title: PDAC KrasG12D cell line sgUsp15 Olaparib Biol rep2 tech rep2

status: Public on Mar 31 2024

type: SRA

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Ave, Room 1080

country: Canada

institute: Lunenfeld- Tanenbaum Research Institute

library_source: transcriptomic

data_processing:
Reads were aligned to mm10 using Hisat2 (2.1.0)
Raw read counts obtained from bam files using featureCounts and mm10 annotation file from ensembl (Mus_musculus.GRCm38.94.gtf)

molecule: total RNA

organism: Mus musculus

source_name: PDAC KrasG12D cell line

growth_protocol: Cells were cutlured in DMEMsupplemented with 10% Fetal bovine serum and 1% Pencillin-Streptomycin antibiotic solution

extract_protocol:
RNA was extracted using Zymoresearch RNA extraction kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with DMSO as a control or with 3uM of Olaparib for 12 hours

tag: cell line

value: PDAC KrasG12D cell line

tag: cell type

value: Epithelial

tag: genotype

value: pdx1-cre KrasG12D sgUsp15

tag: treatment

value: 3uM Olaparib


title: PDAC KrasG12D cell line sgScaf1 DMSO Biol rep2 tech rep2

value: pdx1-cre KrasG12D sgScaf1

value: DMSO


title: PDAC KrasG12D cell line sgScaf1 DMSO Biol rep1 tech rep1


title: PDAC KrasG12D cell line sgLUC DMSO biol rep2

value: pdx1-cre KrasG12D sg Luc


title: PDAC KrasG12D cell line sgScaf1DMSO Biol rep1 tech rep2


title: PDAC KrasG12D cell line sgLUC DMSO biol rep1


title: PDAC KrasG12D cell line sgUsp15 DMSO Biol rep2 tech rep2


title: PDAC KrasG12D cell line sgUsp15 Olaparib Biol rep1 tech rep1


title: PDAC KrasG12D cell line sgLUC Olaparib Biol rep1


title: PDAC KrasG12D cell line sgUsp15  DMSO Biol rep1 tech rep2


title: PDAC KrasG12D cell line sgUsp15  DMSO Biol rep1 tech rep1


title: PDAC KrasG12D cell line sgScaf1 Olaparib Biol rep2 tech rep1


title: HuH-7 cells, siFOXA1-2, replicate 1

city: Tokyo

first: Kiyoshi

last: Yamaguchi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Clinical Genome Research

country: Japan

institute: The University of Tokyo

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.33).
Trimmed sequence reads were aligned to human genome (hg38) using STAR aligner (v2.7.3a).
Raw gene counts from the read alignments were obtained using RSEM (v1.3.3).
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include TPM and FPKM values for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Liver

growth_protocol: HuH-7 cells were maintained in Dulbecco's Modified Eagle Medium, supplemented with 10% fetal bovine serum (Biosera) and antibiotics (Fujifilm Wako Pure Chemical).

extract_protocol:
RNA was extracted from the cells using RNeasy Plus Mini kit (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to manufacturer's instructions.
2 × 100 bp PE

treatment_protocol: The cells were transfected with 10 nM of siRNA using Lipofectamine RNAiMAX (Thermo Fisher Scientific) and harvested after 48 hours of incubation.

tag: tissue

value: Liver

value: Hepatocellular carcinoma

value: FOXA1-2 siRNA


title: PDAC KrasG12D cell line sgScaf1 Olaparib Biol rep2 tech rep2


title: PDAC KrasG12D cell line sgUsp15 DMSO Biol rep2 tech rep1


title: PDAC KrasG12D cell line sgScaf1 Olaparib Biol rep1 tech rep1


title: PDAC KrasG12D cell line sgScaf1 DMSO Biol rep2 tech rep1


title: HuH-7 cells, siFOXA1-2, replicate 2


title: HuH-7 cells, siFOXA1-2, replicate 3


title: PDAC KrasG12D cell line sgUsp15 Olaparib Biol rep1 tech rep2


title: PDAC KrasG12D cell line sgUsp15 Olaparib Biol rep2 tech rep1


title: HuH-7 cells, siFOXA1-1, replicate 2

value: FOXA1-1 siRNA


title: HuH-7 cells, siFOXA1-1, replicate 1


title: HuH-7 cells, siCEBPA-2, replicate 1

value: CEBPA-2 siRNA


title: HuH-7 cells, siFOXA1-1, replicate 3


title: HuH-7 cells, siCEBPA-1, replicate 2

value: CEBPA-1 siRNA


title: HuH-7 cells, siCEBPA-1, replicate 3


title: HuH-7 cells, siCEBPA-2, replicate 3


title: HuH-7 cells, siCEBPA-2, replicate 2


title: HuH-7 cells, siControl, replicate 1

value: Control siRNA


title: HuH-7 cells, siControl, replicate 3


title: HuH-7 cells, CEBPA

library_source: genomic

data_processing:
ChIP-seq reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.33).
Trimmed reads were aligned to the UCSC GRCh38 genome using Bowtie2 (v2.4.1).
Peak calling was performed using MACS2 (v3.6) with the significance cut-off q-value <=0.05.
The bigWig files were generated using the deepTools (v1.5.12). The narrowPeak files were generated using MACS2 with default settings.
Assembly: GRCh38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

extract_protocol:
HuH-7 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and 0.1 M glycine was added to quench the formaldehyde. Chromatin extracts were sheared by micrococcal nuclease digestion (New England Biolabs), and protein-DNA complexes were immunoprecipitated with 5 μg of anti-CEBPA (PA5-77911, Thermo Fisher Scientific) or anti-FOXA1 antibody (17-10267, Merck) bound to Dynabeads Protein G (Thermo Fisher Scientific).
ChIP-seq libraries were prepared using an NEBNext Ultra II DNA Library Prep kit (New England Biolabs) according to manufacturer's instructions. 1 ng of DNA was used for the construction of sequencing libraries.
2 × 150 bp

tag: chip antibody

value: CEBPA(Thermo Fisher Scientific, PA5-77911)


title: HuH-7 cells, siCEBPA-1, replicate 1


title: MCF-7 treated with anti-mir-6501-3p B

city: Brighton

first: Leandro

last: Castellano

address: Falmer, JMS Building

country: United Kingdom

institute: University of Sussex

description:
anti-mir-6501-3p B
MCF7 mir6501-5p B
normalized_counts_MCF-7_miR-6501-3p_+_control.csv

data_processing:
normalized counts generated using DESeq2
Supplementary files format and content: tab-delimited text files with normalized counts

source_name: Breast Cancer

growth_protocol: MCF-7 and HCC1395 cells were cultured in DMEM supplemented with 10%FCS and 1%Pen-Sprep-Glutamine.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions (TRI Reagent, Sigma).
Libraries were prepared with QuantSeq 3' mRNA-Seq Library Prep Kit.
QuantSeq 3' mRNA-Seq

treatment_protocol: Cells were treated with the CRISPR GecKO library for CRISPR screen and with miRNA inhibitors or non-targeting control for QuantSeq 3' mRNA sequencing

value: Breast Cancer

value: ER+ breast cancer


title: MCF-7 treated with anti-mir-6501-3p A

description:
anti-mir-6501-3p A
MCF7 mir6501-5p A
normalized_counts_MCF-7_miR-6501-3p_+_control.csv


title: HuH-7 cells, FOXA1


title: HuH-7 cells, siControl, replicate 2


title: MCF-7 treated with anti-mir-4787-3p A

description:
anti-mir-4787-3p A
MCF7 mir4787-3p A
normalized_counts_MCF-7_miR-4787-3p_+_control.csv


title: HCC1395 treated with anti-mir-4787-3p B

description:
anti-mir-4787-3p B
HCC1395 mir4787-3p B
normalized_counts_HCC1395_miR-4787-3p_+_control.csv

value: triple-negative breast cancer


title: HuH-7 cells, Input


title: PDAC KrasG12D cell line sgScaf1 Olaparib Biol rep1 tech rep2

value: PDAC KrasG12D cell line

value: Epithelial


title: MCF-7 treated with anti-mir-4787-3p B

description:
anti-mir-4787-3p B
MCF7 mir4787-3p B
normalized_counts_MCF-7_miR-4787-3p_+_control.csv


title: HCC1395 treated with anti-mir-4787-3p A

description:
anti-mir-4787-3p A
HCC1395 mir4787-3p A
normalized_counts_HCC1395_miR-4787-3p_+_control.csv


title: MCF-7 treated with anti-mir-301-3p B

description:
anti-mir-301a-3p B
MCF7 mir301-3p B
normalized_counts_MCF-7_miR-310a-3p_+_control.csv


title: MCF-7 treated with anti-mir-301-3p A

description:
anti-mir-301a-3p A
MCF7 mir301-3p A
normalized_counts_MCF-7_miR-310a-3p_+_control.csv


title: HCC1395 treated with anti-mir-4446-3p B

description:
anti-mir-4446-3p B
HCC1395 mir4446-3p B
normalized_counts_HCC1395_miR-4446-3p_+_control.csv


title: HCC1395 treated with anti-mir-4446-3p A

description:
anti-mir-4446-3p A
HCC1395 mir4446-3p A
normalized_counts_HCC1395_miR-4446-3p_+_control.csv


title: PDAC KrasG12D cell line sgLUC Olaparib Biol rep2

value: 3uM Olaparib


title: HCC1395 treated with anti-mir-301-3p B

description:
anti-mir-301a-3p B
HCC1395 mir301-3p B
normalized_counts_HCC1395_miR-310a-3p_+_control.csv


title: MCF-7 treated with anti-mir-1468-5p B

description:
anti-mir-1468-5p B
MCF7 mir1468-5p B
normalized_counts_MCF-7_miR-1468-5p_+_control.csv


title: HCC1395 treated with anti-mir-301-3p A

description:
anti-mir-301a-3p A
HCC1395 mir301-3p A
normalized_counts_HCC1395_miR-310a-3p_+_control.csv


title: HCC1395 treated with anti-mir-1468-5p A

description:
anti-mir-1468-5p A
HCC1395 mir1468-5p A
normalized_counts_HCC1395_miR-1468-5p_+_control.csv


title: HCC1395 treated with anti-miR-483-3p A

description:
anti-miR-483-3p A
HCC1395 mir483-3p A
normalized_counts_HCC1395_miR-483-3p_+_control.csv


title: MCF-7 treated with anti-miR-483-3p A

description:
anti-miR-483-3p A
MCF7 mir483-3p A
normalized_counts_MCF-7_miR-483-3p_+_control.csv


title: HCC1395 growth in 3D for 3 weeks rep1

data_processing:
tab-delimited text files with raw count -values obtained with MAGeCK
Supplementary files format and content: tab-delimited text files with raw count -values
Library strategy: CRISPR screen

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions (TRI Reagent, Sigma).
Libraries were prepared accordingly to Joung J, Nat Protoc, 2017.
CRISPR screen gRNA library

treatment_protocol: Cells were infected with the CRISPR GecKO library for CRISPR screen

value: Infection with CRISPR GecKO Library

tag: culture

value: growth in 3D for 3 weeks


title: HCC1395 treated with anti-mir-1468-5p B

description:
anti-mir-1468-5p B
HCC1395 mir1468-5p B
normalized_counts_HCC1395_miR-1468-5p_+_control.csv


title: HCC1395 treated with anti-miR-483-3p B

description:
anti-miR-483-3p B
HCC1395 mir483-3p B
normalized_counts_HCC1395_miR-483-3p_+_control.csv


title: MCF-7 Time 0 growth in 2D rep1

value: Time 0 growth in 2D


title: MCF-7 treated with anti-miRNA control A

description:
anti-miRNA control A (MCF-7)
MCF7 control A

value: anti-miRNA control


title: MCF-7 growth in 2D for 3 weeks rep1

value: growth in 2D for 3 weeks


title: MCF-7 growth in 3D for 3 weeks rep1


title: MCF-7 treated with anti-miR-483-3p B

description:
anti-miR-483-3p B
MCF7 mir483-3p B
normalized_counts_MCF-7_miR-483-3p_+_control.csv


title: MCF-7 treated with anti-miRNA control B

description:
anti-miRNA control B (MCF-7)
MCF7 control B


title: HCC1395 Time 0 growth in 2D rep1


title: HCC1395 treated with anti-miRNA control B

description:
anti-miRNA control B (HCC1395)
HCC1395 control B


title: HCC1395 treated with anti-miRNA control A

description:
anti-miRNA control A (HCC1395)
HCC1395 control A


title: HCC1395 growth in 2D for 3 weeks rep1


title: MCF-7 treated with anti-mir-1468-5p A

description:
anti-mir-1468-5p A
MCF7 mir1468-5p A
normalized_counts_MCF-7_miR-1468-5p_+_control.csv


