title: YiLi07_Mo_CD8, CITE

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

data_processing:
bcl2fastq (v2.20.0.422) to demultiplex UMIs
count and aggr Cell Ranger (7.0.0) was used to generate filtered and aggregate UMI matrix, respectively
Seurat (4.3.0). Was used to filter, normalize and scale UMI matrix
Tissue identities were inferred by MULTIseqDemux (autoThresh = TRUE and maxiter = 10) from Seurat (v4.3.0) using the UMI matrix
Assembly: mm10 (v3.0.0)
Supplementary files format and content: cd8_cre_annotation.txt.gz for 8562 cells in TAB delimited TXT
Supplementary files format and content: cd8_cre_umi.txt.gz for 8562  cells in TAB delimited TXT
Supplementary files format and content: feature_barcodes.csv.gz Cell Ranger's feature table to deumltiplex TotalSeq C data

molecule: protein

source_name: Colon lamina propria

extract_protocol:
10x Genomics' Single Cell Immune Profiling 5'v2
Libraries were prepared according to manufacturer's recommendations using 10x Genomics' Single Cell Immune Profiling 5'v2 (Dual Index) with Feature Barcoding kit.

value: Colon lamina propria

value: CD8 T cell

value: 8-12 week in the begaining of transfer

tag: strain

value: Bcl6fl/flCd8aCre mice or Bcl6fl/fl

tag: library type

value: Hashtag derived oligonucleotide (HTO)

tag: antibodies/tags


title: s_4_withindex_sequence.txt_TACTCTA.fq

status: Public on Apr 24 2024

type: SRA

city: Boston

first: Abigael

last: Cheruiyot

address: 1 Joslin Place

country: USA

institute: Joslin Diabetes Center

library_source: genomic

data_processing:
A custom Perl script was used to determine the read counts for each sgRNA and map the sgRNAs to their gene IDs in the reference GeCKOv2 library
Supplementary files format and content: Raw read counts for each sgRNAs is provided in GeCKOV2 library B read counts.xls with multiple tabs for different samples

molecule: genomic DNA

organism: Homo sapiens

source_name: Uterus; Cervix

growth_protocol: HeLa cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin at 37°C with 5% CO2 in a humidified incubator.

extract_protocol:
Genomic DNA was extracted using PureLink Genomic DNA kit (ThermoFisher Scientific, K182001)
Two PCR reactions were used to prepare samples for Illumina Next-Gen sequencing. The first PCR was used to amplify sgRNA inserts in the cells, and the second PCR was used to add Illumina sequencing tags as well as index tags for sample identification. To improve the complexity of the library required for deep sequencing, a mixture of 5 forward primers with staggered nucleotides immediately upstream of the sgRNA sequences was used in the second PCR.
Survival screen after genome-wide KO of genes that may be important for survival under HU treatment, but not needed when Exo1 is also depleted

treatment_protocol: Exo1-KO cell lines were generated by transfection of  HeLa with pCRSIPRv2-sgRNA-expressing constructs with sgRNAs targeting human Exo1. Twenty-four hours after transfection, cells were selected withpuromycin(1.5μg/ml) for 2days. Single cells were grown in 96-well plates for amplification. Individual clones were verified bywestern blotto detect the depletion of Exo1. To carry out the screen, HeLa-Cas9 cells were infected with lentiviruses expressing the GeCKOv2 library (containing two sub-libraries) at a multiplicity of infection (MOI) of 0.3 with a 500x coverage of the library, selected 2 days post infection, and then cultured for 10 days. Cells were then treated with 4 mM HU for 24 hours and recovered in fresh DMEM medium for 3 days.

