RNA integrity by the RNA 6000 Nano Chip Kit with the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: After reaching confluency, NHBEs were pretreated with either blank medium or CH223191 for 2 hours, followed by treatment with IL4 and House dust mite extract respectively.

value: Primary normal bronchial epithelial cells (NHBEs)

tag: treatment

tag: inhibitor pre-treatment

value: yes


title: CCR10+/EGFP skin_GFP+ILC_rep2

value: CD3 CD5 CD11b B220 Anti-7-4 Anti-Gr-1 Anti-Ter-120


title: 7H

value: brain

value: tumor


title: 1F_ctrl_rep3

value: clonal line CIW4


title: NHBE CH223191 + HDM [NHBE_23]

description: NHBE CH223191 + HDM


title: CCR10+/EGFP skin_GFP+ILC_rep1

value: CD3 CD5 CD11b B220 Anti-7-4 Anti-Gr-1 Anti-Ter-119


title: CCR10+/EGFP skin_GFP-ILC_rep2

value: CD3 CD5 CD11b B220 Anti-7-4 Anti-Gr-1 Anti-Ter-122


title: NHBE CH223191 + HDM [NHBE_24]

description: NHBE CH223191 + HDM


title: Rag1-/-CCR10+/EGFP skin_GFP+ILC_rep2

value: CD3 CD5 CD11b B220 Anti-7-4 Anti-Gr-1 Anti-Ter-124


title: NHBE CH223191 + HDM + IL4 [NHBE_27]

description: NHBE CH223191 + HDM + IL4


title: NHBE CH223191 + HDM + IL4 [NHBE_26]

description: NHBE CH223191 + HDM + IL4


title: NHBE IL4+HDM [NHBE_21]

description: NHBE IL4+HDM

value: no


title: NHBE IL4+HDM [NHBE_18]

description: NHBE IL4+HDM


title: NHBE IL4+HDM [NHBE_19]

description: NHBE IL4+HDM


title: NHBE IL4+HDM [NHBE_20]

description: NHBE IL4+HDM


title: NHBE IL4+HDM [NHBE_17]

description: NHBE IL4+HDM


title: 7L


title: NHBE CH223191 + HDM + IL4 [NHBE_28]

description: NHBE CH223191 + HDM + IL4


title: Rag1-/-CCR10+/EGFP skin_GFP-ILC_rep1

value: CD3 CD5 CD11b B220 Anti-7-4 Anti-Gr-1 Anti-Ter-125


title: NHBE IL4+HDM [NHBE_16]

description: NHBE IL4+HDM


title: NHBE CH223191 + HDM + IL4 [NHBE_29]

description: NHBE CH223191 + HDM + IL4


title: NHBE CH223191 + HDM [NHBE_22]

description: NHBE CH223191 + HDM


title: NHBE IL4+HDM [NHBE_15]

description: NHBE IL4+HDM


title: NHBE IL4+HDM [NHBE_14]

description: NHBE IL4+HDM


title: FBXW7/AKT1 MS119

first: Daniela

last: Sia

address: 1425 Madison Avenue

department: Liver Diseases

institute: Icahn school of Medicine at Mount Sinai

data_processing:
Alignment: STAR version 2.7.7a with the following code: STAR --runThreadN 8  --genomeDir {genome_star} --sjdbGTFfile {sjdbGTFfile}  --outSAMtype BAM SortedByCoordinate --outSAMmode Full --outFileNamePrefix {output_folder}{name}/{name}_  --outWigType bedGraph --outWigStrand Unstranded --readFilesCommand gunzip -c --quantMode GeneCounts --readFilesIn {file_string}
Counts: Included in STAR code (--quantMode GeneCounts)
Normalization: Normalization was performed using DESeq2 version 1.22.1 Variance Stabilizing Transformation.
Annotation file: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M26/gencode.vM26.annotation.gtf.gz
Genome_build: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M26/GRCm39.genome.fa.gz
Supplementary_files_format_and_content: .txt file with VST normalized counts from DESeq2 package version 1.22.1

growth_protocol: Murine tumors were induced by hydrodynamic tail vein injection of three differet plasmids combination

extract_protocol:
Total RNA was extracted from 30 mg of tissue using Trizol reagent (Invitrogen, Carlsbad, CA) and purified with RNeasy mini kit (Qiagen, Valencia, CA). RNA sample concentration was assessed by Qubit Fluorometric Quantification (Invitrogen, Carlsbad, CA). 1 ug of RNA was poly-A selected, multiplexed RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation kit (Illumina, San Diego, CA) and sequenced on Illumina HiSeq machine (150nt, paired end).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: not applicable

value: liver


title: NICD1/AKT1 MS83


title: YAP1/AKT1 MS24

source_name: YAP1/AKT1 _liver


title: YAP1/AKT1 MS74


title: NHBE HDM [NHBE_10]

description: NHBE HDM

value: HDM


title: YAP1/AKT1 MS26


title: FBXW7/AKT1 MS116


title: NICD1/AKT1 MS35


title: FBXW7/AKT1 MS120


title: KRAS/p19 MS135


title: NHBE HDM [NHBE_11]

description: NHBE HDM


title: KRAS/p19 MS134


title: NICD1/AKT1 MS32


title: KRAS/p19 MS128


title: NHBE HDM [NHBE_12]

description: NHBE HDM


title: NHBE HDM [NHBE_07]

description: NHBE HDM


title: NHBE HDM [NHBE_08]

description: NHBE HDM


title: NHBE Medium [NHBE_01]

description: NHBE Medium

value: Medium


title: Healthy liver MS36

value: Healthy


title: Healthy liver MS33


title: NHBE HDM [NHBE_09]

description: NHBE HDM


title: NHBE Medium [NHBE_05]

description: NHBE Medium


title: NHBE Medium [NHBE_02]

description: NHBE Medium


title: NHBE HDM [NHBE_06]

description: NHBE HDM


title: NHBE Medium [NHBE_04]

description: NHBE Medium


title: NHBE Medium [NHBE_03]

description: NHBE Medium


title: NHBE HDM [NHBE_13]

description: NHBE HDM


title: Healthy liver MS117


title: Sample treated with 1000nM scrambled PNA after INR-Seq – R1

city: Würzburg

first: Jakob

middle: Jeremias

last: Jung

state: Bayern

address: Josef-Schneider-Str. 2/Bau D15

department: Institute of Molecular Infection Biology (IMIB)

institute: University of Würzburg

data_processing:
Library strategy: RIBO-Seq
To remove sequencing adapters from raw reads and remove low-quality bases (Phred quality score <10), BBduk was used
The resulting reads were mapped against the oligo-pool using BBMap (v38.79)
Aligned reads were then assigned mRNAs, rRNAs and tRNAs and quantified using the featureCounts (v2.0.1) method of the Subread package
To facilitate the visualisation of the 3’ ends of reads in coverage plots, wiggle files were created with the bamCoverage (v.3.4.3)
Genome_build: pool of single-stranded DNA oligonucleotides was designed by extracting the sequence of the first 153 nt of each annotated ORF (start codon + 50 codons)
Supplementary_files_format_and_content: Wiggle (.wg) files show 3’end mapped reads for each mRNA. The count table shows counted reads per mRNA

organism: Escherichia coli K-12

source_name: Cell-free mRNA and translational machinery

extract_protocol:
To purify the RET-stalled monosomes, the associated transcripts were cleaved with MNase and the digested samples were subsequently run on sucrose gradients, as is common for bacterial Ribo-seq (Figure 1) (Mohammad et al., 2019). After collection of the 70S peak, RPFs were isolated using acidic phenol-chloroform extraction followed by size selection of 15 – 45 nt long RNA on a denaturing polyacrylamide gel.
RNA 5’ ends were phosphorylated with T4 polynucleotide kinase (New England Biolabs). Adapters were ligated to the 5’ and 3’ ends of the RNA and first-strand cDNA synthesis was performed using M-MLV reverse transcriptase. The cDNA was then amplified using a high fidelity DNA polymerase and purified with Agencourt AMPure XP beads (Beckman Coulter). The cDNA samples were pooled in equimolar amounts and the rDNA within the pool was depleted targeting 24 unique sequences (Table S1) using a CRISPR-Cas9 protocol similar to DASH (Prezza et al., 2020). The final pool was subjected to sequencing on an Illumina NextSeq 500 system using 75 nt single-end read length.