title: LTS (long-term survival) glioblastoma FFPE sample 19

type: genomic

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iSCAN using standard recommended Illumina scanner setting

data_processing: Data loading with method minfi of function champ.load

label: Cy5 and Cy3

source_name: Glioblastoma FFPE tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tumor sample using MagPurix according to standard instructions for automatic extraction of genomic DNA

tag: Sex

value: F

tag: age at diagnosis (years)

tag: kps

tag: overall survival (months)

tag: last follow-up

value: Alive

tag: tumor localization

value: Frontal

tag: tumor side

value: Right


title: LTS (long-term survival) glioblastoma FFPE sample 24

value: Dead

value: Parietal

value: Left


title: LTS (long-term survival) glioblastoma FFPE sample 18

value: M

value: Temporal


title: LTS (long-term survival) glioblastoma FFPE sample 22


title: LTS (long-term survival) glioblastoma FFPE sample 13


title: LTS (long-term survival) glioblastoma FFPE sample 21


title: LTS (long-term survival) glioblastoma FFPE sample 14


title: LTS (long-term survival) glioblastoma FFPE sample 16

value: Fronto-parietal


title: LTS (long-term survival) glioblastoma FFPE sample 27

value: Parieto-occipital


title: LTS (long-term survival) glioblastoma FFPE sample 25


title: LTS (long-term survival) glioblastoma FFPE sample 15


title: LTS (long-term survival) glioblastoma FFPE sample 20


title: LTS (long-term survival) glioblastoma FFPE sample 6


title: LTS (long-term survival) glioblastoma FFPE sample 17


title: LTS (long-term survival) glioblastoma FFPE sample 26

value: Fronto-temporal


title: LTS (long-term survival) glioblastoma FFPE sample 4


title: LTS (long-term survival) glioblastoma FFPE sample 7


title: LTS (long-term survival) glioblastoma FFPE sample 3


title: LTS (long-term survival) glioblastoma FFPE sample 8


title: LTS (long-term survival) glioblastoma FFPE sample 10


title: LTS (long-term survival) glioblastoma FFPE sample 11

value: Occipital


title: LTS (long-term survival) glioblastoma FFPE sample 9


title: LTS (long-term survival) glioblastoma FFPE sample 5


title: LTS (long-term survival) glioblastoma FFPE sample 12


title: LTS (long-term survival) glioblastoma FFPE sample 2


title: Standard survival (control) glioblastoma FFPE sample 24


title: LTS (long-term survival) glioblastoma FFPE sample 1


title: N02_MOLM1_DMSO_4h_B

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

institute: ICGEB

description:
DMSO
Bone marrow derived cell line EVI1High MOLM1 was treated with DMSO with concetration equal to 1 microM for 4h, replica B

data_processing:
The raw sequence files were quality-controlled using FastQC (v 1.3) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, accessed in May 2020).
Transcripts were aligned using the STAR package (v2.7.1a) and quantified using the “quantMode GeneCounts” function with ENSEMBL annotation and the human genome version GRCh38 as a reference.
Read counts generated by STAR were analyzed using the DESeq2 R package to detect differentially expressed genes (DEGs) with an adjusted P value (Adj.P) less than 0.05.
Assembly: human genome version GRCh38 with ENSEMBL annotation from Homo_sapiens.GRCh38.90.gtf model
Supplementary files format and content: Star count matrix file

source_name: Bone marrow

extract_protocol:
RNA was subjected to polyA selection using magnetic oligo-dT beads (Thermo Fisher Scientific, #61002). A 94 °C-incubation for 4 min partially fragmented polyA RNA. Both actinomycin-D (during the first-strand cDNA synthesis) and dUTP (during the second-strand synthesis) were used to keep the strand information.
PolyA-enriched, strand-specific RNA libraries were generated with the TruSeq mRNA stranded sample preparation kit (Illumina, San Diego, CA, USA, #20020594) starting from 1 µg of RNA from each sample. RNA was subjected to polyA selection using magnetic oligo-dT beads (Thermo Fisher Scientific, #61002). A 94 °C-incubation for 4 min partially fragmented polyA RNA. Both actinomycin-D (during the first-strand cDNA synthesis) and dUTP (during the second-strand synthesis) were used to keep the strand information. The libraries were end-repaired and adenylated before being ligated with Y-shape single-indexed adapters and amplified by 11 PCR cycles. The last purification step was performed with Ampure XP beads (Beckman Coulter, #A63882) at 0.8x to remove all adapter dimers. Each library was quantified and quality-controlled using a Qubit 4 fluorometer (Thermo Fisher Scientific) and LabChip GX (Perkin Elmer, Waltham, MA, USA).
The adaptor-tagged pool of libraries was loaded onto Illumina Hiseq2500 rapid-run flow cells (SR100 chemistry) for cluster generation and deep sequencing.

treatment_protocol: UCSD/AML1 and MOLM1 were treated for 16 hr of treatment with AR-42 (0.5 μM and 0.8 μM, respectively) or entinostat (2 μM and 4 μM, respectively).

value: Bone marrow

value: Bone marrow derived cell line

value: DMSO

tag: time point

tag: replicate

value: B

tag: concentration

value: 1 microM


title: N03_MOLM1_DMSO_4h_C

description:
DMSO
Bone marrow derived cell line EVI1High MOLM1 was treated with DMSO with concetration equal to 1 microM for 4h, replica C

tag: cell line

value: C


title: N05_MOLM1_AR42_08_4h_B

description:
AR42
Bone marrow derived cell line EVI1High MOLM1 was treated with AR42 with concetration equal to 0.8microM for 4h, replica B

tag: cell type


title: N01_MOLM1_DMSO_4h_A

description:
DMSO
Bone marrow derived cell line EVI1High MOLM1 was treated with DMSO with concetration equal to 1 microM for 4h, replica A

tag: genotype

value: A


title: N06_MOLM1_AR42_08_4h_C

description:
AR42
Bone marrow derived cell line EVI1High MOLM1 was treated with AR42 with concetration equal to 0.8microM for 4h, replica C

tag: treatment


title: LTS (long-term survival) glioblastoma FFPE sample 23

value: F

value: Alive


title: N08_MOLM1_ENTI_4_4h_B

description:
entinostat
Bone marrow derived cell line EVI1High MOLM1 was treated with entinostat with concetration equal to 4microM for 4h, replica B

tag: tissue


title: N04_MOLM1_AR42_08_4h_A

description:
AR42
Bone marrow derived cell line EVI1High MOLM1 was treated with AR42 with concetration equal to 0.8microM for 4h, replica A


title: Aragene-0882

type: RNA

city: tokyo

first: Kyoko

last: Ohashi-Ito

address: 7-3-1 hongo bunkyo-ku

department: biological sciences

institute: the university of tokyo

description: Estrogen-inducible VND1-GFP transformed cells treated without estrogen for 24h

hyb_protocol: Hybridization, washing, staining procedures were run on Fluidics Station 450 (Affymetrix) with GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G.

data_processing: Data procession was performed with Expression Console Version 1.3 (Affymetrix).

label: biotin

organism: Arabidopsis thaliana

source_name: VND1 culture cell, 24h, uninduced

label_protocol: Sense-strand DNA target preparation was performed in combination with Ambion WT Expression Kit (Affymetrix) and GeneChip WT Terminal Labeling Kit and Controls Kit (Affymetrix)

growth_protocol: Cell suspension was cultured on a rotary shaker at 124 rpm at 23°C in the dark.

extract_protocol: Total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN)

treatment_protocol: Cultured cells were treated with/without 5 μM estrogen for 24h

value: cultured cell suspension

value: estrogen-inducible VND1-GFP transformed

tag: stimulation

value: without estrogen for 24h


title: Standard survival (control) glioblastoma FFPE sample 23

value: Dead

value: Left


title: Aragene-0873

description: Estrogen-inducible VND1-GFP transformed cells treated with estrogen for 24h

source_name: VND1 culture cell, 24h, induced

value: with estrogen for 24h


title: Aragene-0885


title: Aragene-0872


title: N07_MOLM1_ENTI_4_4h_A

description:
entinostat
Bone marrow derived cell line EVI1High MOLM1 was treated with entinostat with concetration equal to 4microM for 4h, replica A


title: N09_MOLM1_ENTI_4_4h_C

description:
entinostat
Bone marrow derived cell line EVI1High MOLM1 was treated with entinostat with concetration equal to 4microM for 4h, replica C


title: N10_MOLM1_DMSO_16h_A

description:
DMSO
Bone marrow derived cell line EVI1High MOLM1 was treated with DMSO with concetration equal to 1 microM for 16h, replica A


title: N11_MOLM1_DMSO_16h_B

description:
DMSO
Bone marrow derived cell line EVI1High MOLM1 was treated with DMSO with concetration equal to 1 microM for 16h, replica B


title: Aragene-0883


title: N12_MOLM1_DMSO_16h_C

description:
DMSO
Bone marrow derived cell line EVI1High MOLM1 was treated with DMSO with concetration equal to 1 microM for 16h, replica C


title: Standard survival (control) glioblastoma FFPE sample 21

value: M

value: Temporo-mesial


title: Aragene-0884


title: N13_MOLM1_AR42_08_16h_A

description:
AR42
Bone marrow derived cell line EVI1High MOLM1 was treated with AR42 with concetration equal to 0.8microM for 16h, replica A

value: Bone marrow


title: N14_MOLM1_AR42_08_16h_B

description:
AR42
Bone marrow derived cell line EVI1High MOLM1 was treated with AR42 with concetration equal to 0.8microM for 16h, replica B

value: Bone marrow derived cell line


title: Standard survival (control) glioblastoma FFPE sample 22

value: Parietal


title: N17_MOLM1_ENTI_4_16h_B

description:
entinostat
Bone marrow derived cell line EVI1High MOLM1 was treated with entinostat with concetration equal to 4microM for 16h, replica B

value: B


title: N16_MOLM1_ENTI_4_16h_A

description:
entinostat
Bone marrow derived cell line EVI1High MOLM1 was treated with entinostat with concetration equal to 4microM for 16h, replica A


title: Standard survival (control) glioblastoma FFPE sample 16

value: Temporo-mesial posterior

value: Right


title: N18_MOLM1_ENTI_4_16h_C

description:
entinostat
Bone marrow derived cell line EVI1High MOLM1 was treated with entinostat with concetration equal to 4microM for 16h, replica C

value: C


title: Standard survival (control) glioblastoma FFPE sample 7


title: N15_MOLM1_AR42_08_16h_C

description:
AR42
Bone marrow derived cell line EVI1High MOLM1 was treated with AR42 with concetration equal to 0.8microM for 16h, replica C


title: N19_AML1_DMSO_4h_A

description:
DMSO
Bone marrow derived cell line EVI1High AML1 was treated with DMSO with concetration equal to 1 microM for 4h, replica A

value: DMSO

value: A

value: 1 microM


title: Standard survival (control) glioblastoma FFPE sample 12

value: Frontal


title: S10min TP RNA Rep1

city: Melbourne

first: Attila

last: Horvath

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description: polysome-associated RNA

data_processing:
Sequencing was performed employing HiSeq 2500 (Illumina provided by by GENEWIZ) using settings compatible with TrueSeq Small RNA Sample Preparation Kit (Illumina) and paired-end reads of 150 nt. Barcoded libraries were mixed in equimolar or otherwise desired proportion, and sequenced with 400 M reads per lane mode; additional lanes were invoked when necessary.  The 150 nt Illumina paired reads were subjected to a quality control using Trimmomatic (SLIDINGWINDOW: 7 nt; phred quality cut-off: 24) followed by adaptor trimming including the (A)20 tract from the reverse transcription primer. The reads containing no 3′ poly(A) or shorter than 17 nt were discarded. To assign reads to the genome, a stepwise alignment strategy was performed as follows. Reads were first filtered to keep only those not mapping to any rRNA species (inferred from the locus: chromosome XII:450,000-491,000). Remaining reads were then mapped to a custom tRNA sequence set based on GtRNAdb (PMC4702915). Unmapped reads from this alignment were then aligned with spliced RNA sequences containing ‘misc_RNA’, ‘ncRNA’, ‘tRNA’ or ‘snoRNA’ primary tags in SacCer3. Finally, the remaining unmapped sequences were aligned to a genomic mRNA reference consisting of all protein-coding gene regions with an up- and downstream 1,000 bp flanking genomic sequences, allowing multiple mappings.
Assembly: sacCer3
Supplementary files format and content: Bedgraphs contain the coverage normalised signal of TCP-seq RS and DS fractions.