tag: tissue

value: Uterus; Cervix

tag: cell line

value: HeLa

tag: cell type

value: epithelial cell

tag: genotype

value: Exo1 KO

tag: treatment


title: Schwann Cells, NF2-WT

city: Heidelberg

first: Aurelio

middle: A

last: Teleman

address: Im Neuenheimer Feld 580

country: Germany

institute: German Cancer Research Center (DKFZ)

library_source: transcriptomic

data_processing:
Data were processed on the Galaxy server
Adapters were trimmed with "Trim Galore !"
Reads were aligned to UCSC hg38
Reads per sgRNA were counted using custom software ("count_features") available at https://github.com/aurelioteleman/Teleman-Lab
Assembly: hg38
Supplementary files format and content: tab-delimited file containing raw read counts for all samples as well as read counts normalized to library size

molecule: total RNA

source_name: Schwannoma

extract_protocol:
Total RNA was isolated using an RNeasy kit from Qiagen
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Schwannoma

value: Schwann Cells


title: YiLi07_Mo_CD8, Gex

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus

tag: age

value: Gene Expression


title: CD4 T-cells, uninfected, day 0, 000035

city: Edinburgh

first: Elisabeth

middle: Margaretha Diana Louise

last: van der Heijden

state: Midlothian

address: Easter Bush Campus

department: Division of Immunology

country: United Kingdom

institute: The Roslin Institute, The University of Edinburgh

data_processing:
Quality control using FastQC (v 0.11.9 - default parameters)
Trimming using TrimGalore (v 0.6.4) (--illumina --length 35 --paired)
Pseudoalignment using kallisto (v 0.46.1 - default parameters - 10 bootstraps)
Import of transcript-level abundances into R using tximport (v 1.24.0)
Differential expression analysis using DESeq2 (v 1.36.0)
Assembly: bosTau 9 (ARS-UCD1.2) and PiroplasmDB T. parva Muguga (GCA_000165365.1)
Supplementary files format and content: Comma-separated values files with raw counts of Bos taurus genes for each sample
Supplementary files format and content: Comma-separated values files with raw counts of Theileria parva genes for each sample

organism: Bos taurus

source_name: CD4 T-cells

growth_protocol: Cells were maintained in RPMI-1640 medium supplemented with 10% FBS, 50mM beta-mercaptoethanol and 1X penicillin-streptomycin, in a humidified incubator at 37C and 5% CO2.

extract_protocol:
Total RNA was isolated using the miRNeasy kit (Qiagen). 500ng of total RNA was use for library preparation.
The NEBNEXT Ultra II Directional RNA Library Prep kit was used with the Poly-A mRNA magnetic isolation module for library construction.

treatment_protocol: Cells were infected with saturating levels of fresh T. parva Muguga sporozoites.

value: CD4 T-cells

tag: time

value: day 0

tag: disease state

value: uninfected


title: s_4_withindex_sequence.txt_ATGACAG.fq

value: untreated


title: formalin-fixed paraffin-embedded prostate tissue :Sample16

status: Public on Apr 23 2024

type: RNA

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalization with lumi Bioconductor v3.2 R package

label: biotin

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted using the RNeasy FFPE KIT (QIAGEN GmgH, Hilden, Germany) according to manufacturer’s instructions. Briefly, punch biopsies, 0.6 mm in diameter, were obtained from each tissue block and were placed in a tube containing 1 ml xylene. Immediately after the 100% ethanol extraction step, an additional 70% ethanol extraction was performed. Proteinase K digestions were at 55uC for 35 min followed by 80uC for 25 min. Genomic DNA was removed by centrifugation in gDNA Eliminator spin columns at 8000 x g for 1 min, after which a volume of 1400 ml ethanol was added to the flow-through fraction, resulting in three passes through the RNeasy MinElute spin column. The first Buffer RPE wash was performed at 8000 x g for 1 min and prior to the final elution the dried spin column membranes were incubated in 30 ml RNase-free water for 10 min at room temperature before centrifugation.

tag: group

value: Local

value: PCa patient


title: formalin-fixed paraffin-embedded prostate tissue :Sample26

value: Advanced


title: formalin-fixed paraffin-embedded prostate tissue :Sample21

value: Metastatic


title: formalin-fixed paraffin-embedded prostate tissue :Sample4


title: formalin-fixed paraffin-embedded prostate tissue :Sample24


title: 22-01-041

city: Houston

first: Akdes

last: Serin Harmanci

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Raw reads from the RNA-seq data were processed using an in-house pipeline that uses STAR for read alignment and FeatureCount for expression count.
Assembly: hg38
Supplementary files format and content: raw expression count matrix

source_name: Meningioma

extract_protocol:
AllPrep DNA/RNA/Protein Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.Paired-end RNA sequencing was performed.