value: treated with 1000nM scrambled PNA


title: Sample treated with 1000nM scrambled PNA after INR-Seq – R2


title: Sample treated with 1000nM PNA after INR-Seq – R3

value: treated with 1000nM acpP PNA


title: Sample treated with 1000nM PNA after INR-Seq – R2


title: Sample treated with 1000nM PNA after INR-Seq – R1


title: Sample treated with 250nM PNA after INR-Seq – R3

value: treated with 250nM acpP PNA


title: Sample treated with 1000nM scrambled PNA after INR-Seq – R3


title: Planktonic_WT_BR3 [PlankWTBR3_S3]

city: Singapore

first: Xianghui

last: Liu

address: 60 Nanyang Drive, SBS-01N-27

country: Singapore

institute: Nanyang Technological Univ. of Singapore

data_processing:
Quality of reads was access using FasQC v0.11.7
Ribosomal RNA reads were discarded using SortMeRNA v4.2.0 and remaining non-RNA reads were trimmed using Trimmomatic v0.38 and mapped against P. aeruginosa PAO1 reference genome (GCA_000006765.1)
Aligned data were used as input for featureCounts function from the Rsubread v2.4.3 to generate a matrix of annotated genes with their corresponding raw counts
The count data were subjected to DESeq2 v1.30.1 for differential gene expression levels and statistical signficance
Assembly: GCA_000006765.1
Supplementary files format and content: couts.all.txt (matrix table with raw gene counts for every gene) and  fpkm_PAO1.txt (tab-delimited text files include FPKM values) and  rlogcounts.all.txt (rlog normalized count table)

organism: Pseudomonas aeruginosa

growth_protocol: For planktonic growth condition, the cells were cultivated in flask with ABTG medium for 4 hours at 37oC (200 rpm, shaking condition). For biofilm growth condition, the cells were cultivated in flow chamber system with continous ABTG medium supplied for 72 hours at  37oC

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit (catalogue number: 74104, Qiagen®, Germany). Then, samples were treated with DNase using Turbo DNA-free™ kit (catalogue number: AM1907, Thermo Fisher Scientific, USA) and purified DNA-free RNA samples were subjected to ribosomal depletion using the Ribo-Zero™ Magnetic Kits (Illumina, USA).  Complementary DNAs (cDNAs) were reverse transcribed using a NEBNext RNA first and second strand synthesis module (NEB®, USA). cDNAs were subjected to Illumina’s TruSeq Stranded mRNA protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Wild-type

tag: mode of growth

value: Planktonic

tag: growth condition

value: 4 hours in shaking condition


title: Planktonic_WT_BR2 [PlankWTBR2_S2]


title: Sample treated with 250nM PNA after INR-Seq – R2


title: R48 (Treated cells were washed with fresh culture medium, and then incubated for 48 hours) Replicate 2

city: Baltimore

first: Ho Lam

last: Tang

state: MD

address: 615 N. Wolfe Street

department: Neurosurgery

institute: The Johns Hopkins University School of Medicine

hyb_protocol: Labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16-20 hours with rocking

scan_protocol: Arrays were scanned with the Illumina iScan BeadArray scanner standard protocol

data_processing: Data were extracted with the Illumina BeadStudio with Gene Expression module, average normalization, to create an output file. These values were imported into Spotfire DecisionSite v9.1.2 and log2 transformed.

source_name: mouse primary liver cells

label_protocol: The RNA was labelled with the SABiosciences C-03 RT² First Strand Kit (SABiosciences - QIAGEN, Frederick, MD) standard protocol

growth_protocol: Primary liver cells were isolated from BALB/c mice by collagenase B according to the manufacturer’s instructions (Worthington Biochemical, Lakewood, NJ) and cultured as described (PMID: 22535522, DOI: 10.1091/mbc.E11-11-0926)

extract_protocol: RNA of all samples was extracted with Trizol reagent. Total RNA was isolated and purified by RNeasy Mini Kit (Qiagen, Cologne, Germany).

treatment_protocol: Mouse primary liver cells were treated with 4.5% ethanol for 5 hours (R0) and then washed and cultured in fresh DMEM F12 10% FBS medium for 3 (R3), 6 (R6), 24 (R24), and 48 (R48) hours.

value: 4.5% EtOH, 5Hr, fresh medium 48Hr


title: R6 (Treated cells were washed with fresh culture medium, and then incubated for 6 hours) Replicate 2

value: 4.5% EtOH, 5Hr, fresh medium 6Hr


title: R24 (Treated cells were washed with fresh culture medium, and then incubated for 24 hours) Replicate 1

value: 4.5% EtOH, 5Hr, fresh medium 24Hr


title: R3 (Treated cells were washed with fresh culture medium, and then incubated for 3 hours) Replicate 3

value: 4.5% EtOH, 5Hr, fresh medium 3Hr


title: Sample treated with 250nM PNA after INR-Seq – R1


title: R48 (Treated cells were washed with fresh culture medium, and then incubated for 48 hours) Replicate 1


title: R0 (Cells were treated with 4.5% ethanol in culture medium for 5 hours. Replicate 1

value: 4.5% EtOH, 5Hr


title: R6 (Treated cells were washed with fresh culture medium, and then incubated for 6 hours) Replicate 3


title: R6 (Treated cells were washed with fresh culture medium, and then incubated for 6 hours) Replicate 1


title: Ctrl (Untreated mouse primary liver cells) Replicate 2

value: Untreated


title: R3 (Treated cells were washed with fresh culture medium, and then incubated for 3 hours) Replicate 1


title: R48 (Treated cells were washed with fresh culture medium, and then incubated for 48 hours) Replicate 3


title: R0 (Cells were treated with 4.5% ethanol in culture medium for 5 hours) Replicate 3


title: Sample treated with 63nM PNA after INR-Seq – R3

value: treated with 63nM acpP PNA


title: R24 (Treated cells were washed with fresh culture medium, and then incubated for 24 hours) Replicate 2


title: Ctrl (Untreated mouse primary liver cells) Replicate 3


title: Ctrl (Untreated mouse primary liver cells) Replicate 1


title: Biofilm_WT_BR2 [BioFWTBR2_S11]

value: Biofilm

value: 72 hours in flow chamber


title: R0 (Cells were treated with 4.5% ethanol in culture medium for 5 hours) Replicate 2


title: R24 (Treated cells were washed with fresh culture medium, and then incubated for 24 hours) Replicate 3


title: Sample treated with 63nM PNA after INR-Seq – R1


title: Biofilm_WT_BR1 [BioFWTBR1_S10]


title: Sample treated with 63nM PNA after INR-Seq – R2


title: Planktonic_WT_BR1 [PlankWTBR1_S1]


title: Sample treated with 16nM PNA after INR-Seq – R3

value: treated with 16nM acpP PNA


title: input_SS01_etoposide-25uM-60min_L2-L3_ext538_AKM349

first: Ana

middle: Karina

last: Morao

address: 29 Washington Place

department: Biology

institute: New York University

data_processing:
Basecalls were performed using CASAVA version 1.8.
ChIP-seq: Bowtie2 version 2.4.2 was used to align 75 bp single-end reads to WS220 with default parameters (Langmead and Salzberg, 2012). Bam sorting and indexing was performed using samtools version 1.11 (Danecek et al., 2021). BamCompare tool in Deeptools version 3.5.0 was used to normalize for the sequencing depth using CPM and create ChIP-Input coverage and ChIP/Input ratios with a bin size of 10 bp and 200 bp read extension (Ramírez et al., 2016). Only reads with a minimum mapping quality of 20 were used, and mitochondrial DNA, PCR duplicates, and blacklisted regions were removed (Amemiya et al., 2019).
Assembly: WS220
Supplementary files format and content: ChIP-seq: bigwig coverage files for individual replicates

source_name: SS01A (top-2::degron::GFP)

growth_protocol: Mixed developmental stage embryos were obtained by bleaching gravid adults. To isolate synchronized L2/L3 worms, gravid adults were bleached and embryos were hatched overnight in M9 buffer. The resulting starved L1s were grown for 24 hours at 22°C. For glp-1 adult worms, gravid adults grown at the permissive temperature (15°C) were bleached and starved L1s were grown at the restrictive temperature (25°C) for three days.