organism: Saccharomyces cerevisiae

source_name: Liquid yeast culture with OD600 0.6-0.8

growth_protocol: Wild-type (WT) yeast of cell line BY4741 was grown in 1 litre of YPD (1% w/v yeast extract (Merck, Sigma-Aldrich cat. no. 70161), 2% w/v peptone (Merck, Sigma-Aldrich cat. no. 70178), 2% w/v dextrose (glucose) (Merck, Sigma-Aldrich cat. no.49139), 40 mg/l adenine sulphate (Amresco)) under the desired conditions (30°C has been used) in an orbital shaker-incubator until the cell culture reached an optical density of 0.6-0.8 AU at 600 nm (OD600).

extract_protocol:
The formaldehyde fixation reaction was quenched by adding a buffer containing glycine (20 mM HEPES-KOH pH 7.4 at 25°C, 100 mM KCl and 2 mM MgCl2, 250 mM glycine) to the cell pellet to neutralise any remaining formaldehyde. The reaction was performed on ice following rigorous cell pellet re-suspension. Upon quenching completion, the cells were pelleted by a centrifugation at 4°C, 5,000×g for 5 minutes. Supernatant was discarded and the cell pellet re-suspended in the same buffer but without added glycine, to reduce glycine contamination. Cells were pelleted once more as described above, supernatant discarded and the cell pellet re-suspended in a small volume of the same buffer without added glycine. Cell suspension was flash-frozen by dripping in liquid nitrogen and stored at -80°C. Frozen cell pellets were further disrupted using a cryo-mixing mill set at 27Hz for 2 minutes under liquid nitrogen temperature. The resultant powdered cell grindate was further re-suspended in a buffer containing 20 mM HEPES-KOH pH 7.4 at 25°C, 100 mM KCl, 2 mM MgCl2, 5 mM DTT, 1× EDTA-free protease inhibitor and 1 U/μl of RNaseOUT RNase inhibitor. The suspension was clarified from cell debris by centrifugation at 4°C, 13,000×g for 5 minutes. The resultant clarified lysate was used for further translation complex isolation by separation via sedimentation over a discontinuous sucrose gradient (10-20% w/v, 50% w/v), allowing particles co-sedimenting with ribosomes or faster (Translated Pool, TP; also total translated, tt) to collect in the bottom 50% w/v sucrose cushion. The tt pool was subsequently subjected to a limited RNase I digestion followed by another round of sedimentation through a continuous 10-40% w/v sucrose gradient. Fractions containing ribosomal small subunit (SSU), mono(ribo)somes (RS) and di(ribo)somes (DS) were identified using in-line UV absorbance readout upon sedimentation completion and isolated. RNA in the isolated fractions has been de-crosslinked using hot acid phenol extraction and ethanol precipitation, followed by the construction of TCP-seq libraries.
Approximately 1 μg of the SSU, RS and DS de-crosslinled RNA was used to construct TCP-seq libraries generally according to the published methods (Archer, et al., Nature 2016, 535: 570-574; Shirokikh, et al., Nature Protocols, 2017, 12:697-731; Janapala et al., JoVE, 2021, e62639). Briefly, RNA was end-repaired with T4 bacteriophage polynucleotide kinase, 3'-polyadenylated with Escherichia coli poly(A) polymerase, primed with a split-adaptor circularisation DNA oligonucleotide and converted into cDNA using SuperScript IV reverse transcriptase. The resultant cDNA was circularised using CircLigase II and the original RNA degraded with A/T RNase mix. The circularised cDNA was then PDD-treated (Archer, et al., BMC Genomics 2014, 15:401; Archer, et al., Current Protocols in Human Genetics 2015, 85:11.15.1-11.15.36) using a set of probes designed based on the previously-encountered ribosomal(r)RNA TCP-seq library contaminants. Upon the PDD treatment, the cDNA was amplified for 14-28 cycles with primers containing indices and structures compatible with Illumina’s TrueSeq Small RNA Sample Preparation Kit. The amplified libraries were size-selected using non-denaturing agarose gel electrophoresis separation and cleaned-up with phenol:chloroform extraction and ethanol precipitation. The resultant amplified and indexed libraries were paired-end sequenced to 150 nt read length with Illumina HiSeq 2500.  RNA-seq libraries were made using the same fixed cell material as the TCP-seq counterparts and included Total cell lysate (TCL; also Total, T) and Translated Pool (TP; also total translated, tt) fractions. ~1 μg of the RNA obtained from each T and tt was directed for making rRNA depleted RNA-seq libraries using GENEWIZ services and the following general approach. The rRNA was depleted using an rRNA removal kit. The VAHTS Total RNA-seq (HMR) Library Prep Kit for Illumina was used for library preparation. The rRNA-depleted RNA was fragmented and reverse-transcribed. First cDNA strand was synthesised using ProtoScript II Reverse Transcriptase with random primers and Actinomycin D. The cDNA second-strand was synthesised using Second Strand Synthesis Enzyme Mix including dACG-TP/dUTP. The double-stranded cDNA was bead-purified and then treated with End Prep Enzyme Mix to repair both ends and create dA-tailing in one reaction, followed by a T-A ligation to add amplification adaptors to both ends. Size selection of the adaptor-ligated DNA was then performed using beads, and fragments of ~400 bp (with the approximate insert size of 300 bp) were recovered. The dUTP-labelled second strand was digested with Uracil-Specific Excision Reagent enzyme. Each sample was then amplified by PCR using Illumina’s P5 and P7 index-containing primers. The PCR products were cleaned up using beads and assessed by Nano quality control (Nano QC) to identify library concentration. High-throughput sequencing libraries were then multiplexed and sequenced similarly to the TCP-seq libraries, to obtain at least 100 M reads per each multiplexing barcode.
TCP-seq with PDD rRNA depletion, RNA-seq with RNA-stage rRNA depletion

treatment_protocol: The cells were immediately snap-chilled by mixing with 25% w/v of crushed ice and 37% w/v formaldehyde solution (methanol-stabilised solution; ‘formalin’; Merck (Sigma-Aldrich cat. no. F11635-500ML)) was added to a final concentration of 2.2% w/v for 10 minutes. The cells were then subjected to polysome sedimentation profile analysis, separation of the cytosolic RNA/(poly)ribosomes into translated and non-translated fractions (based on their co-sedimentation with (poly)ribosomes), and further separation of the translated RNA fraction into fractions co-sedimenting with SSU, RS and DS complexes upon RNase digestion. RNA was extracted and TCP-seq and RNA-seq libraries were made and deep sequenced from thee fractions generally according to the published methods.  For glucose starvation experiments, prior to the snap-chilling and fixation, the cells were briefly pelleted using centrifugation at 30°C, 5,000×g for 1 minute. The cell pellet was immediately resuspended in warm (30°C) YP media (containing no added glucose) and incubated as earlier in the culture for 10 minutes more at 30°C in an orbital shaker-incubator.

tag: strain

value: wild type

value: glucose (-)


title: Standard survival (control) glioblastoma FFPE sample 9

tag: Sex

value: F

value: Dead

value: Temporal

value: Left


title: Standard survival (control) glioblastoma FFPE sample 15

value: M

tag: age at diagnosis (years)

value: Frontal, basal ganglia and corpus callosum


title: Standard survival (control) glioblastoma FFPE sample 20

tag: kps

value: Temporo-parieto-occipital


title: N20_AML1_DMSO_4h_B

description:
DMSO
Bone marrow derived cell line EVI1High AML1 was treated with DMSO with concetration equal to 1 microM for 4h, replica B

value: Bone marrow

value: Bone marrow derived cell line

value: B


title: CTR TP RNA Rep1

description: polysome-associated RNA

value: glucose (+)


title: Standard survival (control) glioblastoma FFPE sample 11

tag: overall survival (months)

value: Parietal

value: Right


title: Standard survival (control) glioblastoma FFPE sample 4

tag: last follow-up


title: Standard survival (control) glioblastoma FFPE sample 10

tag: tumor localization

value: Parieto-occipital


title: CTR TCL RNA Rep1

description: total cell lysate RNA


title: N23_AML1_AR42_05_4h_B

description:
AR42
Bone marrow derived cell line EVI1High AML1 was treated with AR42 with concetration equal to 0.5microM for 4h, replica B


title: N22_AML1_AR42_05_4h_A

description:
AR42
Bone marrow derived cell line EVI1High AML1 was treated with AR42 with concetration equal to 0.5microM for 4h, replica A

value: A


title: Standard survival (control) glioblastoma FFPE sample 2

tag: tumor side


title: Standard survival (control) glioblastoma FFPE sample 17

value: Frontal


title: Standard survival (control) glioblastoma FFPE sample 6


title: Standard survival (control) glioblastoma FFPE sample 19


title: Standard survival (control) glioblastoma FFPE sample 5


title: S10min DS Rep1

description:
selected ribosomal footprints
S10m_DS_m.bed.gz

data_processing:
Library strategy: TCP-seq
Sequencing was performed employing HiSeq 2500 (Illumina provided by by GENEWIZ) using settings compatible with TrueSeq Small RNA Sample Preparation Kit (Illumina) and paired-end reads of 150 nt. Barcoded libraries were mixed in equimolar or otherwise desired proportion, and sequenced with 400 M reads per lane mode; additional lanes were invoked when necessary.  The 150 nt Illumina paired reads were subjected to a quality control using Trimmomatic (SLIDINGWINDOW: 7 nt; phred quality cut-off: 24) followed by adaptor trimming including the (A)20 tract from the reverse transcription primer. The reads containing no 3′ poly(A) or shorter than 17 nt were discarded. To assign reads to the genome, a stepwise alignment strategy was performed as follows. Reads were first filtered to keep only those not mapping to any rRNA species (inferred from the locus: chromosome XII:450,000-491,000). Remaining reads were then mapped to a custom tRNA sequence set based on GtRNAdb (PMC4702915). Unmapped reads from this alignment were then aligned with spliced RNA sequences containing ‘misc_RNA’, ‘ncRNA’, ‘tRNA’ or ‘snoRNA’ primary tags in SacCer3. Finally, the remaining unmapped sequences were aligned to a genomic mRNA reference consisting of all protein-coding gene regions with an up- and downstream 1,000 bp flanking genomic sequences, allowing multiple mappings.
Assembly: sacCer3
Supplementary files format and content: Bedgraphs contain the coverage normalised signal of TCP-seq RS and DS fractions.

tag: fraction

value: disomal (disomes, DS)

value: wild type

value: glucose (-)


title: S10min DS Rep2


title: Standard survival (control) glioblastoma FFPE sample 3

value: F

value: Dead


title: Standard survival (control) glioblastoma FFPE sample 13

value: M

value: Temporal

value: Left


title: N25_AML1_ENTI_2_4h_A

description:
entinostat
Bone marrow derived cell line EVI1High AML1 was treated with entinostat with concetration equal to 2microM for 4h, replica A

value: Bone marrow

tag: time point

tag: replicate


title: SAMPLE 6_FSHD2 iPSC without dCas9 nor sgRNAs transfection

city: Kyoto

first: Mitsuru

last: Sasaki-Honda

address: Shogoin, Sakyoku

department: Dept. of Clinical Application

institute: CiRA

description: FSHD2 iPSCs sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Illumina iScan System

data_processing: R (ChAMP package v.2.21.1 )

source_name: genomic DNA from FSHD2 iPSC

growth_protocol: Cells were cultured in StemFit on iMatrix (laminin511)

extract_protocol: genome DNA was extracted with GenElute Mammalian Genomic DNA Miniprep Kit (Sigma-Aldrich) and bisulphite converted by EZ DNA Methylation Kit (ZYMO RESEARCH)

tag: gender

value: Male

tag: subject status/id

value: FSHD2 donor 2


title: CTR DS Rep4

description:
selected ribosomal footprints
NS_DS_m.bed.gz

tag: genotype

value: glucose (+)


title: CTR DS Rep3

tag: treatment


title: SAMPLE 5_FSHD2 iPSC with constitutive dCas9_KAL with transient sgRNAs transfection

description: FSHD2 iPSCs sample

value: Female

value: FSHD2 donor 1


title: Standard survival (control) glioblastoma FFPE sample 14

value: Parieto-occipital


title: CTR DS Rep2


title: N26_AML1_ENTI_2_4h_B

description:
entinostat
Bone marrow derived cell line EVI1High AML1 was treated with entinostat with concetration equal to 2microM for 4h, replica B

tag: tissue

tag: cell line

tag: cell type

value: Bone marrow derived cell line

value: B

tag: concentration


title: CTR DS Rep1

tag: strain

value: disomal (disomes, DS)


title: Standard survival (control) glioblastoma FFPE sample 8

tag: Sex

tag: age at diagnosis (years)

tag: kps

value: Right


title: N29_AML1_DMSO_16h_B

description:
DMSO
Bone marrow derived cell line EVI1High AML1 was treated with DMSO with concetration equal to 1 microM for 16h, replica B

value: DMSO

value: 1 microM


title: SAMPLE 7_FSHD2 iPSC without dCas9 nor sgRNAs transfection

description: FSHD2 iPSCs sample


title: Standard survival (control) glioblastoma FFPE sample 1

tag: overall survival (months)