tag: class

value: C


title: 22-01-049


title: formalin-fixed paraffin-embedded prostate tissue :Sample17


title: 22-01-044

value: A


title: 22-01-048


title: formalin-fixed paraffin-embedded prostate tissue :Sample10


title: 22-01-043


title: formalin-fixed paraffin-embedded prostate tissue :Sample15


title: formalin-fixed paraffin-embedded prostate tissue :Sample25


title: formalin-fixed paraffin-embedded prostate tissue :Sample14


title: formalin-fixed paraffin-embedded prostate tissue :Sample19


title: 22-01-042


title: formalin-fixed paraffin-embedded prostate tissue :Sample23


title: formalin-fixed paraffin-embedded prostate tissue :Sample22


title: formalin-fixed paraffin-embedded prostate tissue :Sample3


title: formalin-fixed paraffin-embedded prostate tissue :Sample27


title: formalin-fixed paraffin-embedded prostate tissue :Sample18


title: formalin-fixed paraffin-embedded prostate tissue :Sample13


title: formalin-fixed paraffin-embedded prostate tissue :Sample1


title: formalin-fixed paraffin-embedded prostate tissue :Sample2


title: formalin-fixed paraffin-embedded prostate tissue :Sample20


title: formalin-fixed paraffin-embedded prostate tissue :Sample12


title: 22-01-035


title: 22-01-039


title: 22-01-034


title: 22-01-033


title: 22-01-026


title: 22-01-023


title: 22-01-022


title: 22-01-019

value: B


title: 22-01-012


title: 22-01-016


title: 22-01-014


title: 22-01-015


title: 22-01-008


title: 21-01-099


title: 22-01-001


title: 21-01-101


title: 22-01-021


title: 21-01-097


title: 21-01-095


title: 21-01-094


title: 21-01-093


title: 21-01-096


title: 21-01-098


title: 21-01-091


title: 21-01-090


title: 21-01-086


title: 21-01-084


title: F1-AGVT_c45_AG (MS356_063)

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: F1-AGVT (NCLCN-261), d8hPGCLC, expansion culture c45 BMP2(+) AG(+)

data_processing:
All reads were processed with cutadapt v1.18 for trimming adaptor and poly-A, then mapped onto GRCh38.p12 transcript references using Tophat v2.1.1.
Resulting BAM files were processed with HTseq v0.9.1 to calculate read counts per gene.
Read counts per gene were divided by total read counts in all chromosomal genes to estimate RPM values for genes.
Resulting BAM files were separately processed with SNPsplit v0.3.2 to split into alleles. Resulting bam files were processed with Htseq v0.9.1 to calculate read counts per gene.
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: NCLCN AGVT

extract_protocol:
Total RNA was extracted from cells by NucleoSpin RNA XS (MACHEREY-NAGEL, U0902A) according to the manufacturer’s instructions.
1 ng of extracted RNA was used for the reverse transcription and the cDNA amplification described in the previous report (Nakamura, 2015). Sequencing libraries were generated from amplified cDNA as described previously (Murase, 2020).
SC3-seq (Nakamura, 2015)