extract_protocol:
ChIP-seq: embryos, L2/L3s and adult worms were dounce-homogenized in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) and sonicated in 0.1% sarkosyl to obtain chromatin fragments between 200 and 800 bp. 2 mg of protein extract and 3 to 10 ug of antibody was used per ChIP.
ChIP-seq: half of the ChIP DNA and 30 ng of input DNA were ligated to Illumina TruSeq adapters and amplified by PCR. Library DNA between 250 and 600 bp was gel purified.

treatment_protocol: Auxin treatment: synchronized L2/L3s were washed three times with M9 and split into two aliquots. Half of the worms were transferred to NGM plates containing 1mM of indole-3-acetic-acid (Fisher 87-51-4) prepared as in (Zhang et al., 2015). The other half were placed in normal NGM plates (no-auxin control) for the indicated time. Worms were then washed one time with M9 and processed accordingly to future application. For ChIP and Hi-C, L2/L3 worms were incubated in 2% formaldehyde for 30 minutes, followed by quenching with glycine, one wash with M9 and two washes with PBS, PMSF and protease inhibitors. For RNA-seq, worms were stored in Trizol. Etoposide treatment: synchronized L2/L3 worms were washed three times with M9 and incubated for one hour in etoposide (Sigma-Aldrich, E1383-100MG) diluted at the desired concentration in 5mL of M9. Similar results were obtained with 12.5 μM, 25 μM and 50 μM.

value: SS01A (top-2::degron::GFP)

tag: antibody target

value: input

value: etoposide 25uM


title: input_SS01_etoposide-12uM-60min_L2-L3_ext539_AKM350

value: etoposide 12uM


title: R3 (Treated cells were washed with fresh culture medium, and then incubated for 3 hours) Replicate 2


title: input_SS01_L2-L3_ext407_AKM314

value: no-auxin


title: input_AM05_L2-L3_ext498_AKM288

source_name: AM05 (top-1::degron::GFP)

value: AM05 (top-1::degron::GFP)

value: auxin


title: input_SS01_etoposide-50uM-30min_L2-L3_ext537_AKM348

value: etoposide 50uM


title: Biofilm_WT_BR3 [BioFWTBR3_S12]

value: Wild-type


title: Sample treated with 16nM PNA after INR-Seq – R1


title: input_AM05_L2-L3_ext497_AKM287


title: input_AM05_L2-L3_ext531_AKM321


title: input_AM05_L2-L3_ext530_AKM320


title: Sample treated with 5nM PNA after INR-Seq – R2

value: treated with 5nM acpP PNA


title: Sample treated with 5nM PNA after INR-Seq – R1


title: Sample treated with 16nM PNA after INR-Seq – R2


title: Sample treated with 0.5nM PNA after INR-Seq – R3

value: treated with 0.5nM acpP PNA


title: TOP-2_SS01_etoposide-50uM-30min_L2-L3_ext537_AKM332_input_AKM348_ChIP-seq

value: GFP

tag: antibody (vendor, cat#, lot#)

value: Abcam, ab290


title: input_SS01_L2-L3_ext409_AKM315


title: Sample treated with 5nM PNA after INR-Seq – R3


title: TOP-2_SS01_etoposide-12uM-60min_L2-L3_ext539_AKM336_input_AKM350_ChIP-seq


title: TOP-2_SS01_etoposide-25uM-60min_L2-L3_ext538_AKM334_input_AKM349_ChIP-seq


title: DPY-27_SS01_etoposide-25uM-60min_L2-L3_ext538_AKM335_input_AKM349_ChIP-seq

value: Covance Research Products Inc, JL00001_DPY27


title: Sample treated with 0.5nM PNA after INR-Seq – R2


title: Untreated sample after INR-Seq – R3

value: untreated


title: Untreated sample after INR-Seq – R5


title: DPY-27_SS01_etoposide-50uM-30min_L2-L3_ext537_AKM333_input_AKM348_ChIP-seq


title: Untreated sample after INR-Seq – R4


title: Untreated sample after INR-Seq – R2


title: Sample treated with 0.5nM PNA after INR-Seq – R1


title: TOP-2_SS01_1h_auxin_L2-L3_ext409_AKM308_input_AKM315_ChIP-seq


title: Group 3 innate lymphoid cells-KO rep3

city: hangzhou

first: lie

last: wang

state: zhejiang

address: Zijingang Campus, Zhejiang University，Yuhangtang Road 866

department: immunology

institute: zhejiang universiry

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12).  .
The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Mus

source_name: small intestine

extract_protocol:
Total RNA was extracted from the tissues using RNeasy Mini kit (QIAGEN, 74104) according to the manual instruction. Limited RNA（more than 200pg, high-quality）was amplified.
Limited RNA（more than 200pg, high-quality）was amplified with oligo-dT and dNTPs,  incubated at 72℃ and immediately put back on ice, then reverse transcribed to cDNA based on   polyA tail. The template was switched to the 5' end of the RNA and the full-length cDNA was  generated by PCR. Agilent 2100 bioanalyzer instrument (Thermo Fisher Scientific, MA, USA)  was used to determine the average molecule length of PCR product. Purified cDNA from previous   steps was fragmented into small pieces with fragment buffer by PCR, and the product was purified   and selected by the Agencourt AMPure XP-Medium kit (Thermo Fisher Scientific, USA). cDNA   was quantified by Agilent Technologies 2100 bioanalyzer. The double stranded PCR product   undergo QC step was heat denatured and circularized by the splint oligo sequence. The single   strand circle DNA (ssCir DNA) was formatted as the final library. The final library was quantitated   in two ways in order to ensure the high quality of the sequencing data: Determined the average   molecule length used the Agilent 2100 bioanalyzer instrument, quantified library used real-time   quantitative PCR (qPCR).The final library was amplified with phi29(Thermo Fisher Scientific,   MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular ,   DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on   BGISEQ500 platform(BGI-Shenzhen, China) .

treatment_protocol:
All samples were sorted from siLP
DMEM containing 3% FBS, 0.2%Hanks, 5 mM EDTA, and 0.145 mg/ml DTT

value: small intestine

value: innate lymphoid cells

value: ThPOK-deficient


title: Untreated sample after INR-Seq – R1


title: TOP-2_SS01_1h_no-auxin_L2-L3_ext407_AKM307_input_AKM314_ChIP-seq

value: SS01A (top-2::degron::GFP)


title: Group 3 innate lymphoid cells-WT rep3


title: TOP-2_SS01_1h_auxin_L2-L3_ext406_AKM306_input_AKM155_ChIP-seq


title: TOP-1_AM05_1h_auxin_L2-L3_ext498_AKM310_input_AKM288_ChIP-seq


title: TOP-1_AM05_1h_no-auxin_L2-L3_ext497_AKM309_input_AKM287_ChIP-seq


title: TOP-2_SS01_1h_no-auxin_L2-L3_ext404_AKM305_input_AKM153_ChIP-seq


title: Group 3 innate lymphoid cells-KO rep2


title: Group 3 innate lymphoid cells-WT rep2


title: dpe2/phs1, Prior Period,3

city: Potsdam-Golm

first: Joerg

last: Fettke

state: Brandenburg

address: Karl-Liebknechtstr. 24/25, Building 20

institute: University of Potsdam

data_processing:
Original image data file is transformed to sequenced reads by CASAVA base recognition (Base Calling). Raw reads filtering is as follows: (1) Remove reads containing adapters; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
Clean reads were mapped to the reference genome or the transcriptome with HISAT2.
The RNA-seq reads were assembled according to the reference genomes using Rockhopper(R. McClure, et al, 2013)
Gene expression level of different samples represented by FPKM, quantified by software FeatureCounts.
Assembly: ensemblplants_arabidopsis_thaliana_tair10_gca_000001735_1
Supplementary files format and content: txt file include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: cells of whole shoot