tag: last follow-up

value: Dead

tag: tumor localization

value: Parietal


title: N28_AML1_DMSO_16h_A

description:
DMSO
Bone marrow derived cell line EVI1High AML1 was treated with DMSO with concetration equal to 1 microM for 16h, replica A

tag: time point

value: A


title: N27_AML1_ENTI_2_4h_C

description:
entinostat
Bone marrow derived cell line EVI1High AML1 was treated with entinostat with concetration equal to 2microM for 4h, replica C

tag: replicate

value: C


title: S10min RS Rep2

description:
selected ribosomal footprints
S10m_RS_m.bed.gz

tag: fraction

value: monosomal (ribosomes, RS)

value: wild type

value: glucose (-)


title: N31_AML1_AR42_05_16h_A

description:
AR42
Bone marrow derived cell line EVI1High AML1 was treated with AR42 with concetration equal to 0.5microM for 16h, replica A

value: Bone marrow


title: CTR RS Rep1

description:
selected ribosomal footprints
NS_RS_m.bed.gz

value: glucose (+)


title: N32_AML1_AR42_05_16h_B

description:
AR42
Bone marrow derived cell line EVI1High AML1 was treated with AR42 with concetration equal to 0.5microM for 16h, replica B


title: SAMPLE 4_FSHD2 iPSC with constitutive dCas9_KAL with transient sgRNAs transfection

description: FSHD2 iPSCs sample

tag: gender

value: Female

tag: subject status/id

value: FSHD2 donor 1


title: S10min SSU Rep2

description:
selected ribosomal footprints
S10m_SSU_m.bed.gz

value: small ribosomal subunit (SSU)

tag: genotype

tag: treatment


title: CTR RS Rep2


title: N24_AML1_AR42_05_4h_C

description:
AR42
Bone marrow derived cell line EVI1High AML1 was treated with AR42 with concetration equal to 0.5microM for 4h, replica C

tag: tissue

tag: cell line

value: Bone marrow derived cell line


title: S10min RS Rep1


title: S10min SSU Rep1


title: N34_AML1_ENTI_2_16h_A

description:
entinostat
Bone marrow derived cell line EVI1High AML1 was treated with entinostat with concetration equal to 2microM for 16h, replica A

tag: cell type

tag: concentration


title: S10min TCL RNA Rep1

description: total cell lysate RNA

tag: strain


title: N33_AML1_AR42_05_16h_C

description:
AR42
Bone marrow derived cell line EVI1High AML1 was treated with AR42 with concetration equal to 0.5microM for 16h, replica C


title: Standard survival (control) glioblastoma FFPE sample 18

tag: Sex

value: F

tag: age at diagnosis (years)

value: Mesial frontal

tag: tumor side

value: Left


title: N35_AML1_ENTI_2_16h_B

description:
entinostat
Bone marrow derived cell line EVI1High AML1 was treated with entinostat with concetration equal to 2microM for 16h, replica B

value: B


title: N30_AML1_DMSO_16h_C

description:
DMSO
Bone marrow derived cell line EVI1High AML1 was treated with DMSO with concetration equal to 1 microM for 16h, replica C

value: DMSO

value: 1 microM


title: CTR SSU Rep1

description:
fragmented ribosome-associated RNA
NS_SSU_m.bed.gz


title: CTR SSU Rep2

description:
selected ribosomal footprints
NS_SSU_m.bed.gz


title: SAMPLE 3_FSHD2 iPSC with constitutive dCas9_NN with transient sgRNAs transfection

description: FSHD2 iPSCs sample


title: IMR90, mock, TFIIIC, ChIP-seq

city: Parma

first: Giorgio

last: Dieci

address: Parco Area delle Scienze 23/A

department: Deparment of Life Sciences

institute: University of Parma

description: ChIP-seq single end (SE)

data_processing:
ChIP-seq peak calling. Analysis of sequence data was carried out as previously described (Ferrari et al., 2014) with minor modifications. Reads were aligned to the hg38 human genome reference sequence (GRCh38) using Bowtie (Langmead et al., 2009) and aligning parameters of unique- ness (-S –m1 –v2 –t –q).
Assembly: hg38
Supplementary files format and content: bigwig, bed

source_name: Lung

growth_protocol: IMR90 primary human fetal lung fibroblasts were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin at 37ºC in 5% CO2.

extract_protocol:
Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014).
Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach  saturation with a coverage of 4 reads/bp of the human genome for each condition.

treatment_protocol: Cells were infected with the dl1500 adenovirus-based mutant or mock-infected

value: Lung

value: IMR90 human primary lung fetal fibroblasts

value: Contact-inhibited IMR90

tag: chip antibody

value: in house anti-GTF3C2

value: WT

value: mock-infected


title: IMR90, dl1500, RPC39, ChIP-seq

description: ChIP-seq single end (SE)


title: IMR90, dl1500, TFIIIC, ChIP-seq

description: ChIP-seq single end (SE)


title: IMR90, mock, RPC39, ChIP-seq

description: ChIP-seq single end (SE)


title: IMR90, dl1500, BDP1, ChIP-seq

description: ChIP-seq single end (SE)

value: in-house anti-BDP1 rabbit polyclonal


title: H3_BC_rep1

city: Wuhan

first: Wenxing

last: Chen

address: No.1, Shizishan Street, Hongshan District

country: China

institute: Huazhong Agricultural University

description: H3 DNA

data_processing:
Basecalls performed using CASAVA version 1.8
The ChIP-seq reads were mapped to  apple whole genome (GDDH13_11.1) using Bowtie (Langmead, 2010) with up to two mismatches allowed
The raw sequencing reads were processed using custom Python scripts developed in the Comai laboratory and available online (http://comailab.genomecenter.ucdavis.edu/index.php/Barcoded_data_preparation_tools)
ChIP-seq tag-enriched regions were identified by SICER version 1.1 (Zang et al., 2009) with a window size setting = 200 bp and gap size = 200 bp for H3K4me3; window size settings = 200 bp and gap size = 600 bp for H3K27me3. Input material and H3 reads were used for background subtraction and a false discovery rate (FDR) of 0.01 was employed.
For quantitative comparison of H3K4me3 and H3K27me3 signals in different stages, libraries were normalized through the DiffReps pipeline (Shen et al., 2013)
Genome_build: apple genome (GDDH13_11.1, Daccord et al., 2017)

organism: Malus domestica

source_name: Flower buds

growth_protocol: The one-year old middle branches bearing flower buds at terminal position were sampled from apple trees (Malus×domestica Borkh. ‘Fuji’) grown at the experimental farm of the Department of Agriculture, Shinshu University (Nagano, Japan; 36’ N and 139’ E) on 11 November, 2016

extract_protocol:
Preparation of chromatin samples and immunoprecipitation were performed as described previously (Gendrel et al., 2005). Three to four flower buds were used as one replicate. Cross-link was conducted as described previously (Saito et al., 2015) with minor modifications. In brief, each flower bud was first cut longitudinally by razor and divided into 8 equal parts.
The immunoprecipitated chromatin samples were amplified and used for library construction using the ThruPLEX DNA-seq Kit (Takara Bio USA) as per the manufacturer’s instructions.

treatment_protocol: The flower buds used for ChIP experiment were collected before incubation (before chilling, sample “BC”) and after chilling exposure for 60 d (after chilling, sample “AC”). After 60 d of chilling exposure, branches were then moved to forcing condition in a growth chamber, 22 °C under long-photoperiod conditions (16 h light/8 h dark) with a light intensity of 100 μmol m-2 s-1 provided by cool-white fluorescent lights.

value: terminal flower buds

tag: developmental stage

value: before chilling exposure

value: H3 (ab1791; Abcam)


title: H3_BB_rep2

description: H3 DNA

value: approaching bud break


title: H3_BC_rep2

description: H3 DNA


title: SAMPLE 1_FSHD2 iPSC with constitutive dCas9_NN with transient sgRNAs transfection

description: FSHD2 iPSCs sample

value: Female

value: FSHD2 donor 1


title: H3_AC_rep2

description: H3 DNA

value: after chilling exposure


title: N36_AML1_ENTI_2_16h_C

description:
entinostat
Bone marrow derived cell line EVI1High AML1 was treated with entinostat with concetration equal to 2microM for 16h, replica C

value: Bone marrow

value: Bone marrow derived cell line

tag: time point

value: C


title: Input_BB_rep2

description: input DNA

value: input DNA


title: hypoxia HSPC

city: Xining

first: Haijing

last: Wang

address: 23 Xinning Road

institute: Northwest Institute of Plateau Biology, Chinese Academy of Sciences

description: HSPCs enriched from bone marrow of hypoxic group mice

data_processing:
Sequenced reads were aligned to the GRCm38 murine transcriptome(bowtie2)
Quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline
Matrix table with raw gene counts for every gene and every sample
Genome_build: GRCm38
Supplementary_files_format_and_content: raw counts

source_name: hypoxic

extract_protocol:
For cell collection, the bone marrow cells suspension was enriched for Lin- cells by nagetivate selection with magnetic beads (Lineage Cell Depletion Kit; 130-090-858; Miltenyi Biotec) according to the manufacturer's instructions.
Library construction was performed using a BD Rhapsody™ Single-Cell Analysis System following a standard protocol provided by the manufacturer (BD Biosciences)

treatment_protocol: The hypoxic group was placed in an altitude chamber for 13 days. The chamber with a pressure of 52.93 KPa, corresponding to an altitude of 5000 m. The concentration of oxygen in the chamber was 19.5%. The control group were sacrificed upon arrival at Xining.

value: ICR mice

tag: age

value: 7~8 week

value: bone marrow


title: Input_AC_rep1

description: input DNA


title: Input_BC_rep2

description: input DNA


title: Input_AC_rep2

description: input DNA


title: Input_BC_rep1

description: input DNA


title: Disomes_Acetate2

city: Wako

first: Tilman

last: Schneider-Poetsch

state: Saitama

address: 2-1 Hirosawa

institute: RIKEN

description: RNA-Seq

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: Human Genome hg38
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Library strategy: Ribo-seq

growth_protocol: HEK293T flpIn cells grown in DMEM with 10% FBS and antibiotics at 37 deg C under 5% CO2

extract_protocol:
Cells were collected in lysis buffer, cleared of debris and lysates were snap frozen with liquid nitrogen and stored at -80 deg C
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification. For RNA-Seq, Poly(A) selection and cDNA synthesis were performed using Illumina Stranded mRNA Prep, Ligation (Illumina) and subsequent steps were performed by TruSeq Stranded Total RNA Library Prep Gold (Illumina).

treatment_protocol: Cells were treated with Acetate solvent or indicated concentration of GC7 overnight

value: wild type

value: Acetate


title: Disomes_Acetate1

description: RNA-Seq


title: Rv1_Luc_Cas_SNX631_Rep9

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

country: USA

institute: University of South Carolina

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by cutadapt (v 2.8) with parameters -m 75 -q 30
Reads were aligned to a hybrid reference genome consisting of both the human GRCh38.p13 primary assembly genome and the mouse GRCm39 primary assembly genome, utilizing STAR (v 2.7.2b) with parameter --outFilterMismatchNoverReadLmax 0.01 --outFilterMultimapNmax 1
Read counts over annotated genes were obtained using featureCount (subreads | version: 2.0.3) with parameters -T 12 -B -O --fraction -s 2 -p --countReadPairs -d 50 -D 800 -g gene_id
Assembly: GRCh38.p13 & GRCm39
Supplementary files format and content: tab-delimited text files include human and mouse gene counts for each sample

source_name: xenograft

growth_protocol: 22Rv1 and its derivatives were cultured in RPMI-1640 media supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 1.5 g/L sodium bicarbonate, 10 mM HEPES, 0.45% D-glucose, and either 10% fetal bovine serum (FBS) or charcoal stripped FBS (CSS), plus 1% penicillin-streptomycin (P/S).   Cells were inoculated s.c. (2x10^6 cells in 0.1 mL 50% Matrigel per animal) in the right flank of intact or castrated male NSG mice to form xenograft tumors

extract_protocol:
Tumor tissues were first submerged in 500 μL RNA-Later stabilization solution (Thermo Fisher Scientific) at room temperature. After stabilization, RNA samples were extracted from tumor tissues using the mRNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol.  RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit

treatment_protocol: For SNX631 in vivo treatment, animals were randomly allocated to two study groups when the mean tumor size reached 100-200 mm^3. For Rv1-WT study, the treatment group received SNX631-medicated diet (500 ppm, producing 30-60 mg/kg/day dosage on average) and the control group received the control diet.  For Rv1-Luc study, the animals in the control group were dosed with vehicle (70% PEG-400/30% Propylene Glycol, 5 mL/kg, p.o., b.i.d.) and the treatment group was dosed with SNX631 (6 mg/mL solution in the vehicle, 5 mL/kg, p.o., b.i.d.) at 60 mg/kg/day.