tag: transgene

value: TFAP2C-EGFP, DDX4-tdTomato knock-in

value: differentiated hPGCLC

value: WT

value: culture day 45

value: Expansion culture with BMP signalling


title: 22-01-018


title: 22-01-020


title: 21-01-082


title: 21-01-080


title: 21-01-083


title: 21-01-076


title: 21-01-069


title: 21-01-059_B2_Rep2


title: 21-01-064


title: 21-01-059_B2_Rep1


title: 21-01-058


title: 21-01-065


title: 22-01-002


title: 21-01-092


title: 21-01-056


title: 21-01-063


title: 21-01-062


title: 21-01-050


title: 21-01-057


title: 21-01-051


title: 21-01-049


title: 21-01-048


title: 21-01-046


title: 21-01-044


title: 21-01-085


title: 21-01-041


title: 21-01-039


title: 21-01-028


title: 21-01-038


title: 21-01-035


title: 21-01-037


title: 21-01-031


title: 21-01-021


title: 21-01-019


title: 21-01-027


title: 21-01-054


title: 21-01-024


title: 21-01-010


title: 21-01-004


title: 21-01-022


title: 9Myc-Swd2 strain 1

city: Chuncheon

first: Seho

last: Kim

address: 강원 춘천시 우석로79번길 15-5

department: Department of biomedical science

country: South Korea

institute: Kangwon National Unversity

data_processing:
The Illumina Hiseq generates raw images utilizing HCS(HiSeq Control Software v2.2) for system control
Base calling through an integrated primary analysis software called RTA(Real Time Analysis. v1.18)
The BCL(base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq(v1.8.4)
Adapters are not trimmed away from the reads.
Genome_build: sacCer3
Supplementary_files_format_and_content: abundance measurements

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cells are cultured at 10ml YPD(1% Yeast extract, 2% Peptone, 2% Glucose) in 100ml flask (30℃, 230rpm) and harvested at OD600=1.0

extract_protocol:
RNA was harvested according to the MN RNA-isolation kit(MN;#7409555.50) standard protocols. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina(NEB #E7420S) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 9Myc tag at N-terminal of Swd2


title: 21-01-016


title: WT strain 2

address: 강원 춘천시 우석로79번길 15-5

value: wildtype


title: 21-01-011


title: 21-01-013


title: 21-01-009


title: WT strain 1

address: 강원 춘천시 우석로79번길 15-5


title: 21-01-015


title: 21-01-018


title: 21-01-007


title: 21-01-005


title: 9Myc-Swd2 strain 2

address: 강원 춘천시 우석로79번길 15-5


title: Adipose O3 22

city: Research Triangle Park

first: Thomas

last: Jackson

state: NC

address: 109 TW Alexander Dr

department: CPHEA

institute: United States Environmental Protection Agency

data_processing:
Partek Alignment to Rat Genome
Partek Quatification (Gene) using EM
Only genes with 1 or more reads in 10 or more samples retained
Genes rounded to integers in preparation for DESeq2
Normalized Counts from DESeq2
Assembly: rn6 ensemble release 83
Supplementary files format and content: Processed_Adrenal_Norm.csv is a csv file showing the normalized counts for Adrenals
Supplementary files format and content: Processed_HT_Norm.csv is a csv file showing the normalized counts for hypothalamus
Supplementary files format and content: Processed_Liver_Norm.csv is a csv file showing the normalized counts for liver
Supplementary files format and content: Processed_Lung_Norm.csv is a csv file showing the normalized counts for lung
Supplementary files format and content: Processed_Muscle_Norm.csv is a csv file showing the normalized counts for muscle
Supplementary files format and content: Processed_Adipose_Norm.csv is a csv file showing the normalized counts for adipose

organism: Rattus norvegicus

source_name: Adipose

extract_protocol:
Tissues were removed and flash frozen on dry ice. Total RNA was isolated from each tissue using Qiagen RNAeasy Mini kits (liver, lung), Qiagen Fibrous Tissue Mini kits (muscle), Qiagen Lipid Tissue Mini kits (adipose; Germantown, MD), or Direct-Zol RNA MiniPrep kits from Zymo Research (hypothalamus, adrenals; Irvina, California). RNA quality was examined using Agilent Bioanalyzer (Agilent Technologies, Santa Clara, California). RNA samples were processed and run in Apollo324 automated sample processing system for mRNA selection (Wafergen Biosystems, Fremont, California). RNA-Seq library was prepared with Wafergen’s PrepX mRNA 48 Protocol. cDNA libraries were amplified and dsDNA from each library was quality checked by Agilent Bioanalyzer with an RIN cutoff of 7 (Agilent Technologies, Santa Clara, California). Each library was sequenced according to Illumina NextSeq 500 protocols (1.8 pM + 5% PhiX from Illumina, Inc, San Diego, California). An n=6 per tissue per exposure were included, except for adipose where only 5 air and 5 ozone samples passed QC.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adipose