extract_protocol:
RNA was harvested using Trizol protocol (Invitrogen, US) . 1 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

value: cells of whole shoot

value: whole shoot from dpe2/phs1 of 3 weeks

tag: time

value: Prior Period (3 weeks after germination)


title: dpe2/phs1, Recovery Period,3

value: whole shoot from dpe2/phs1 of 7 weeks

value: Recovery Period (7weeks after germination)


title: dpe2/phs1, Prior Period,1


title: AM12_2hours-auxin_L2-L3_RNA_rep2_AKM328_RNA-seq

data_processing:
Basecalls were performed using CASAVA version 1.8.
RNA-seq:We aligned reads to the WS220 genome version using HISAT2 version 2.2.1 (Kim et al., 2019) using the parameter --rna-strandness R. Count data was calculated using HTSeq version 0.13.5 (Anders et al., 2015). The raw counts were normalized FPKM using cufflinks version 2.2.1 (Roberts et al., 2011), and then FPKM was converted to TPM. The raw counts were used for the R package DESeq2 version 1.30.0 (Love et al., 2014).
Assembly: WS220
Supplementary files format and content: RNA-seq: normalized counts (TPM and FPKM) for individual replicates. Log2fold change values generated using DEseq2

growth_protocol: Mixed developmental stage embryos were obtained by bleaching gravid adults. To isolate synchronized L2/L3 worms, gravid adults were bleached and embryos were hatched overnight in M9 buffer. The resulting starved L1s were grown for 24 hours at 22°C.

extract_protocol:
RNA-seq: Total RNA was purified following Trizol manufacturer’s instructions after freeze-cracking samples five times. RNA was cleaned up using Qiagen RNeasy MinElute Cleanup kit. mRNAs were purified using Sera-Mag Oligo (dT) beads (Thermo Scientific) from 10 µg of total RNA. cDNA preparation was done in the presence of dUTP to prepare stranded RNA-seq libraries as in PMID:19620212, cDNA synthesis was performed in the presence of dUTP in order to prepare stranded mRNA-seq libraries.
RNA-seq: cDNA was ligated to Illumina adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: Auxin treatment: synchronized L2/L3s were washed three times with M9 and split into two aliquots. Half of the worms were transferred to NGM plates containing 1mM of indole-3-acetic-acid (Fisher 87-51-4) prepared as in (Zhang et al., 2015). The other half were placed in normal NGM plates (no-auxin control) for the indicated time. Worms were then washed one time with M9 and processed accordingly to future application. For ChIP and Hi-C, L2/L3 worms were incubated in 2% formaldehyde for 30 minutes, followed by quenching with glycine, one wash with M9 and two washes with PBS, PMSF and protease inhibitors. For RNA-seq, worms were stored in Trizol.

value: auxin


title: dpe2/phs1, Prior Period,2


title: TOP-1_AM05_1h_no-auxin_L2-L3_ext530_AKM318_input_AKM320_ChIP-seq

value: AM05 (top-1::degron::GFP)

value: no-auxin


title: dpe2/phs1, Recovery Period,2


title: AM12_2hours-auxin_L2-L3_RNA_rep1_AKM325_RNA-seq


title: TOP-1_AM05_1h_auxin_L2-L3_ext531_AKM319_input_AKM321_ChIP-seq


title: DPY-27_SS01_etoposide-12uM-60min_L2-L3_ext539_AKM337_input_AKM350_ChIP-seq

value: etoposide 12uM


title: AM11_2hours-auxin_L2-L3_RNA_rep1_AKM323_RNA-seq


title: Pcgf4-/-Pcgf2flfl_RA_TAM_rep2

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

institute: University of Oxford

description:
Pcgf2fl_nucRNASeq_48hRA_TAM_mm10_downsampledSpikeInInp_MERGED_FORWARD.bw
Pcgf2fl_nucRNASeq_48hRA_TAM_mm10_downsampledSpikeInInp_MERGED_MinusStrand.bw
Pcgf2fl_RA.NucRNAseq_spikenormalised_DESeq2.csv

data_processing:
Paired-end reads were aligned using Bowtie 2 (with “--very-fast”, “--no-mixed” and “--no-discordant” options) against the concatenated mm10 and dm6 rRNA genomic sequence (GenBank: BK000964.3 and M21017.1), to filter out reads mapping to rRNA fragments. All unmapped reads from the first step, were aligned against the genome sequence of concatenated mm10 and dm6 genomes using the STAR RNA-seq aligner (Dobin et al. 2012). To improve mapping of intronic sequences for nascent transcripts abundant in nuclear RNA-seq, reads which failed to map using STAR were aligned against the mm10+dm6 concatenated genome using Bowtie 2 (with “--sensitive-local”, “--no-mixed” and “ --no-discordant” options). Reads that were mapped more than once were discarded. PCR duplicates were removed using SAMTools.
To internally calibrate RNA-seq, we spiked-in a fixed number of Drosophila SG4 to each experimental sample. For data visualisation, mm10 reads were randomly subsampled using factors that reflected the total number of dm6 reads in each sample.
Read counts from biological quadruplicates were determined using custom scripts utilising SAMTools for a custom-built, non-redundant mm10 gene set. Briefly, mm10 refGene genes were filtered to remove very short genes with poor sequence mappability and highly similar transcripts which resulted in the final set of 20,633 genes. Raw mm10 reads prior to spike-in normalisation were used for read counts quantitation for differential expression analysis.
The final set of 20,633 genes were used for differential analysis using a custom R script adapting DESeq2 (Love et al., 2014) for spike-in calibrated RNA-seq data. To incorporate spike-in calibration into this analysis, read counts for the spike-in genome at a control set of intervals were supplied to calculate DESeq2 size factors which were then used for DESeq2 normalisation of raw mm10 read counts. A set of unique dm6 refGene genes was used for spike-in normalisation of cnRNA-seq. Prior to quantitation, spike-in reads were pre-normalised to accurately reflect the actual spike-in ratio. For a change to be called significant, we applied a threshold of p-adj < 0.05 and fold change > 1.5.
Genome_build: mm10, dm6
Supplementary_files_format_and_content: Stranded bigWig files were generated using genomeCoverageBed from BEDTools representing genome coverage of merged spike-in normalised biological replicates.
Supplementary_files_format_and_content: DESeq2 results tables for differential gene expression analysis containing normalised read counts, raw and shrunk log2-fold changes (LFC), and statistical significance levels for a non-redundant set of mm10 refGene genes.

organism:
Drosophila melanogaster
Mus musculus

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, tamocifen-treated, retinoic acid treated; Pcgf4-/-Pcgf2 fl/fl

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. ). Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech). For RA differentiation, 4x10^6 ES cells were allowed to attach to gelatinised 15cm dishes for 6-8 hours and treated with 1 µM retinoic acid (Sigma-Aldrich) in EC-10 medium (DMEM supplemented with 10% fetal bovine serum, L-Glutamine, beta-mercaptoethanol, non-essential amino acids and penicillin/streptomycin) for 48 hours.