value: xenograft

value: prostate cancer cells

value: Luciferase-expressing

value: Rv1-Luc xenograft (Luc_Cas_Snx_#8) growing castrated NSG male mice, SNX631 treatment group (Cas-Snx)


title: H3K4me3_BB_rep2

value: terminal flower buds

value: approaching bud break

value: H3K4me3 (ab8580; Abcam)


title: IMR90, mock, BDP1, ChIP-seq

description: ChIP-seq single end (SE)

value: Lung

value: IMR90 human primary lung fetal fibroblasts

value: Contact-inhibited IMR90

value: in-house anti-BDP1 rabbit polyclonal

value: WT

value: mock-infected


title: H3K4me3_BB_rep1


title: control HSPC

description: HSPCs enriched from bone marrow of control group mice

source_name: control

value: ICR mice

value: 7~8 week


title: Monosome_Acetate2

description: RNA-Seq

value: wild type


title: Rv1_Luc_Cas_SNX631_Rep7

value: Rv1-Luc xenograft (Luc_Cas_Snx_#7) growing castrated NSG male mice, SNX631 treatment group (Cas-Snx)


title: H3K4me3_BC_rep1

value: before chilling exposure


title: H3_AC_rep1

description: H3 DNA

value: after chilling exposure

value: H3 (ab1791; Abcam)


title: Rv1_Luc_Cas_SNX631_Rep6

value: xenograft

value: prostate cancer cells

value: Luciferase-expressing

value: Rv1-Luc xenograft (Luc_Cas_Snx_#5) growing castrated NSG male mice, SNX631 treatment group (Cas-Snx)


title: Rv1_Luc_Cas_SNX631_Rep5

value: Rv1-Luc xenograft (Luc_Cas_Snx_#1) growing castrated NSG male mice, SNX631 treatment group (Cas-Snx)


title: H3K4me3_BC_rep2

value: terminal flower buds

value: H3K4me3 (ab8580; Abcam)


title: Monosomes_GC7

description: RNA-Seq

value: 30 µM GC7


title: H3_BB_rep1

description: H3 DNA

value: approaching bud break


title: N21_AML1_DMSO_4h_C

description:
DMSO
Bone marrow derived cell line EVI1High AML1 was treated with DMSO with concetration equal to 1 microM for 4h, replica C

value: Bone marrow

value: Bone marrow derived cell line

value: DMSO

tag: replicate

value: C

value: 1 microM


title: H3K4me3_AC_rep1


title: Rv1_Luc_Cas_SNX631_Rep8

value: Rv1-Luc xenograft (Luc_Cas_Snx_#6) growing castrated NSG male mice, SNX631 treatment group (Cas-Snx)


title: H3K27me3_BB_rep2

value: H3K27me3 (07-449; Millipore)


title: Rv1_Luc_Cas_SNX631_Rep4

value: Rv1-Luc xenograft (Luc_Cas_Snx_#2) growing castrated NSG male mice, SNX631 treatment group (Cas-Snx)


title: Disomes_GC7

description: RNA-Seq

value: wild type


title: Rv1_Luc_Cas_SNX631_Rep3

value: xenograft

value: prostate cancer cells

value: Rv1-Luc xenograft (Luc_Cas_Snx_#4) growing castrated NSG male mice, SNX631 treatment group (Cas-Snx)


title: Monosome_Acetate1

description: RNA-Seq

value: Acetate


title: H3K27me3_BB_rep1

value: terminal flower buds


title: Input_BB_rep1

description: input DNA

value: input DNA


title: H3K27me3_AC_rep1

value: after chilling exposure


title: Rv1_Luc_Cas_SNX631_Rep2

value: Luciferase-expressing

value: Rv1-Luc xenograft (Luc_Cas_Snx_#9) growing castrated NSG male mice, SNX631 treatment group (Cas-Snx)


title: H3K27me3_AC_rep2


title: Rv1_Luc_Cas_Ctrl_Rep8

value: Rv1-Luc xenograft (Luc_Cas_Ctrl_#1) growing castrated NSG male mice, control group (Cas-Ctrl)


title: H3K27me3_BC_rep1

value: before chilling exposure


title: Rv1_Luc_Cas_Ctrl_Rep7

value: Rv1-Luc xenograft (Luc_Cas_Ctrl_#3) growing castrated NSG male mice, control group (Cas-Ctrl)


title: Rv1_Luc_Cas_Ctrl_Rep6

value: Rv1-Luc xenograft (Luc_Cas_Ctrl_#4) growing castrated NSG male mice, control group (Cas-Ctrl)


title: Rv1_Luc_Cas_Ctrl_Rep3

value: Rv1-Luc xenograft (Luc_Cas_Ctrl_#5) growing castrated NSG male mice, control group (Cas-Ctrl)


title: HVP-3

city: shenzhen

first: Chunling

address: 广东省深圳市南山区学苑大道1088号

institute: southern university of science and technology

data_processing:
fastp 0.23.2 is the software for data quality control
HISAT2 2.2.1 is used for recounts of the reference genome
FeatureCounts 2.0.3 of the expression volume is used in the calculation of recounts
DESeq2 1.34.0 is used for recounting the differences
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: huh 7

growth_protocol: huh7 cells were maintained in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using a high-purity total RNA extraction kit (BioTeke, China) . Total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using ABclonal mRNA-seq Lib Prep Kit（ABclonal, China）following manufacturers‘ protocols

value: huh 7

value: hepatoma cell line

tag: time

value: 2 day

value: acute HEV infection


title: P6-3

address: 广东省深圳市南山区学苑大道1088号

value: chronic HEV infection


title: Rv1_Luc_Cas_Ctrl_Rep2

value: xenograft

value: prostate cancer cells

value: Rv1-Luc xenograft (Luc_Cas_Ctrl_#9) growing castrated NSG male mice, control group (Cas-Ctrl)


title: P6-2

address: 广东省深圳市南山区学苑大道1088号


title: P6-1

address: 广东省深圳市南山区学苑大道1088号


title: HVP-2

address: 广东省深圳市南山区学苑大道1088号


title: HVP-1

address: 广东省深圳市南山区学苑大道1088号


title: CTR-3

address: 广东省深圳市南山区学苑大道1088号

value: control


title: Rv1_Luc_Cas_SNX631_Rep1

value: Rv1-Luc xenograft (Luc_Cas_Snx_#3) growing castrated NSG male mice, SNX631 treatment group (Cas-Snx)


title: H3K27me3_BC_rep2

value: terminal flower buds

value: H3K27me3 (07-449; Millipore)


title: Rv1_WT_Cas_SNX631_Rep4

value: WT

value: Rv1-WT xenograft (WT_Cas_Snx_#6) growing castrated NSG male mice, SNX631 treatment group (Cas-Snx)


title: H3K4me3_AC_rep2

value: after chilling exposure

value: H3K4me3 (ab8580; Abcam)


title: CTR-1

address: 广东省深圳市南山区学苑大道1088号


title: Rv1_WT_Cas_SNX631_Rep5

value: Rv1-WT xenograft (WT_Cas_Snx_#7) growing castrated NSG male mice, SNX631 treatment group (Cas-Snx)


title: Rv1_WT_Cas_SNX631_Rep3

value: Rv1-WT xenograft (WT_Cas_Snx_#2) growing castrated NSG male mice, SNX631 treatment group (Cas-Snx)


title: CTR-2

address: 广东省深圳市南山区学苑大道1088号

value: huh 7

value: hepatoma cell line


title: AP6-3

address: 广东省深圳市南山区学苑大道1088号

value: 2 day

value: chronic HEV infection+aicar


title: Rv1_WT_Cas_SNX631_Rep2

value: xenograft

value: Rv1-WT xenograft (WT_Cas_Snx_#5) growing castrated NSG male mice, SNX631 treatment group (Cas-Snx)


title: AP6-2

address: 广东省深圳市南山区学苑大道1088号


title: Rv1_Luc_Cas_Ctrl_Rep4

value: prostate cancer cells

value: Luciferase-expressing

value: Rv1-Luc xenograft (Luc_Cas_Ctrl_#8) growing castrated NSG male mice, control group (Cas-Ctrl)


title: AP6-1

address: 广东省深圳市南山区学苑大道1088号


title: Rv1_Luc_Cas_Ctrl_Rep5

value: Rv1-Luc xenograft (Luc_Cas_Ctrl_#2) growing castrated NSG male mice, control group (Cas-Ctrl)


title: ACTR-3

address: 广东省深圳市南山区学苑大道1088号

value: AICAR


title: ACTR-1

address: 广东省深圳市南山区学苑大道1088号


title: Rv1_WT_Cas_Ctrl_Rep3

value: WT

value: Rv1-WT xenograft (WT_Cas_Ctrl_#10) growing castrated NSG male mice, control group (Cas-Ctrl)


title: ACTR-2

address: 广东省深圳市南山区学苑大道1088号


title: Rv1_WT_Cas_Ctrl_Rep1

value: Rv1-WT xenograft (WT_Cas_Ctrl_#7) growing castrated NSG male mice, control group (Cas-Ctrl)


title: Rv1_WT_Cas_Ctrl_Rep5

value: Rv1-WT xenograft (WT_Cas_Ctrl_#2) growing castrated NSG male mice, control group (Cas-Ctrl)


title: iPSC-mesodem cells,CYT387 treament3

city: Shanghai

first: su

last: yao

address: 1239 Siping Road

institute: Tongji university

data_processing:
For RNAseq, sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using hisat2 v2.1.0 with parameters -p 8 --dta -x -1 -2 -S. Raw transcripts were assembled using the StringTie (v1.3.4). Counts per million (cpm) were calculated by the DESeq2 (v1.42.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

growth_protocol: iPSC-mesoderm cell were produced from ZSSY001 (Nuwacell) by regulating Wnt signaling pathway. hPSCs were grown on Matrigel.

extract_protocol:
The total RNA was extracted by TRIzol extraction reagent (Invitrogen, 15596018). Furthermore, the purity and concentration of RNA were examined by measuring the absorbance value at 260 and 280 nm.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: iPSC-mesoderm cell were treated with CYT387 for 48h

value: iPSC-mesoderm cells

value: crodiomyocyte differentiation


title: iPSC-mesodem cells,CYT387 treament2


title: iPSC-mesodem cells,CYT387 treament1


title: Rv1_WT_Cas_Ctrl_Rep4

value: Rv1-WT xenograft (WT_Cas_Ctrl_#8) growing castrated NSG male mice, control group (Cas-Ctrl)


title: Rv1_WT_Int_SNX631_Rep6

value: Rv1-WT xenograft (WT_Int_Snx_#9) growing intact NSG male mice, SNX631 treatment group (Int-Snx)


title: SAMPLE 2_FSHD2 iPSC with constitutive dCas9_KAL with transient sgRNAs transfection

description: FSHD2 iPSCs sample

tag: gender

value: Female

tag: subject status/id

value: FSHD2 donor 1


title: iPSC-mesodem cells,control3

tag: treatment

value: DMSO


title: Rv1_WT_Cas_Ctrl_Rep2

tag: tissue

value: xenograft

tag: genotype

value: Rv1-WT xenograft (WT_Cas_Ctrl_#3) growing castrated NSG male mice, control group (Cas-Ctrl)


title: Rv1_WT_Int_SNX631_Rep4

tag: cell line

tag: cell type

value: prostate cancer cells

value: Rv1-WT xenograft (WT_Int_Snx_#5) growing intact NSG male mice, SNX631 treatment group (Int-Snx)


title: Rv1_WT_Int_SNX631_Rep3

value: Rv1-WT xenograft (WT_Int_Snx_#1) growing intact NSG male mice, SNX631 treatment group (Int-Snx)


title: iPSC-mesodem cells,control2


title: Rv1_WT_Int_SNX631_Rep2

value: Rv1-WT xenograft (WT_Int_Snx_#6) growing intact NSG male mice, SNX631 treatment group (Int-Snx)


title: iPSC-mesodem cells,control1


title: Rv1_WT_Int_SNX631_Rep1

value: WT

value: Rv1-WT xenograft (WT_Int_Snx_#10) growing intact NSG male mice, SNX631 treatment group (Int-Snx)


title: SH-SY5Y cells, DNAJC12KO, rep2

first: Xi

last: Mo

address: Dongfang Road

department: Pediatric Translational Medicine Institute

institute: Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine

data_processing:
Raw sample files in fastq form were trimmed for illumina adaptations using the "cutadapt 3.5", followed by FastQC v0.119 analysis to confirm proper trimming.  Reads were then selective alignment and quantified to the Homo sapiens GENCODE 45(GRCh38.p14) transcriptome using the alignment-free transcript quantifier Salmon v1.10.0. A decoy-aware transcriptome index was prepared, and comprehensive transcript level estimates were calculated. The resulting sample gene level count matrix was size factor normalized and analyzed for pairwise differential gene expression using R Bioconductor package DESeq2 v1.42.1
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-separated file of gene  quantification

extract_protocol:
Lyse cells directly in a culture dish by adding 1 mL TRIzol reagent and mix thoroughly. add 200μL chloroform, vortex mix for 15 seconds. incubate the mix for 5 minutes at room temperature and two layer should form. centrifuge at 12000 g at 4 °C for 10 minutes. Carefully transfer the top layer into the new tubes.add 1:1V of isopropanol to each tube and mix by inversion. Centrifuge at 12000 g at 4 °C for 15 minutes. Discard the supernatant and wash the pellet with 1 mL 75%  ethanol. Centrifuge at 12000g at 4 °C for 10 minutes. Remove all of residential ethanol with a pipet and air dry for 5 min. redissolve RNA in 30-50 μL  DEPC treated water.
Total RNA was isolated from cultivated cells using TRIzol (15596026, Invitrogen, Amercia) according to  manufacturer’s instructions. Comlementary DNA was synthesised from 1 μg total RNA using the Hifair®Ⅱ1st Strand cDNA Synthesis Kit (11121ES60, Yeasen, China) according to manufacturer’s instructions. The rRNA-depleted sequencing libraries from total RNA were prepared using Illumina TruSeq® Stranded Total RNA Gold preparation Kit. About 1 μg total RNA was used as input material, and Ribo-Zero Gold kit was used to remove both cytoplasmic and mitochondrial rRNA. Purified RNA was then fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis. These cDNA fragments were then subjected to end-repair, phosphorylation and 'A' base addition according to Illumina's library construction protocol. The products were purified and enriched with PCR, and the AMPure XP Beads (Beckmen, Norway) were used to clean up the amplified target fragments to create the final cDNA library.