value: Wistar-Kyoto


title: Adipose O3 21


title: 20-01-061


title: Adipose O3 16


title: 20-01-059


title: 20-01-063


title: 21-01-002


title: Adipose Air 12

value: Air


title: 20-01-081


title: Adipose Air 9


title: 20-01-074


title: 20-01-082


title: Adipose O3 23


title: 20-01-050


title: Adipose O3 19


title: 20-01-069


title: 20-01-048


title: 20-01-055


title: 20-01-045


title: 20-01-072


title: 22-01-010


title: Adipose Air 5


title: Muscle O3 24

source_name: Muscle

value: Muscle


title: Muscle O3 23


title: 20-01-036


title: Muscle O3 17


title: Adipose Air 2


title: Muscle O3 15


title: 20-01-040


title: 20-01-033


title: 20-01-026


title: 20-01-025


title: 20-01-021


title: Muscle Air 11


title: 20-01-027


title: 20-01-018


title: Muscle O3 13


title: Muscle Air 7


title: Muscle Air 9


title: 20-01-020


title: Muscle Air 3


title: 20-01-039


title: 20-01-011


title: Muscle Air 2


title: Adipose Air 6


title: Muscle Air 4


title: 20-01-010


title: Lung O3 19

source_name: Lung

value: Lung


title: 20-01-006


title: 20-01-009


title: Muscle O3 16


title: Lung O3 16


title: Lung O3 15


title: 20-01-004


title: Lung O3 20


title: Lung O3 14


title: 19-01-099


title: 20-01-002


title: Lung O3 13


title: 20-01-003


title: Lung Air 9


title: 19-01-097


title: Lung Air 10


title: 19-01-096


title: 19-01-094


title: 20-01-014


title: Lung Air 8


title: 19-01-095


title: 19-01-091


title: 19-01-090


title: Lung Air 7


title: 19-01-089


title: Liver O3 19

source_name: Liver

value: Liver


title: Lung Air 1


title: 19-01-087


title: Liver O3 20


title: Liver O3 18


title: Liver O3 16


title: 19-01-083


title: 19-01-080


title: 19-01-079


title: Liver O3 14


title: Liver O3 13


title: 19-01-078


title: Liver Air 10


title: Liver Air 9


title: 19-01-074


title: Liver Air 6


title: 19-01-072


title: 19-01-061


title: Lung Air 2


title: Liver Air 7


title: 19-01-063


title: Hypothalamus O3 18

source_name: Hypothalamus

value: Hypothalamus


title: Liver Air 1


title: 19-01-057


title: 19-01-055

value: C


title: 19-01-051


title: Hypothalamus O3 14


title: Hypothalamus O3 17


title: Hypothalamus O3 16


title: Hypothalamus O3 13


title: 19-01-047


title: Hypothalamus Air 4


title: 19-01-032


title: 19-01-029


title: 19-01-064

value: A


title: 19-01-049

value: B


title: 19-01-054


title: Hypothalamus Air 6


title: Hypothalamus Air 7


title: 19-01-030


title: 19-01-038


title: Hypothalamus Air 2


title: Hypothalamus O3 15


title: 19-01-023


title: Liver Air 2


title: Hypothalamus Air 3


title: Adrenal O3 19

source_name: Adrenal

value: Adrenal


title: 19-01-018


title: Hypothalamus Air 1


title: 19-01-026


title: 19-01-017


title: Adrenal O3 17


title: Adrenal O3 20


title: Adrenal O3 14


title: Adrenal O3 15


title: 19-01-027


title: Adrenal O3 16


title: Adrenal Air 9


title: Adrenal Air 7


title: 19-01-016


title: 19-01-008


title: 19-01-007


title: 19-01-005