extract_protocol:
2 x 10^7 mouse ESCs were mixed with 8 x 10^6 Drosophila SG4 cells in PBS. Nuclei were isolated in 1 ml HS Lysis buffer (50 mM KCl, 10 mM MgSO4.7H20, 5 mM HEPES, 0.05 % NP40 (IGEPAL CA630)), 1 mM PMSF, 3 mM DTT) for 1 min at room temperature. They were then recovered by centrifugation at 1000 × g for 5 min at 4°C, followed by a total of three washes with ice-cold RSB buffer (10 mM NaCl, 10 mM Tris (pH 8.0), 3 mM MgCl2). Nuclei integrity was assessed using 0.4% Trypan Blue staining (ThermoScientific). Next, nuclei were resuspended in 1 ml of TRIzol reagent (ThermoScientific) and RNA was extracted according to the manufacturer’s protocol, followed by treatment with the TURBO DNA-free Kit (ThermoScientific). Quality of RNA was assessed using 2100 Bioanalyzer RNA 6000 Pico kit (Agilent) and high-quality RNA samples were depleted of rRNA using the NEBNext rRNA Depletion kit (NEB).
RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA-seq kit (NEB) following manufacturer’s guidelines. RNA-seq were sequenced as 80 bp (Med13/13lflfl) or 40 bp (Pcgf4-/-Pcgf2flfl) paired-end reads on the Illumina NextSeq 500 platform in biological quadruplicates

treatment_protocol: To induce conditional removal of CDK-MED or cPRC1, cells were treated with 800 nM 4-hydroxytamoxifen (TAM, Sigma) for 96 hours (Med13/13l fl/fl) or 72h (Pcgf4-/-Pcgf2fl/fl). To induce differentiation of ES cells, cells were treated with 1 µM retinoic acid (RA, Sigma-Aldrich)

tag: tag

value: Pcgf4-/-Pcgf2 flfl

value: tamoxifen

tag: treatment time

tag: additional treatment

value: retinoic acid

tag: additional treatment time

tag: spike-in reference organism

value: Drosophila melanogaster

tag: spike-in cell line

tag: protocol

value: calibrated nuclear RNA-seq


title: dpe2/phs1, mature leaves,3

source_name: cells from Mature leaves and petioles

tag: cell type

value: cells from Mature leaves and petioles

value: mature leaves and petioles from dpe2/phs1

value: Retard Period (5weeks after germination)


title: Pcgf4-/-Pcgf2flfl_RA_UNT_rep4

description:
Pcgf2fl_nucRNASeq_48hRA_UNT_mm10_downsampledSpikeInInp_MERGED_FORWARD.bw
Pcgf2fl_nucRNASeq_48hRA_UNT_mm10_downsampledSpikeInInp_MERGED_MinusStrand.bw
Pcgf2fl_RA.NucRNAseq_spikenormalised_DESeq2.csv

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, untreated control, retinoic acid treated; Pcgf4-/-Pcgf2 fl/fl

tag: strain

value: untreated


title: BshPTB_C

city: Belle Mead

first: Bitha

last: Narayanan

state: New Jersey

address: 241 Berkley Ave

institute: Rutgers

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: B2.7 Jurkat cells

growth_protocol: Cells were cultured in RPMI media with 10% FBS

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

treatment_protocol: Cells were not treated

value: T cell lymphoma cell line


title: DshPTB_C

source_name: D1.1 Jurkat cells


title: Pcgf4-/-Pcgf2flfl_RA_TAM_rep4

tag: treatment


title: Group 3 innate lymphoid cells-KO rep1

tag: tissue

value: small intestine

value: innate lymphoid cells

value: ThPOK-deficient


title: BshPTB_B


title: dpe2/phs1, Recovery Period,1

value: cells of whole shoot

tag: genotype

value: whole shoot from dpe2/phs1 of 7 weeks

value: Recovery Period (7weeks after germination)


title: Pcgf4-/-Pcgf2flfl_RA_TAM_rep1


title: dpe2/phs1, mature leaves,2


title: Pcgf4-/-Pcgf2flfl_RA_TAM_rep3


title: DshPTB_B


title: dpe2/phs1, young leaves,3

source_name: cells from young leaves and petioles

value: cells from young leaves and petioles

value: young leaves and petioles from dpe2/phs1


title: dpe2/phs1, mature leaves,1


title: Group 3 innate lymphoid cells-WT rep1

value: Wild-type


title: BshCtrl_B


title: BshCtrl_C


title: Pcgf4-/-Pcgf2flfl_RA_UNT_rep1

value: Pcgf4-/-Pcgf2 flfl

value: retinoic acid


title: AM11_2hours-auxin_L2-L3_RNA_rep2_AKM331_RNA-seq

city: New York

tag: developmental stage

value: auxin


title: Pcgf4-/-Pcgf2flfl_ESC_TAM_rep3

description:
Pcgf2fl_nucRNASeq_ESC_TAM_mm10_downsampledSpikeInInp_MERGED_FORWARD.bw
Pcgf2fl_nucRNASeq_ESC_TAM_mm10_downsampledSpikeInInp_MERGED_MinusStrand.bw

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, tamoxifen-treated, Pcgf4-/-Pcgf2 fl/fl

value: tamoxifen

value: Drosophila melanogaster

value: calibrated nuclear RNA-seq


title: DshCtrl_C


title: Pcgf4-/-Pcgf2flfl_ESC_TAM_rep1


title: Pcgf4-/-Pcgf2flfl_RA_UNT_rep2

value: untreated


title: Pcgf4-/-Pcgf2flfl_ESC_TAM_rep2


title: Pcgf4-/-Pcgf2flfl_ESC_TAM_rep4


title: dpe2/phs1, young leaves,2

value: Retard Period (5weeks after germination)


title: DshCtrl_B

value: T cell lymphoma cell line


title: Pcgf4-/-Pcgf2flfl_RA_UNT_rep3


title: Pcgf4-/-Pcgf2flfl_ESC_UNT_rep3

description:
Pcgf2fl_nucRNASeq_ESC_UNT_mm10_downsampledSpikeInInp_MERGED_FORWARD.bw
Pcgf2fl_nucRNASeq_ESC_UNT_mm10_downsampledSpikeInInp_MERGED_MinusStrand.bw

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, untreated control, Pcgf4-/-Pcgf2 fl/fl


title: Pcgf4-/-Pcgf2flfl_ESC_UNT_rep2


title: dpe2/phs1, young leaves,1


title: K562, ABBS experiment (A.M. library prep)

city: Carlsbad

first: Benjamin

last: Delatte

address: 1914 Palomar Oaks Way STE 150

department: Advanced Research

institute: Active Motif

data_processing:
Raw reads (FastQ files) were aligned to human hg19 or E. coli K12 genomes using Bismark (https://github.com/FelixKrueger/Bismark) following the command line: $ bismark <genome path> -p 4 --parallel 6 -q --pbat -o <output folder> -1 read1.fastq.gz -2 read2.fastq.gz.
PCR duplicates were removed following these arguments: $ deduplicate_bismark -p --output_dir <output folder> -- bam <input bam file>
MAPQ filter of 20 was applied using samtools (https://github.com/samtools/samtools): $ samtools view -h -q 20 <input bam file> -o <output folder bam file>.
Methylated cytosines were extracted with Bismark Methylation Extractor following the following arguments: $ bismark_methylation_extractor --parallel 10 -p --no_overlap --ignore 7 -- ignore_r2 7 --ignore_3prime 5 --ignore_3prime_r2 5 -o <output folder> --report --bedGraph -- zero_based --cutoff 1 --CX --remove_spaces --cytosine_report --genome_folder <genome path> <input bam file>
bam files were sorted and indexed using samtools sort and samtools index
Bigwig coverage files were obtained with deeptools bamcoverage (https://github.com/deeptools/deepTools): $ bamCoverage -b <input bam file> -o <output folder bigwig file> --normalizeUsing RPKM --binSize 5 --numberOfProcessors 16
Genome_build: E. coli K12 or hg19
Supplementary_files_format_and_content: Bigwig (bw) files are RPKM-normalized
Supplementary_files_format_and_content: Methylation bedgraph files contain methylation percentages and coverage information