value: neuroblastoma cells

value: DNAJC12 knockout


title: Rv1_WT_Int_SNX631_Rep5

value: Rv1-WT xenograft (WT_Int_Snx_#3) growing intact NSG male mice, SNX631 treatment group (Int-Snx)


title: SH-SY5Y cells, DNAJC12KO, rep3


title: SH-SY5Y cells, DNAJC12KO, rep1


title: SH-SY5Y cells, WT, rep3


title: Rv1_WT_Int_Ctrl_Rep6

value: Rv1-WT xenograft (WT_Int_Ctrl_#3) growing intact NSG male mice, control group (Int-Ctrl)


title: Rv1_WT_Int_Ctrl_Rep5

value: Rv1-WT xenograft (WT_Int_Ctrl_#6) growing intact NSG male mice, control group (Int-Ctrl)


title: SH-SY5Y cells, WT, rep2


title: SH-SY5Y cells, WT, rep1


title: Rv1_WT_Int_Ctrl_Rep3

value: Rv1-WT xenograft (WT_Int_Ctrl_#7) growing intact NSG male mice, control group (Int-Ctrl)


title: Rv1_WT_Int_Ctrl_Rep2

value: Rv1-WT xenograft (WT_Int_Ctrl_#10) growing intact NSG male mice, control group (Int-Ctrl)


title: Rv1_WT_CSS_SNX631_3d_Rep3

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by cutadapt (v 2.8) with parameters -m 75 -q 30
Reads were aligned to a hybrid reference genome consisting of both the human GRCh38.p13 primary assembly genome and the mouse GRCm39 primary assembly genome, utilizing STAR (v 2.7.2b) with parameter --outFilterMismatchNoverReadLmax 0.01 --outFilterMultimapNmax 1
Read counts over annotated genes were obtained using featureCount (subreads | version: 2.0.3) with parameters -T 12 -B -O --fraction -s 2 -p --countReadPairs -d 50 -D 800 -g gene_id
Assembly: GRCh38.p13 & GRCm39
Supplementary files format and content: tab-delimited text files include gene counts for each sample

growth_protocol: 22Rv1 and its derivatives were cultured in RPMI-1640 media supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 1.5 g/L sodium bicarbonate, 10 mM HEPES, 0.45% D-glucose, and either 10% fetal bovine serum (FBS) or charcoal stripped FBS (CSS), plus 1% penicillin-streptomycin (P/S).

extract_protocol:
Total RNA was extracted using RNAeasy Mini Kit (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit

treatment_protocol: To evaluate effects of CDK8/19 inhibition under androgen-supplemented conditons, cells were seeded into 12-well plates at the density of 2 X 10^5/well in FBS media, incubated overnight, and then treated with 0.1% DMSO (vehicle control) or 500 nM SNX631 in FBS media for 3 days. To evaluate effects of CDK8/19 inhibition under androgen-deprived conditions, cells were first sub-cultured in CSS media for one passage (3-4 days) and then seeded into 12-well plates at the density of 3x10^5 /well in CSS media, incubated overnight, and then treated with 0.1% DMSO (vehicle control) or 500 nM SNX631 in CSS media for 3 days.

value: Rv1-WT cells treated with 500 nM SNX631 for 72 hours, in CSS media


title: Rv1_WT_Int_Ctrl_Rep4

value: Rv1-WT xenograft (WT_Int_Ctrl_#8) growing intact NSG male mice, control group (Int-Ctrl)


title: Rv1_WT_Int_Ctrl_Rep1

value: xenograft

value: Rv1-WT xenograft (WT_Int_Ctrl_#1) growing intact NSG male mice, control group (Int-Ctrl)


title: Rv1_WT_CSS_SNX631_3d_Rep2

value: prostate cancer cells


title: DU145_oeSOX4_1

city: shanghai

first: jing

state: shanghai

address: Rm 1515, Bldg 17, 160 Pujian Rd, Shanghai 200127, China

institute: Shanghai jiaotong university

data_processing:
Raw Reads were filtered to remove adapters and low quality reads (including Reads with N ratio greater than 10% were removed, and Reads with bases quality value Q<=10 accounting for more than 50% of the entire Read were removed), and then high-quality Clean Reads provided in FASTQ format were obtained for subsequent information analysis. The libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads, according to the manufacturer’s instructions.
The Bowtie2 software was used to compare the high-quality Reads obtained from the sequencing of each sample with the reference genome to obtain the alignment efficiency of the sample Reads and the position information of the Reads on the genome. DeepTools v2.07 was used to map the density distribution of sequencing Read in the 3 kb of interval upstream and downstream of the TSS of each gene, and the results were presented as heat maps.
Use the STAR alignment tool to align sequencing reads to the reference genome. Upon alignment, calculate the genome coverage at each position using the aligned sequence data. Utilize the 'wigToBigWig' tool to convert the coverage data from WIG format to BigWig format based on the coverage information.
MACS2 v2.1.1 software was used to perform peak extraction.MACS2 contained four steps:(1) removing redundant Reads；(2) adjusting the Read position；(3) calculating Peak enrichment；(4) estimating the empirical false detection rate (FDR)；Finally, FDR<0.05(default) was selected as the identified peak.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence (hg19). Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: prostate

growth_protocol: DU145 cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10%  FBS and 1% penicillin/streptomycin.

extract_protocol:
For RNA-seq, 1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit. 1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x100 paired end flow cell. For the ATAC-seq assay, 50000 cells were centrifuged at 500 g for 5 min at 4℃, and the supernatant was removed. Cells were washed once with cold PBS. Subsequently, the cells were again centrifuged at 500 g for 5 min at 4℃ and the supernatant was removed. The cells were then suspended in cold lysis buffer. Next, the cells were again centrifuged at 500 g for 10 min at 4℃ and the supernatant was removed. The transposition reaction system was performed using Tn5 transposase. The cell nuclear content was added to the transposing reaction system mixture, and the DNA were purified after incubation at 37℃ for 30 min. The PCR system was performed with purified DNA, and PCR amplification was performed. For ATAC-seq, 40 000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 ℃. The transposed DNA fragments were purified immediately after with a MinElute PCR Purification Kit (Qiagen). After Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligoattached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. ATAC was performed according to ATAC-seq protocol by Biomarker Technologies Biotechnology Ltd. In brief, native nuclei were purified from cell as previously described (Buenrostro et al.,2015). The Nextera DNA Library Preparation Kit (Illumina) was used to perform the transposition according to the manufacturer’s manual. 40 000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 ℃. The transposed DNA fragments were purified immediately after with a MinElute PCR Purification Kit (Qiagen). After Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen) and subjected to sequencing on Illumina Novaseq 6000 using PE150.

treatment_protocol: All cells were incubated at 37°C in 5% CO2.

value: prostate

value: Human prostate cancer

value: SOX4 overexpression


title: DU145_Vector_2

value: Vector


title: DU145_Vector_1


title: DU145_shSOX4_3

value: SOX4 knockdown


title: Rv1_WT_FBS_SNX631_3d_Rep2

value: WT

value: Rv1-WT cells treated with 500 nM SNX631 for 72 hours, in FBS media


title: Rv1_WT_CSS_SNX631_3d_Rep1


title: DU145_shSOX4_1


title: DU145_shSOX4_2


title: DU145_shCon_1

value: Scramble


title: Rv1_WT_CSS_Ctrl_3d_Rep3

value: Rv1-WT cells treated with 0.1% DMSO (vehicle control) for 72 hours, in CSS media


title: Rv1_WT_CSS_Ctrl_3d_Rep2


title: Rv1_WT_FBS_SNX631_3d_Rep3


title: DU145_shCon_3


title: Rv1_WT_FBS_SNX631_3d_Rep1


title: Rv1_WT_CSS_Ctrl_3d_Rep1


title: UC72_LC_S23

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

data_processing:
Low quality sequences were trimmed or removed with Trimmomatic; STAR (version 2.6.0a) was used to align reads on reference genome (human genome hsGRCh38_94 ); The resulting transcriptome-aligned sequences were used for expression quantification by using RSEM (version 1.3.3) with “–forward-prob 0 ” option.
Assembly: GRCm38 Ensembl 94
Supplementary files format and content: tab-delimited text file includes batch corrected counts for each Sample.

source_name: Colon

growth_protocol: Healthy and CD organoids were embedded in matrigel and cultured for 7 days using WNT, R-Spondin, Noggin conditioned media. EDMs were made by digesting organoids enzymatically and mechanically into single cells and seeded onto transwell inserts.

extract_protocol:
Cell recovery was used to extract the organoids from the matrigel domes. Organoids and EDMs were lysed with RNA lysis buffer following the manufacturer's instructions for the Zymo Research Quick-RNA MicroPrep Kit.
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: Organoids were allowed to proliferate for 7 days. EDMs differentiated for 48h.

value: Colon

tag: group

value: ORG

tag: behavior at diagnosis

value: Pancolitis


title: UC73_LC_S28

value: Left sided


title: UC73_LC_S21


title: Rv1_WT_FBS_Ctrl_3d_Rep2

value: Rv1-WT cells treated with 0.1% DMSO (vehicle control) for 72 hours, in FBS media


title: DU145_oeSOX4_2


title: UC72_LC_S16


title: Rv1_WT_FBS_Ctrl_3d_Rep3


title: Rv1_WT_FBS_Ctrl_3d_Rep1


title: UC71_R_S26

value: Proctitis


title: LNCaP_R1000_Snx631_72h_Rep3

source_name: LNCaP

growth_protocol: LNCaP cells were cultured in RPMI-1640 media supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 1.5 g/L sodium bicarbonate, 10 mM HEPES, 0.45% D-glucose, and either 10% fetal bovine serum (FBS) or charcoal stripped FBS (CSS), plus 1% penicillin-streptomycin (P/S). grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine.  LNCaP cells were seeded into 12-well plates at the density of 3 X 105/well and cultured in CSS media for 72 hours before start of treatment.

treatment_protocol: In study 1, cells were treated with DMSO (0.1%), Senexin B (1 μM), R1881 (0.1 nM), or a combination of Senexin B and R1881 for 24 hours. In study 2, the cells were treated with DMSO (0.1%), SNX631 (500 nM), R1881 (1 nM), or a combination of SNX631 and R1881, for 72 hours.