title: Adrenal Air 8


title: 18-01-016


title: Adrenal Air 11


title: 17-01-027


title: Adrenal Air 2


title: 17-01-038


title: 18-01-010


title: 17-01-041


title: RelA_p53_Sequential_2.0h

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

data_processing:
Demultiplexed reads where mapped to the NCBI37/mm9 genome using Hisat2.
Homer peak-calling (FDR < 0.01) was used to identify binding sites.
Binding sites were annotated to the closest gene (mm9).
Assembly: mm9
Supplementary files format and content: bedGraph files for each sample represent the strength of binding at each genomic location.

source_name: BMDM

growth_protocol: Bone marrow was extracted from hip, femur, tibia, and fibula of wild-type (C57/B16) or Nfkb1-/- mice. Cells were differentiated for 6-days in cell culture using 8% M-CSF prior to stimulation.

extract_protocol:
Samples were prepared as previously described (Barish et al., 2010). Crosslinking conditions of 1.0mM DSG and 1.0% formaldehyde were used for p50 and RelA ChIP-seq. Crosslinking conditions of 3.0mM DSG and 1.0% formaldehyde were used for IkBz ChIP-seq. Chromatin shearing was done using either the Bioruptor or Covaris M220. Immunoprecipitation was performed with either anti-RelA, anti-IkBz, or anti-p50 antibodies.
Using the Kapa LTP Library Preparation Kit, libraries were constructed according to manufacturers instructions.

value: BMDM

value: Wild-type (C57/B16)

value: 2.0h Lipid A


title: 16-01-004


title: 16-01-027


title: 19-01-003


title: 16-01-026


title: RelA_IkBz_Sequential_2.0h


title: 17-01-037


title: RelA_p50_Sequential_2.0h


title: RelA_in_p50_KO_2.0h_R1


title: Ikbz_in_p50_KO_Input_R3


title: 13-01-003


title: Adrenal Air 6


title: IkBz_in_p50_KO_2.0h_R2


title: Ikbz_in_p50_KO_Input_R1_R2


title: 15-01-040


title: IkBz_in_p50_KO_2.0h_R1


title: IkBz_in_p50_KO_2.0h_R3


title: 11-01-004


title: IkBz_Input_R3

value: Input


title: 16-01-031


title: RelA_Sequential_2.0h


title: 18-01-054


title: Sequential_Input


title: IkBz_2.0h_R3


title: IkBz_Input_R2


title: IkBz_6.0h_R2

value: 6.0h Lipid A


title: IkBz_2.0h_R2


title: 15-01-041


title: 15-01-037


title: PRP_18, PRP, week2

city: Rochester

first: Tao

last: Ma

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

data_processing:
Samples were sequenced using a 2x100bp Paired End (PE) configuration with Illumina HiSeq instrument (4000)
Image analysis and base calling were performed with Illumina BCL2FASTQ v2.19.0
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR 2.6.1c
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Assembly: HG38
Supplementary files format and content: tab-delimited text files include raw count and RPKM values for each Sample

source_name: Patient skin biopsy

extract_protocol:
RNA was isolated using miRNeasy Mini Kit (Qiagen). 20 ng of Total RNA was used to prepare the sequencing libraries.
RNA libraries for RNA-seq were prepared using the Illumina TruSeq® RNA Exome Library Prep kit (San Diego, CA), following manufacturer's protocols.