source_name: human erythroleukemic cell line

growth_protocol: Escherichia coli K12 cells were acquired from Neb (#E4104), MA and two clones were obtained by streaking an E. coli suspension on a LB agar plate, and further cultured in liquid LB containing no antibiotics, at 37C. Optical density was measured at 600nm every twenty minutes until bacteria reached a plateau phase, then the culture was quickly placed on ice and spun on a Sorvall centrifuge at 7500 RPM / 4C for 10 minutes, then washed twice with ice cold 1x PBS and aliquots were snap frozen in liquid nitrogen and kept at -80C for further genomic DNA extraction.  K562 cells were grown in RPMI-1640 supplemented with L-glutamine, 10% FBS and 1X penicillin G + streptomycin, at 37C / 5% CO2. Cells were then trypsinized and counted with a haemocytometer while viability was assessed with Trypan Blue staining. The culture was quickly placed on ice and spun on a Sorvall centrifuge at 3000 RPM / 4C for 5 minutes, then washed twice with ice cold 1x PBS and aliquots were snap frozen in liquid nitrogen and kept at -80C for further genomic DNA extraction.

extract_protocol:
Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen, Germany) following the manufacturer’s protocol.
3μg of E. coli or 10μg of K562 genomic DNA spiked with 1% of unmethylated Lambda DNA was bisulfite-converted with Zymo Lightning kit (Zymo Research, CA) following the manufacturer’s  instructions, then eluted in 2x10μl of Tris-HCl 10mM pH8.0 (of note, desulfonation was performed for 20mins, on column). An additional 15-minute sonication was achieved using PIXUL Multisample sonicator (Active Motif, CA) with the default settings. DNA was heated at 95C for 3 minutes then placed on ice and quantification was done using Nanodrop (Thermo Fisher Scientific, MA) while profiles were measured with RNA TapeStation (Agilent, CA) to ensure for proper sonication. Bacterial non-converted DNA was sonicated for 30 minutes using PIXUL Multisample sonicator with the default settings and DNA was further heated at 95C for 3 minutes and stored at -80C.  Second strand synthesis was performed as follow: 100ng of genomic DNA was diluted in Neb 1x NEBuffer 2, supplemented with 0.25mM dNTPs and 6.5μM (K562 cells) or 0.65μM (E. coli K12 cells) ABBS primers (NNNNNSuperG) or WGBS primers (NNNNNN) in 29 μl, then heated at 94C for 2 minutes and rapidly placed on ice for 3-5 minutes. One microliter of Neb Klenow exo minus (5 units/μl) was added to the reaction that was gradually heated from 4C to 37C at a rate of 0.1C/second. Samples were then incubated for 30 minutes at 37C and purified with 45μl of Ampure XP beads (Beckman Coulter, CA). DNA was eluted in 20μl Tris-HCl 10mM pH8.0 supplemented with 0.05% Tween-20 and quantified with Qubit 2.0 dsDNA HS kit (Thermo Fisher Scientific, MA).  Double stranded library preparation was performed either with Neb NEBNext® UltraTM II DNA Library Prep Kit for Illumina or Active Motif Next Gen DNA Library Kit, following manufacturers’ recommendations, with the exception that libraries amplification was performed using KAPA HiFi HotStart Real-Time Library Amp Kit (Roche, Switzerland). After a final purification using 0.75 volumes of Ampure XP beads, libraries were resuspended in 12μl of Tris-HCl 10mM pH8.0 supplemented with 0.05% Tween-20 and quantified with Qubit 2.0 dsDNA HS kit while profiles were measured with HS dsDNA TapeStation to calculate molarity

treatment_protocol: No cell treatment was applied.

value: Bisulfite

tag: primer used

value: ABBS

tag: library prep kit used

value: Active Motif


title: wild type, Prior Period,3

value: cells of whole shoot

value: whole shoot from Col-0 of 3 weeks

value: Prior Period (3 weeks after germination)


title: Pcgf4-/-Pcgf2flfl_ESC_UNT_rep1


title: wild type, Prior Period,2


title: Med1313lfl_RA_TAM_rep4

description:
nucRNAseq_MED13-13LcKO_RA_TAM_mm10_downsampleddm6tomm10RNA_MERGED_FORWARD.bw
nucRNAseq_MED13-13LcKO_RA_TAM_mm10_downsampleddm6tomm10RNA_MERGED_MinusStrand.bw
Med13fl_RA.NucRNAseq_spikenormalised_DESeq2.csv

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, tamoxifen-treated, retinoic acid treated; Med13/13l flfl

value: Med13;Med13l flfl


title: K562, ABBS experiment

value: NEB


title: K562, WGBS experiment

value: WGBS


title: wild type, Recovery Period,3

value: whole shoot from Col-0 of 7 weeks

value: Recovery Period (7weeks after germination)


title: Med1313lfl_RA_TAM_rep3

value: tamoxifen

value: retinoic acid


title: wild type, Prior Period,1


title: Med1313lfl_RA_TAM_rep2

value: Drosophila melanogaster

value: calibrated nuclear RNA-seq


title: Med1313lfl_RA_UNT_rep3

description:
nucRNAseq_MED13-13LcKO_RA_UNT_mm10_downsampleddm6tomm10RNA_MERGED_FORWARD.bw
nucRNAseq_MED13-13LcKO_RA_UNT_mm10_downsampleddm6tomm10RNA_MERGED_MinusStrand.bw
Med13fl_RA.NucRNAseq_spikenormalised_DESeq2.csv

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, untreated control, retinoic acid treated; Med13/13l flfl

value: untreated


title: Pcgf4-/-Pcgf2flfl_ESC_UNT_rep4

value: Pcgf4-/-Pcgf2 flfl


title: Med1313lfl_RA_UNT_rep4


title: Med1313lfl_RA_UNT_rep2


title: wild type, Recovery Period,1


title: Med1313lfl_ESC_TAM_rep4

description:
nucRNAseq_MED13-13LcKO_ESC_TAM_mm10_downsampleddm6tomm10RNA_MERGED_FORWARD.bw
nucRNAseq_MED13-13LcKO_ESC_TAM_mm10_downsampleddm6tomm10RNA_MERGED_MinusStrand.bw

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, tamoxifen-treated, Med13/13l flfl


title: MCF-7 cells - TBX2_Rep2

city: Belfast

last: Mullan

address: 97 Lisburn Road

department: PGJCCR

institute: Queen's University Belfast

data_processing:
Basecalls performed using RTA v2
FASTQ files were de-multiplexed on Sanger indexes and quality of sequencing confirmed with the FastQC tool.
Single-end FASTQ files were aligned to human genome hg38 primary assembly using Bowtie2 (end-to-end mode).
Aligned BAM files were filtered on a minimum MAPQ of 10 to retain unique alignments.
NarrowPeaks were called on BAM files of individual ChIP replicates vs matched input controls using MACS2 callpeak (tag extension size=250bp, keep-dup=auto). Peaks were then called on pooled replicates as before.
MACS2 output bedGraph files were converted to binary bigWig format for genome browser viewing of ChIP-enriched regions.
Reproducible peaks were classed as regions in pooled data overlapping at least 1bp with narrowPeaks called in each individual replicate.
Genome_build: hg38
Supplementary_files_format_and_content: Peak text files contain genomic coordinates of reproducible peaks and enrichment scores
Supplementary_files_format_and_content: BigWig files contain mapped read counts scaled to RPM/CPM

source_name: Homo sapiens MCF-7 cell line

growth_protocol: Purchased cell lines were authenticated from ATCC and mycoplasma-tested prior to conducting experiments. MCF7 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% foetal calf serum, 1mM sodium pyruvate, 50 mg/ml penicillin–streptomycin and 2mM L-glutamine (Life Technologies, Inc., Paisley, UK).