value: LNCaP

value: LNCaP cells treated with 1 nM R1881 and 500 nM SNX631 for 72 hours


title: DU145_shCon_2

value: prostate


title: LNCaP_R1000_Snx631_72h_Rep4

value: prostate cancer cells


title: UC41_LC_S21


title: UC71_LC_S13


title: LNCaP_R1000_Ctrl_72h_Rep2

value: LNCaP cells treated with 1 nM R1881 for 72 hours


title: LNCaP_R1000_Snx631_72h_Rep2


title: UC41_LC_S14


title: LNCaP_R1000_Ctrl_72h_Rep3


title: H14_colon_S22

value: Healthy


title: LNCaP_R1000_Ctrl_72h_Rep4


title: CD74_LC_S18

value: Stricturing, fistulizing/ penetrating


title: LNCaP_AD_Snx631_72h_Rep3

value: WT

value: LNCaP cells treated with 500 nM SNX631 for 72 hours


title: CD69_LC_S25

value: fistulizing/ penetrating


title: H14_colon_S29


title: CD74_LC_S11


title: LNCaP_AD_Snx631_72h_Rep2


title: CD69_LC_S18


title: LNCaP_AD_Snx631_72h_Rep4


title: UC71_LC_S20


title: LNCaP_AD_Snx631_72h_Rep1


title: CD68_LC_S17

value: inflammatory (NSNP)


title: LNCaP_R1000_Ctrl_72h_Rep1


title: LNCaP_R1000_Snx631_72h_Rep1


title: LNCaP_AD_Ctrl_72h_Rep4

value: LNCaP cells treated with 0.1% DMSO (vehicle control) for 72 hours


title: CD61_LC_S27

value: Colon

value: ORG

value: Stricturing


title: CD68_LC_S10


title: LNCaP_AD_Ctrl_72h_Rep3


title: UC71_R_S19


title: LNCaP_AD_Ctrl_72h_Rep2


title: CD23_LC_S12


title: LNCaP_R100_SnxB_24h_Rep2

value: LNCaP cells treated with 0.1 nM R1881 and 1μM Senexin B for 24 hours


title: LNCaP_AD_Ctrl_72h_Rep1


title: CD23_LC_S19


title: LNCaP_R100_SnxB_24h_Rep3


title: CD61_LC_S20


title: siRPS27-2

city: Urumqi

first: Jingzhan

last: Zhang

state: Xinjiang

address: NO. 91, Tianchi Road, Tianshan District

department: Dermatology

institute: People’s Hospital of Xinjiang Uygur Autonomous Region

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. While several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with P value <0.05 and fold change>1.5 or < 0.67.
The threshold for RASE detection was set to an RASE ratio >0.2 and P-value <0.05.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include reads counts for each Sample.
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.

source_name: HUVEC

extract_protocol:
Total RNA was extracted from RPS27 siRNA group and RPS27 siRNA NC group using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Following RNA extraction, the DNA was digested with DNase I. RNA quality was determined by measuring the A260/A280 ratio using a NanodropTM One/OneC spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Electrophoresis (1.5% agarose gel) was performed to confirm the RNA integrity. Qualified RNAs were quantified using the Qubit™ RNA Assay Kit (Life Technologies, Carlsbad, CA, USA).
An RNA-seq library was prepared from 2 µg of total RNA using a KCTM Stranded mRNA Library Prep Kit for Illumina (cat. no. DR08402, Wuhan Seq health Co., Ltd., Wuhan, China). Polymerase chain reaction (PCR) products corresponding to 200–500 bp were enriched.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions. A NovaSeq 6000 sequencer (Illumina, San Diego, CA, USA) with a PE150 model was used for quantification and final sequencing.

value: HUVEC

value: Normal human umbilical vein endothelial cells

value: RPS27 siRNA (RPS27 gene silent)


title: LNCaP_R100_Ctrl_24h_Rep1

value: LNCaP

value: LNCaP cells treated with 0.1 nM R1881 for 24 hours


title: siRPS27-3


title: LNCaP_R100_SnxB_24h_Rep1

value: prostate cancer cells


title: LNCaP_R100_Ctrl_24h_Rep2


title: LNCaP_R100_Ctrl_24h_Rep3


title: NC-3

value: NC siRNA (negative control)


title: NC-1


title: Hs, 293T, ANKRD11 KD, rep2

first: Shaobo

last: Liang

state: Hubei Sheng

address: BaYi Road, LUOJIA HILL

institute: Wuhan University

data_processing:
Raw reads were cleaned with trim-galore and mapped to the Drosophila melanogaster genome (dm6, FlyBase) and Homo sapiens genome (hg38, Ensembl) using STAR for mRNA sequencing and Bowtie2 for sequencing of CUT&Tag and ChIP assays.
For mRNA sequencing, the reads at the gene level were summarized by featureCounts, followed by DESeq2 R package for analysis of differential expression.
For CUT&Tag and ChIP sequencing, duplicate reads were removed by picard, and peaks were called using MACS2.
Supplementary files format and content: narrow peaks of Cut&Tag and ChIP sequencing
Supplementary files format and content: read count of RNAseq

extract_protocol:
RNA was harvested using TRI Reagent (Sigma-Aldrich). 1 ug of total RNA was used for the construction of sequencing libraries. ChIP DNA was pulled down by H3K9ac antibody in HEK293T cells. DNA for CUT&Tag-seq was cleavaged Under Target & Tagmentation by RNPC3 or HDAC3 antibody in HEK293T cells.
RNA libraries for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2 following manufacturer's protocols. DNA libraries for CUT&Tag-seq were prepared using CUT&Tag Assay Kit (pAG-Tn5) following manufacturer's protocols. DNA libraries for ChIP-seq were prepared using Scale ssDNA-seq Lib Prep Kit following manufacturer's protocols.

value: HsANKRD11 KD


title: LNCaP_AD_SnxB_24h_Rep1

value: WT

value: LNCaP cells treated with 1μM Senexin B for 24 hours


title: LNCaP_AD_SnxB_24h_Rep2


title: Hs, 293T, ANKRD11 KD, rep1


title: Hs, 293T, ANKRD11 KD, rep3


title: NC-2


title: LNCaP_AD_Ctrl_24h_Rep3

value: LNCaP cells treated with 0.1% DMSO (vehicle control) for 24 hours


title: LNCaP_AD_Ctrl_24h_Rep2


title: siRPS27-1


title: LNCaP_AD_Ctrl_24h_Rep1


title: LNCaP_AD_SnxB_24h_Rep3


title: Hs, 293T, 65K KD, rep2

value: Hs65K KD


title: Hs, 293T, 65K KD, rep1


title: Rv1_WT_Cas_Ctrl_Rep6

value: xenograft

value: Rv1-WT xenograft (WT_Cas_Ctrl_#5) growing castrated NSG male mice, control group (Cas-Ctrl)


title: IMR90, mock, replicate 2, RNA-seq

data_processing:
Libraries were sequenced using Illumina HiSeq 4000 (dl1500, mock, dl312) or Illumina NovaSeq (dl1500_mut, mock_mut, RB-_mut, p300-_mut, p400-_mut) to obtain 100 or 150 bp-long reads, respectively.
RNA-seq reads were aligned to the GRCh38 human reference genome using STAR. Only uniquely mapped reads were considered for downstream analyses and subjected to counting with the featureCounts tool of the SubRead Python package.
Alus identified by the pipeline were subsequently filtered for an expression coverage of at least 1000 nt, corresponding to 5 paired-end reads of length 100 nt. The union of these Alus from all the samples in the experiment, considered only once, constitute the single, comprehensive list of expression-positive Alus. To be considered as expressed in a sample, each of the Alus in the comprehensive list needs to have more than 0 read counts in it.
Differentially expressed Alu sequences were identified using the DESeq2 package. Alu sequences with a log2 fold-change ≥ 0.5 or ≤ -0.5 and an adjusted p-value < 0.05 were deemed as differentially expressed.
Assembly: hg38
Assembly: AC_000008.1 (Human adenovirus 5)
Supplementary files format and content: bigWig (samples *.CM.bw are mapped to the hg38 human genome, whereas samples *_CPM.bw are mapped to the AC_000008.1 Adenovirus5 genome)

extract_protocol:
24 hours post-infection, cells were lysed with Trizol and total RNA was extracted using the Direct-zol RNA MiniPrep Plus (Zymo research). Eluted RNA was treated with DNase (Invitrogen).
Total RNA (1 μg) from dl1500, dl312 and mock infections was processed using a Ribo-Zero rRNA Removal Kit (Epicentre) to remove rRNA. Total RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA library Preparation kit. For the Adenovirus5 mutants experiment, total RNA (1 μg) from wt e1a (dl1500), e1a_RB-b-, e1a_p300-b-, e1a_p400-b- and mock infections was processed using the RiboCop rRNA Depletion Kit (Lexogen), and total RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA library Preparation kit.

treatment_protocol: Low passage IMR90 lung fibroblasts were grown to confluence in 60 mm dishes and incubated two more days without changing the medium to arrest cells in G1/0. On the day of infection, the medium was collected (conditioned medium) and confluent cells were incubated with mock or with the indicated Ad5-based vectors for 1 hr in PBS. At the end of the infection, cells were washed and transferred back to conditioned medium. The infections were performed at multiplicity of infection (MOI) 40 for dl1500 and dl312, 160 MOI for e1a_RB-b-, 60 MOI for e1a_p300-b- and 6 MOI for e1a_p400-b-, in order to achieve comparable amounts of wt and mutant e1a protein expression as assayed by Western blotting.

value: Lung

value: IMR90 human primary lung fetal fibroblasts

value: Contact-inhibited IMR90

value: Mock-infected


title: IMR90, dl312, replicate 2, RNA-seq


title: Hs, 293T, Ctrl, rep3

value: Ctrl


title: IMR90, dl312, replicate 1, RNA-seq


title: Hs, 293T, Ctrl, rep2


title: Hs, 293T, Ctrl, rep1


title: Hs, 293T, ANKRD11KD, input


title: IMR90, mock, replicate 1, RNA-seq


title: Hs, 293T, 65K KD, input


title: IMR90, dl1500, replicate 1, RNA-seq


title: Hs, 293T, ANKRD11 KD, ChIP, rep2

value: H3K9ac (ab4441, abcam)


title: Hs, 293T, Ctrl, input


title: Heyc2_TET1

city: Taipei

first: Hung-Cheng

last: Lai

address: No.250, Wuxing St.

department: Department of Obstetrics and Gynecology, School of Medicine, College of Medicine,

country: Taiwan

institute: Taipei Medical University

data_processing:
The RNA reads were aligned to the human reference genome hg19, using Bowtie2 V2.2.6 (SourceForge, Slashdot Media, La Jolla, CA, USA), and relative gene expression was quantified as transcripts per million (TPM) and Fragments Per Kilobase of transcript per Million (FPKM) mapped reads, using RSEM v1.2.17 (GitHub, San Francisco, CA, USA).
Genome_build: hg19
Supplementary_files_format_and_content: FPKMs

source_name: Ovarian cancer cells

extract_protocol:
Total RNA was quantified using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA), checked for purity and integrity on a Bioanalyzer-2100 device (Agilent Technologies, Santa Clara, CA), and performed the next-generation sequencing. Libraries were prepared using TruSeq RNA Sample Preparation Kits (Illumina, San Diego, CA, USA), according to the manufacturer’s protocols. Specifically, each library was paired-end sequenced (2 × 150 bp) on a HiSeq-4000 platform (Illumina, San Diego, CA, USA). The RNA reads were then aligned to the human reference genome hg19, using Bowtie2 V2.2.6 (SourceForge, Slashdot Media, La Jolla, CA, USA), and relative gene expression was quantified as transcripts per million (TPM) and Fragments Per Kilobase of transcript per Million (FPKM) mapped reads, using RSEM v1.2.17 (GitHub, San Francisco, CA, USA).
Libraries were prepared using TruSeq RNA Sample Preparation Kits (Illumina, San Diego, CA, USA), according to the manufacturer’s protocols. Specifically, each library was paired-end sequenced (2 × 150 bp) on a HiSeq-4000 platform (Illumina, San Diego, CA, USA).

treatment_protocol: 3 μg pCMV6/TET1or empty plasmid were transfected using lipofectamine 2000 (Invitrogen,Thermo Fisher Scientific Waltham, MA, USA), following a standard protocol. Cells were selected and cultivated with fresh culture medium containing 400 μg/ml Geneticin®.