value: Patient skin biopsy

value: patient skin tisuse

value: R


title: PRP_48, PRP, week2


title: IkBz_0.5h_R2

value: 0.5h Lipid A


title: PRP_31, PRP, week2

value: NR


title: IkBz_0.0h_R2

value: Unstimulated


title: IkBz_Input_R1


title: PRP_04, PRP, week2


title: IkBz_6.0h_R1


title: PRP_24, PRP, week2


title: PRP_06, PRP, week2


title: PRP_28, PRP, week2


title: PRP_21, PRP, week2


title: PRP_36, PRP, week2


title: PRP_42, PRP, week2


title: PRP_33, PRP, week0

value: PRP


title: IkBz_0.5h_R1


title: IkBz_1.0h_R1

value: 1.0h Lipid A


title: IkBz_0.0h_R1


title: PRP_10, PRP, week0


title: PRP_20, PRP, week2


title: PRP_14, PRP, week0


title: PRP_46, PRP, week2


title: p50_Input_R2


title: p50_6.0h_R2


title: IkBz_1.0h_R2


title: p50_2.0h_R2


title: PRP_38, PRP, week0


title: p50_0.5h_R2


title: p50_0.0h_R2


title: PRP_29, PRP, week0


title: PRP_16, PRP, week0


title: PRP_08, PRP, week0


title: p50_6.0h_R1


title: PRP_02, PRP, week0


title: p50_2.0h_R1


title: p50_0.5h_R1


title: PRP_26, PRP, week0


title: p50_0.0h_R1


title: IkBz_2.0h_R1


title: PRP_11, PRP, week0


title: PRP_17, Ctrl, week2

value: Ctrl


title: GBS_only_I_R2_total_RNA

city: Cologne

first: Till

middle: David

last: Sauerwein

address: Gleueler Str. 60

department: Data Science and Services

institute: ZB MED - Information Centre for Life Sciences

description: GBS only replicate 2

data_processing:
Adapter filtering: Illumina’s TruSeq “Read 1” adapter sequence using cutadapt version: 1.15
Trimming of reads with a Phred score below 20 using cutadapt version 1.15
Poly(A) clipping reads using READemption 0.4.3
Discarding of reads with a length below 20 using READemption version 0.4.3
Aligning of reads to both genomes using segemehl version 0.2.0
Gene quantification using READemption version 0.4.3
Differential gene expression analysis using DESeq2 version: 1.18.1, R version: 3.4.4
Genome_build: Human: GENCODE version: 26, NCBI assembly name: GRCh38.p10 / Streptococcus: accession number: HG939456.1, Genbank assembly accession number: GCA_000689235.1
Supplementary_files_format_and_content: csv files containing DESeq2 results

organism: Streptococcus sp. 'group B'

source_name: Group B Streptococcus (GBS)

growth_protocol: Human: Growth of hCMEC/D3 cell line: hCMEC/D3 cells were maintained on tissue culture flasks coated with 1% rat tail collagen in EndoGRO MV medium (Millipore-Sigma). Cells were split onto 24-well tissue culture plastic dishes for experiments and allowed to grow to confluency (4 days) before infection experiments were conducted. Streptococcus: Wild-type GBS strains were cultivated in Todd-Hewitt broth (THB) at 37C in static culture/

extract_protocol:
Total RNA was collected using the MirVana RNA (Thermo Scientific) isolation kit
Sequencing was performed on a NextSeq500 platform (Illumina) in single-end mode for 75 cycles

treatment_protocol: iPSC-BECs were differentiated and infected with GBS at an MOI of 10 for 5 hours