extract_protocol:
Briefly, 20 million cells were subjected to fixation with 16% formaldehyde prior to cytoplasmic and nuclear lysis. Nuclear lysates were sonicated for 33 cycles (30 sec on/30 sec off) and precleared with Dynabeads Protein G. Precleared lysates were incubated overnight with 6 micrograms of ChIP antibody, after which antibody-DNA complexes were captured onto Dynabeads Protein G for 4 hours. The beads were washed several times in a series of lysis buffers prior to elution and Proteinase K treatment. ChIP DNA was purified using a phenol chloroform isoamyl alcohol extraction method.
1ng of input or ChIP DNA were used to generate Illumina-compatible indexed libraries using a MicroPlex Library Preparation Kit v2 (Diagenode) following the manufacturer’s instructions. Libraries were size-selected to an average fragment size of 300-400bp. The ChIP library pool was sequenced with an Illumina Next Seq 500 High Output Kit for 75 cycles in single-end mode.

tag: antibody

value: TBX2 (abcam, ab33298)

tag: line

tag: Sex

value: female

tag: health state

value: breast cancer (adenocarcinoma)

tag: dev stage

value: adult

tag: age

value: 69 year

tag: biological replicate number


title: wild type, Recovery Period,2

value: cells of whole shoot

tag: time


title: MCF-7 cells - Input_Rep2


title: Med1313lfl_ESC_TAM_rep2

tag: tag

value: Med13;Med13l flfl

tag: treatment time

tag: additional treatment

tag: additional treatment time

tag: spike-in reference organism

tag: spike-in cell line

tag: protocol


title: wild type, mature leaves,2

tag: cell type

value: cells from Mature leaves and petioles

tag: genotype

tag: treatment

value: Mature leaves and petioles from Col-0

value: Retard Period (5weeks after germination)


title: Med1313lfl_ESC_TAM_rep3

tag: strain


title: Med1313lfl_RA_UNT_rep1


title: TPM3-NTRK1_S5_PDX

city: Worcester

first: Matthew

last: Hemming

state: MA

address: 364 Plantation Street

institute: UMass Medical School

data_processing:
RNA-seq data were aligned using STAR with expression quantification using Cufflinks to generate gene expression values in FPKM units.
Genome_build: hg19
Supplementary_files_format_and_content: Processed RNA-seq data files with FPKM are in text format

molecule: polyA RNA

source_name: NTRK PDX

growth_protocol: Cells were grown in DMEM/F12 containing 10% FBS, 2 mM L- glutamine, 100 mg/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
Total RNA was isolated using an RNeasy Plus Kit (Qiagen). RNA was normalized to cell count, then ERCC RNA Spike-In Control (Ambion) was added to allow for cell count normalization of gene expression changes.
Libraries for Illumina NextSeq 500 sequencing were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) and equimolar multiplexed libraries were sequenced with single-end 75 bp reads.

tag: sample type

value: xenograph


title: Med1313lfl_ESC_UNT_rep4

description:
nucRNAseq_MED13-13LcKO_ESC_UNT_mm10_downsampleddm6tomm10RNA_MERGED_FORWARD.bw
nucRNAseq_MED13-13LcKO_ESC_UNT_mm10_downsampleddm6tomm10RNA_MERGED_MinusStrand.bw

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, untreated control, Med13/13l flfl


title: wild type, mature leaves,3


title: Med1313lfl_RA_TAM_rep1

value: tamoxifen


title: Med1313lfl_ESC_TAM_rep1


title: Med1313lfl_ESC_UNT_rep3


title: Med1313lfl_ESC_UNT_rep1


title: Med1313lfl_ESC_UNT_rep2


title: wild type, young leaves,3

value: cells from young leaves and petioles

value: young leaves and petioles from wild type Col-0


title: MCF-7 cells - TBX2_Rep1

tag: antibody

tag: line

tag: Sex

tag: health state


title: TPM3-NTRK1_S5

source_name: NTRK tumor

value: tumor


title: Med1313lfl_NChIP_Input_TAM_rep3

description: input for H3K27me3 ChIPs in Med13:Med13lflfl

data_processing:
For cChIP-seq, Bowtie2 was used to align paired-end reads to the concatenated mouse and spike-in genome sequences (mm10+dm6 for native cChIP-seq for histone modifications; mm10+hg19 for cross-linked cChIP-seq) with the “--no-mixed” and “--no-discordant” options. Non-uniquely mapping reads were discarded, and PCR duplicates were removed with Sambamba.
For visualization of cChIP-seq, the data were internally calibrated using dm6 or hg19 spike-in as described previously (Fursova et al. 2019). Briefly, uniquely aligned mm10 reads were randomly subsampled based on the total number of spike-in (dm6 or hg19) reads in each sample. To account for variations in the spike-in cell mixing, we used the ratio of spike-in/mouse total read counts in the corresponding Input samples to correct the subsampling factors. After normalisation, read coverages across genomic regions of interest were compared for individual biological replicates using multiBamSummary and plotCorrelation from deepTools. For each experimental condition, biological replicates correlated well (Pearson correlation coefficient > 0.9) and were merged for downstream analysis.
Genome_build: mm10; dm6; hg19
Supplementary_files_format_and_content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2.

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, tamoxifen treated, Med13/13l flfl, input

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. HEK293T celles were grown in EC-10 medium (DMEM supplemented with 10% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.4 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor). Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).

extract_protocol:
For cross-linked ChIP, 50x10^6 ES cells were fixed for 45min with with 2mM DSG (ThermoFisher scientific) in PBS and 12.5 min with 1% formaldehyde (methanol-free, ThermoFisher scientific). Reactions were quenched by the addition of glycine to a final concentration of 125 µM and the fixed cells were washed in ice-cold 1xPBS and snap frozen in liquid nitrogen. 50x10^6 HEK293T cells were fixed as above, snap frozen in 2x106 aliquots, and stored at -80°C until further use. For calibrated ChIPseq, 2x10^6 HEK293T cells were resuspended in 1ml ice-cold lysis buffer (50mM HEPES pH 7.9, 140mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100) and added to 50x10^6 fixed ESCs, resuspended in 9ml lysis buffer. The cell suspension was incubated for 10 min at 4°C. The released nuclei were then washed (10mM Tris-HCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) for 10 min at 4°C. The chromatin pellet was resuspended in 1mL of ice-cold sonication buffer (10mM Tris-HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine) and sonicated for 25 min using a BioRuptor Pico sonicator (Diagenode), shearing genomic DNA to produce fragments between 300bp and 1kb. Following sonication, Triton X-100 was added to a final concentration of 1%. Two hundred and fifty µg chromatin diluted 10-fold in ChIP dilution buffer (1% Triton-X100, 1mM EDTA, 20mM Tris-HCl (pH 8.0), 150mM NaCl) was used per IP. Three reactions were set up per condition to allow for maximal DNA recovery suitable for library preparation. Chromatin was precleared with protein A Dynabeads blocked with 0.2 mg/ml BSA and 50 µg/ml yeast tRNA and incubated with the respective antibodies overnight at 4°C. Antibody-bound chromatin was purified using blocked protein A Dynabeads for 3 hours at 4°C. ChIP washes were performed as described in Farcas et al 2012. ChIP DNA was eluted in ChIP elution buffer (1% SDS, 100mM NaHCO3) and reversed cross-linked overnight at 65°C with 200mM NaCl and RNase A (Sigma). The reverse cross-linked samples were treated with 20 μg/ml Proteinase K and purified using ChIP DNA Clean and Concentrator kit (Zymo research). The three reactions per condition were pooled at this stage. For each sample, corresponding Input DNA was also reverse cross-linked and purified. The efficiency of the ChIP experiments was confirmed by quantitative PCR. Prior to library preparation, 5-10ng ChIP material was diluted to 50ul in TLE buffer (10mM Tris-HCl pH8.0, 0.1mM EDTA) and sonicated with Bioruptor Pico sonicator for 17 min (30 sec on/off). The antibodies used for ChIPseq experiments were rabbit polyclonal anti-CDK8 (A302-500A, Bethyl laboratories, 2.5μl), rabbit monoclonal anti-RING1B (5694, Cell signaling, 3 μl), rabbit polyclonal anti-PCGF2 (sc-10744, Santa Cruz, 3ul), rabbit monoclonal anti-T7-Tag (D9E1X) (13246, Cell signaling, 3ul). The antibodies used for ChIP-qPCR for TetO targeting experiments were rabbit polyclonal anti-FS2 (produced in house, 59, 3ul), polyclonal anti-MED12 (A300-774A, Bethyl laboratories, 3ul), polyclonal anti-MED1 (A300-793A, Bethyl laboratories, 3ul), polyclonal anti-CCNC (A301-989A, Bethyl laboratories, 3ul). For native ChIP, 50x10^6 ESCs were mixed with 20x10^6 SG4 Drosophila cells and washed with 1x PBS prior to chromatin isolation. Nuclei were released in ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 3mM MgCl2, 0.1% NP40), washed and resuspended in 1ml ice cold digestion buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 0.25M sucrose, 3mM CaCl2, 1x cOmplete protease inhibitor cocktail (Roche)). Chromatin was digested with 200mM MNase (ThermoFisher scientific) for 5 min at 37°C and the reaction was stopped by the addition of 4mM EDTA pH 8.0. The samples were centrifuged at 1500g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300μl of nucleosome release buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 0.2mM EDTA, 1x protease inhibitor cocktail (Roche)) at 4°C for 1 h, passed five times through a 27G needle using a 1mL syringe, and spun at 1500g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 sample from above. Digestion to mostly mononucleosomes was confirmed on a 1.5% agarose gel. The prepared native chromatin was aliquot, snap frozen in liquid nitrogen and stored at -80°C until further use. ChIPs were performed as described in Fursova et al 2019, using 5ul of H3K27me3 antibody prepared in-house.
cChIP-seq libraries for both ChIP and Input samples were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries were analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR quantification using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads in biological triplicate or quadruplicate on Illumina NextSeq 500 platform.