value: Ovarian cancer cells

value: TET1 overexpressed


title: Heyc2_Ctrl

value: Wild-type


title: Skov3_Ctrl


title: Hs, 293T, ANKRD11 KD, ChIP, rep3


title: Hs, 293T, ANKRD11 KD, ChIP, rep1


title: Skov3_TET1


title: Hs, 293T, 65K KD, ChIP, rep3


title: AM633_DMSO_d0.005_Rep06 [AM6330093]

city: Indianapolis

first: Shreedharan

last: Sriram

address: 9330 Zionsville Road

institute: Corteva Agriscience

data_processing:
Adapter sequences remaining within the reads were trimmed (using parameters minlength=35 trimq=20 ktrim=r qtrim=rl k=23 mink=11 hdist=1) using the bbmap tool (v 38.18)
any reads aligning to Zebrafish rRNA sequences were removed using the bbmap tool (v38.18) from the JGI bbtools software package.
Zebrafish transcript abundances were calculated on a per sample basis using the Salmon software (v.1.2.0) 11 (with parameters “--seqBias --validateMappings --numBootstraps 100 --libType SR”) processed against the D. rerio GRCz11 reference genome and annotation 4 downloaded from Ensembl
Following transcript level abundance estimation, gene level expression counts were summarized from the salmon output using the tximport package (v1.26) 12 in R
any protein coding gene with less than an abundance count of ten across all samples were removed from further analysis
The DESeq2 analysis package (v1.34.0) in R 13 (version 4.1.3) was used for data normalization (using the variance stabilizing transformation (vst) method), handling batch effects and identification of differentially expressed genes between control groups and dose treatment groups for each molecule tested.
Assembly: D. rerio GRCz11 reference genome
Supplementary files format and content: tab-delimited text file which includes raw gene count values for each Sample
Supplementary files format and content: tab-delimited text file which includes vst-normalized and batch corrected gene expression table (filtered for low expressing genes)

organism: Danio rerio

source_name: embryo

growth_protocol: Please refer to associated manuscript

extract_protocol:
Total RNA was isolated from zebrafish embryo samples from BioBide using the Qiagen RNeasy Mini kit following the manufacturer’s protocol. RNA samples had RNA Quality Scores ≥7 as determined with a 5200 Fragment Analyzer System (Agilent, Santa Clara, CA).
The Illumina Stranded mRNA Sample Preparation kit (Illumina, San Diego, California, U.S.A.) was used to generate RNAseq libraries following the manufacturer’s recommended protocol. First, poly-A containing mRNA was purified from 800 ng of total RNA using poly-T oligo-attached magnetic beads. Purified mRNA was fragmented to approximately 200 bp average length using divalent cations under high temperature. Following fragmentation, SuperScript II reverse transcriptase and random hexamers were used to synthesize first strand cDNA. Second strand synthesis was completed using dUTP-containing Second Strand Marking Master Mix. The resulting blunt end double stranded cDNA fragments underwent end repair, poly A-tailing, and ligation to Illumina index-anchors.  Anchor-ligated library products were enriched with dual-indexed Illumina adapters (IDT for Illumina DNA/RNA Indexes sets) with 13 cycles of PCR. Individual sample libraries were analyzed for fragment quality and quantity using a Tapestation 4200 with D1000 screentape.  Individual libraries were pooled together based on equal nmol amount.  The pooled library was quantitated by Qubit fluorometer (Thermo Scientific, Waltham, Massachusetts, U.S.A.) and further diluted to 2 nM. The normalized and pooled library was further diluted to 2 pM and loaded onto an Illumina NovaSeq6000 following manufacturer’s protocol and sequenced with single-read 100 bp configuration to generate raw RNAseq reads

treatment_protocol: Please refer to associated manuscript

value: embryo

value: 5 days post fertilization

tag: strain

value: Transgenic zebrafish (Danio rerio) Tg(cmlc2:CopEGFP)

tag: loading dose_level_(mg/kg)


title: Hs, 293T, 65K KD, ChIP, rep2

tag: chip antibody


title: AM633_DMSO_d0.005_Rep04 [AM6330091]

tag: developmental stage


title: Hs, 293T, 65K KD, ChIP, rep1


title: Hs, 293T, Ctrl, ChIP, rep3


title: AM633_Pro_d70_Rep03 [AM6330090]


title: AM633_DMSO_d0.005_Rep05 [AM6330092]


title: Hs, 293T, Ctrl, ChIP, rep2


title: AM633_Pro_d70_Rep02 [AM6330089]


title: AM633_Pro_d40_Rep03 [AM6330087]


title: Hs, 293T, ANKRD11 KD, HDAC3, Cut&Tag, rep3

data_processing:
Raw reads were cleaned with trim-galore and mapped to the Drosophila melanogaster genome (dm6, FlyBase) and Homo sapiens genome (hg38, Ensembl) using STAR for mRNA sequencing and Bowtie2 for sequencing of CUT&Tag and ChIP assays.
For mRNA sequencing, the reads at the gene level were summarized by featureCounts, followed by DESeq2 R package for analysis of differential expression.
For CUT&Tag and ChIP sequencing, duplicate reads were removed by picard, and peaks were called using MACS2.
Supplementary files format and content: narrow peaks of Cut&Tag and ChIP sequencing
Supplementary files format and content: read count of RNAseq
Library strategy: Cut&Tag

value: HsANKRD11 KD

value: HDAC3 (10255-1-AP, Proteintech)


title: IMR90, dl1500, replicate 2, RNA-seq

value: WT


title: AM633_Pro_d70_Rep01 [AM6330088]


title: Rv1_Luc_Cas_Ctrl_Rep1

value: xenograft

value: prostate cancer cells

value: Luciferase-expressing

value: Rv1-Luc xenograft (Luc_Cas_Ctrl_#6) growing castrated NSG male mice, control group (Cas-Ctrl)


title: Hs, 293T, Ctrl, ChIP, rep1


title: AM633_Pro_d40_Rep01 [AM6330085]


title: AM633_Pro_d40_Rep02 [AM6330086]


title: Hs, 293T, ANKRD11 KD, HDAC3, Cut&Tag, rep1


title: AM633_Pro_d15_Rep03 [AM6330084]


title: Hs, 293T, 65K KD, rep3

value: Hs65K KD


title: Hs, 293T, Ctrl, HDAC3, Cut&Tag, rep2


title: Hs, 293T, Ctrl, HDAC3, Cut&Tag, rep3


title: Hs, 293T, Ctrl, HDAC3, Cut&Tag, rep1


title: AM633_Pro_d5_Rep03 [AM6330081]


title: Hs, 293T, ANKRD11 KD, 65K, Cut&Tag, rep3

value: 65K/RNPC3 (25820-1-AP, Proteintech)


title: AM633_Pro_d5_Rep02 [AM6330080]


title: Hs, 293T, ANKRD11 KD, 65K, Cut&Tag, rep2


title: AM633_Nit_d80_Rep02 [AM6330077]


title: Hs, 293T, Ctrl, 65K, Cut&Tag, rep2

value: Ctrl


title: Rv1_WT_Cas_SNX631_Rep1

value: Rv1-WT xenograft (WT_Cas_Snx_#9) growing castrated NSG male mice, SNX631 treatment group (Cas-Snx)


title: Hs, 293T, Ctrl, 65K, Cut&Tag, rep3


title: AM633_Nit_d80_Rep03 [AM6330078]


title: Rv1_DKO_19M_Cas_Rep4

value: CDK8/19-double kncokout, re-expressing human CDK19-D173A kinase-dead mutant

value: Rv1-dKO-CDK19M xenograft (dKO-19M_Cas_#5) growing castrated NSG male mice


title: AM633_Pro_d5_Rep01 [AM6330079]


title: Hs, 293T, ANKRD11 KD, 65K, Cut&Tag, rep1


title: AM633_Nit_d40_Rep02 [AM6330074]


title: AM633_Nit_d40_Rep01 [AM6330073]


title: Rv1_DKO_19M_Cas_Rep2

value: Rv1-dKO-CDK19M xenograft (dKO-19M_Cas_#2) growing castrated NSG male mice


title: AM633_Nit_d40_Rep03 [AM6330075]

value: embryo


title: AM633_Pro_d15_Rep02 [AM6330083]

value: 5 days post fertilization


title: Rv1_DKO_19M_Cas_Rep3

value: Rv1-dKO-CDK19M xenograft (dKO-19M_Cas_#4) growing castrated NSG male mice


title: AM633_Nit_d10_Rep03 [AM6330072]

value: Transgenic zebrafish (Danio rerio) Tg(cmlc2:CopEGFP)


title: Rv1_DKO_19_Cas_Rep4

value: CDK8/19-double kncokout, re-expressing human wt CDK19

value: Rv1-dKO-CDK19 xenograft (dKO-19_Cas_#1) growing castrated NSG male mice


title: Hs, 293T, Ctrl, 65K, Cut&Tag, rep1


title: Rv1_DKO_19_Cas_Rep3

value: xenograft

value: Rv1-dKO-CDK19 xenograft (dKO-19_Cas_#3) growing castrated NSG male mice


title: AM633_Nit_d10_Rep01 [AM6330070]


title: AM633_Met_d200_Rep03 [AM6330069]


title: Rv1_DKO_19_Cas_Rep2

value: prostate cancer cells

value: Rv1-dKO-CDK19 xenograft (dKO-19_Cas_#2) growing castrated NSG male mice


title: AM633_Nit_d80_Rep01 [AM6330076]


title: AM633_Met_d200_Rep02 [AM6330068]


title: Rv1_DKO_19_Cas_Rep1

value: Rv1-dKO-CDK19 xenograft (dKO-19_Cas_#5) growing castrated NSG male mice


title: AM633_Met_d200_Rep01 [AM6330067]


title: Rv1_DKO_19M_Int_Rep4

value: Rv1-dKO-CDK19M xenograft (dKO-19M_Int_#4) growing intact NSG male mice


title: AM633_Nit_d10_Rep02 [AM6330071]


title: AM633_Met_d50_Rep03 [AM6330066]


title: AM633_Met_d50_Rep02 [AM6330065]


title: AM633_Met_d50_Rep01 [AM6330064]


title: Rv1_DKO_19M_Int_Rep3

value: Rv1-dKO-CDK19M xenograft (dKO-19M_Int_#2) growing intact NSG male mice


title: Rv1_DKO_19M_Int_Rep1

value: Rv1-dKO-CDK19M xenograft (dKO-19M_Int_#1) growing intact NSG male mice


title: AM633_Met_d6_Rep03 [AM6330063]


title: Rv1_DKO_19_Int_Rep2

value: Rv1-dKO-CDK19 xenograft (dKO-19_Int_#2) growing intact NSG male mice


title: AM633_Met_d6_Rep01 [AM6330061]


title: AM633_Met_d1_Rep02 [AM6330059]


title: Rv1_DKO_19_Int_Rep1

value: Rv1-dKO-CDK19 xenograft (dKO-19_Int_#4) growing intact NSG male mice


title: AM633_Met_d1_Rep03 [AM6330060]


title: Rv1_Luc_Int_SNX631_Rep4

value: Luciferase-expressing

value: Rv1-Luc xenograft (Luc_Int_Snx_#4) growing intact NSG male mice, SNX631 treatment group (Int-Snx)


title: Rv1_DKO_19M_Cas_Rep1

value: CDK8/19-double kncokout, re-expressing human CDK19-D173A kinase-dead mutant

value: Rv1-dKO-CDK19M xenograft (dKO-19M_Cas_#3) growing castrated NSG male mice


title: AM633_Fen_d8_Rep03 [AM6330057]

value: embryo

value: 5 days post fertilization

value: Transgenic zebrafish (Danio rerio) Tg(cmlc2:CopEGFP)


title: Rv1_Luc_Int_SNX631_Rep3

value: xenograft

value: Rv1-Luc xenograft (Luc_Int_Snx_#3) growing intact NSG male mice, SNX631 treatment group (Int-Snx)


title: AM633_Fen_d8_Rep02 [AM6330056]


title: AM633_Fen_d8_Rep01 [AM6330055]


title: Rv1_DKO_19M_Int_Rep2

value: prostate cancer cells

value: Rv1-dKO-CDK19M xenograft (dKO-19M_Int_#5) growing intact NSG male mice


title: Rv1_DKO_19_Int_Rep4

value: CDK8/19-double kncokout, re-expressing human wt CDK19

value: Rv1-dKO-CDK19 xenograft (dKO-19_Int_#1) growing intact NSG male mice


title: Rv1_Luc_Int_Ctrl_Rep4

value: Rv1-Luc xenograft (Luc_Int_Ctrl_#3) growing intact NSG male mice, control group (Int-Ctrl)


title: Rv1_Luc_Int_SNX631_Rep1

value: Rv1-Luc xenograft (Luc_Int_Snx_#1) growing intact NSG male mice, SNX631 treatment group (Int-Snx)


title: AM633_Fen_d4_Rep02 [AM6330053]


title: Rv1_Luc_Int_SNX631_Rep5

value: Rv1-Luc xenograft (Luc_Int_Snx_#2) growing intact NSG male mice, SNX631 treatment group (Int-Snx)


title: Rv1_Luc_Int_Ctrl_Rep5

value: Rv1-Luc xenograft (Luc_Int_Ctrl_#1) growing intact NSG male mice, control group (Int-Ctrl)


title: AM633_Met_d6_Rep02 [AM6330062]


title: Rv1_DKO_19_Int_Rep3

value: Rv1-dKO-CDK19 xenograft (dKO-19_Int_#3) growing intact NSG male mice


title: AM633_Fen_d4_Rep01 [AM6330052]


title: Rv1_Luc_Int_Ctrl_Rep2

value: Luciferase-expressing

value: Rv1-Luc xenograft (Luc_Int_Ctrl_#4) growing intact NSG male mice, control group (Int-Ctrl)