treatment_protocol: Med13/13lfl/fl ERT2-Cre ESCs were treated with 800nM 4-hydroxytamoxifen (Sigma) for 96 hours. Pcgf4-/-/Pcgf2fl/fl ERT2-Cre ESCs were treated with 800nM 4-hydroxytamoxifen (Sigma) for 72 hours. For RA differentiation, ESCs were treated with 1µM retinoic acid (Sigma-Aldrich) for 48h.

tag: cell line

tag: replicate

value: Drosophila melanogster

tag: type of chip

value: native

tag: ChIP

value: rabbit polyclonal anti-H3K27me3, in-house


title: TPM3-NTRK1_S3_Cell

source_name: NTRK Cell Line

value: cell line


title: TPM3-NTRK1_S3_PDX


title: wild type, young leaves,1

tag: time


title: Med1313lfl_NChIP_Input_TAM_rep2

tag: treatment time

tag: additional treatment

tag: additional treatment time

tag: spike-in reference organism


title: Med1313lfl_NChIP_Input_TAM_rep1

tag: spike-in cell line


title: TPM3-NTRK1_S3


title: Med1313lfl_NChIP_Input_UNT_rep3

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, untreated control, Med13/13l flfl, input

tag: treatment

value: untreated


title: Med1313lfl_NChIP_Input_UNT_rep2

tag: strain


title: H37_MYC+BCL2+

first: Michal

middle: Marek

last: Hoppe

address: 14 Medical Dr

department: Cancer Science Institute of Singapore

institute: National University of Singapore

description:
primary tonsil B-cells with MYC, BCL2 overexpression
H37

data_processing:
Raw read counts are provided by HTSeq-count 0.13.5
Mapping is using STAR
Gene expression quantification is based on featureCounts
raw files were processed via the publicly available portal: https://csibioinfo.nus.edu.sg/
Assembly: hg38
Supplementary files format and content: raw counts

source_name: B-cells primary tonsil tissue

growth_protocol: Fresh, tonsil tissue was sourced from the Addenbrooke’s ENT Department, Cambridge with written informed consent of the patient/parent/guardian and processed directly to preserve viability. Ethical approval for the use of human tissue was granted by the Health Research Authority Cambridgeshire Research Ethics Committee (REC no. 07/MRE05/44). GC B cells were purified using the human B cell negative selection isolation Kit II (MACS, Miltenyi Biotec) as per the manufacturer’s instructions. The protocol was modified to include negative selection antibodies IgD-BIOT (IADB6; SouthernBiotech 9030- 08, 1:100) and CD44-BIOT (F10-44-2; SouthernBiotech 9400-08, 1:100) to remove naïve and memory B cells. Cells were stained for CD38 (HB7; BioLegend #12- 0388-42, 1:500), CD20 (2H7; BioLegend #17-0209-41, 1:500), CD19 (HIB19; BioLegend #302223, 1:500), and CD10 (97C5; MiltenyiBiotec, 130-093-450, 1:500) to confirm enrichment of GC B cells. B cell genomic DNA was screened for EBV status using a quantitative real-time PCR (qPCR) assay and cells from EBV-positive patients were discarded. GC B cells were plated onto irradiated YK6-CD40lg-IL21 and split every 2–3 days. Fresh YK6-CD40lg-IL21 cells (irradiated 30 Gy) were added with each split. Primary human GC B cells were cultured in Advanced Roswell Park Memorial Institute medium (Advanced RPMI-1640, Invitrogen, Carlsbad, CA) with GlutaMAX containing 20% FBS, 100 IU/ml penicillin, and 100 µg/ml streptomycin and kept at 37 °C in a humidified incubator (5% CO2 and 95% atmosphere). For more details see Caeser et al. 2019 Nat Commun.

extract_protocol:
TRIzol extraction
250~300 bp insert cDNA library (Eukaryotic mRNA)

treatment_protocol: MYC, BCL2, BCL6 were cloned into MSCV-based vectors using synthetic double-stranded DNA and Gibson Assembly. For overexpression of multiple human genes, CDS sequences were cloned into the MSCV-IRES-huDC2 vector (kind gift of Dr Martin Turner, the Babraham Institute, UK) with the t2A peptides linking genes, such as BCL6-t2A-BCL2, or MYC-t2A-BCL2. Retroviral packaging plasmids pHIT60 (kind gift of Dr. Louis Staudt, National Cancer Institute, USA) and GaLV WT were used as follows: 1 μg pHIT60 (gag-pol), 1 μg GaLV WT (envelope), and 4 μg of a retroviral construct was used to transfect each 10 cm2 dish of HEK-293T, after mixing with 1 ml of Opti-MEM media (Invitrogen) and 18 μl of TransIT-293 (Mirus). The packaging line Lenti-X 293T Cell Line (Clontech Laboratories) was used for all transfections. After 36–48 h, the virus supernatant was filtered through a 0.45 μM filter. If needed, media was replenished and harvested again at 16 h later. For retroviral/lentiviral transduction, 1–2 × 106 target cells were resuspended with viral supernatant and infected by centrifugation (1500 × g, 90 min at 32 °C) with the addition of 10 μg/ml Polybrene (INSIGHT Biotechnology) and 25 μM HEPES (ThermoFisher) in 12- or 24-well plates. Viral supernatant was replaced with fresh media immediately after centrifugation for retroviral infection. Cells were maintained at 37 °C with 5% CO2 for 2–4 days before analyzing by FACS.

tag: tissue

value: primary tonsil

tag: cell type

value: B cells

tag: overexpression


title: ETV6-NTRK3

tag: sample type


title: MCF-7 cells - Input_Rep1

tag: antibody

tag: line

tag: Sex

value: female

tag: health state

value: breast cancer (adenocarcinoma)

tag: dev stage

value: adult

tag: age

value: 69 year

tag: biological replicate number