value: uninfected


title: GBS_only_I_R3_total_RNA

description: GBS only replicate 3


title: PRP_35, Ctrl, week2


title: PRP_40, PRP, week0


title: PRP_19, Ctrl, week2


title: PRP_44, PRP, week0


title: PRP_45, Ctrl, week2


title: U2OS_siRFXANK_Nutlin_3_RNAseq

city: Jena

first: Martin

last: Fischer

state: Thuringia

address: Beutenbergstraße 11

department: Computational Biology

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

description: DESeq2_U2OS_siControl-vs-siRFXANK_Nutlin.tsv

data_processing:
Quantification and quality check of libraries were performed using the Agilent Bioanalyzer 2100 in combination with the DNA 7500 Kit. Sequence information was extracted in FastQ format using Illumina's bcl2fastq v2.20.0.422.
We utilized Trimmomatic v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming according to inspections made from FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.9 reports. Illumina universal adapter as well as mono- and di-nucleotide content was clipped using Cutadapt v2.10. Potential sequencing errors were detected and corrected using Rcorrector v1.0.3.1. Ribosomal RNA (rRNA) transcripts were artificially depleted by read alignment against rRNA databases through SortMeRNA v2.1. The preprocessed data was aligned to the reference genome hg38, retrieved along with its gene annotation from Ensembl v.92, using the mapping software segemehl v0.3.4 with adjusted accuracy (95%) and split-read option enabled (RNA-seq) or disabled (ChIP-seq). Mappings were filtered by Samtools v1.10 for uniqueness and properly aligned mate pairs. We removed duplicated reads with Picard MarkDuplicates v2.23.4.
Read quantification was performed on exon level using featureCounts v1.6.5, parametrized according to the strand specificity inferred through RSeQC v3.0.0. Differential gene expression and its statistical significance was identified using DeSeq2 v1.20.0.
Assembly: Genome_build: hg38
Supplementary files format and content: Supplementary_files_format_and_content: .tsv DESeq2 output

source_name: bone

extract_protocol:
Total cellular RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) following the manufacturer protocol.
Libraries were constructed from 500 ng of total RNA using NEBNext Ultra II RNA - polyA+ (mRNA) Library Preparation Kit following the manufacturer's description.

treatment_protocol: Treated for 24h with 10 µM Nutlin-3a or DMSO solvent control

value: bone

value: epithelial cells

value: wild-type

value: Nutlin-3a 10 µM 24 h


title: GBS_only_I_R1_total_RNA

description: GBS only replicate 1


title: U2OS_siRFXANK_Nutlin_2_RNAseq


title: PRP_03, Ctrl, week2


title: U2OS_siRFXANK_DMSO_2_RNAseq

description: DESeq2_U2OS_siControl-vs-siRFXANK_DMSO.tsv

value: DMSO 24 h


title: U2OS_siRFXANK_DMSO_3_RNAseq


title: PRP_32, Ctrl, week2


title: U2OS_siRFXANK_Nutlin_1_RNAseq


title: PRP_23, Ctrl, week2


title: U2OS_siRFXANK_DMSO_1_RNAseq


title: RPE-1_siRFXANK_Nutlin_3_RNAseq

description: DESeq2_RPE-1_siControl-vs-siRFXANK_Nutlin.tsv

source_name: retina

value: retina


title: PRP_27, Ctrl, week2


title: PRP_22, Ctrl, week2


title: PRP_47, Ctrl, week2


title: RPE-1_siRFXANK_Nutlin_2_RNAseq


title: PRP_41, Ctrl, week2


title: RPE-1_siRFXANK_Nutlin_1_RNAseq


title: RPE-1_siRFXANK_DMSO_3_RNAseq

description: DESeq2_RPE-1_siControl-vs-siRFXANK_DMSO.tsv


title: PRP_34, Ctrl, week0


title: RPE-1_siRFXANK_DMSO_2_RNAseq


title: PRP_13, Ctrl, week0


title: RPE-1_siRFXANK_DMSO_1_RNAseq


title: C4,control,replicate3,snRNA-seq

city: Oxford

first: Rui

last: Qi

state: Oxford

address: Old Road Campus

institute: University of Oxford

description: 10X Genomics

data_processing:
Libraries were then sent to the Oxford Genomics Centre or Novogene for Illumina NovoSeq6000 Sequencing. SubsequentIllumina runs were demultiplexed and the resulting fastq files were processed through the 10X Genomics Cellranger pipeline on the command line. Filtered gene matrix data was then analysed in R using the Seurat package. snRNA-Seq data were filtered on gene features >500-750 or <5000-6000, gene count <18,000-25,000, and mitochondrial % <15-25. Data was log normalized, variable features identified, and linear transformation scaling performed. PCA dimensionality reduction was run before the human snRNA-Seq data was Harmony integrated to remove batch effects. The first 30 principle components were selected and clusters identified using the ‘FindClusters’ method in Seurat with at a 0.5 resolution.  oThe ‘FindAllMarkers’ function was used to identify genes that characterized each cluster and differential expression of genes was tested between clusters. Cluster annotation was performed manually based on the top markers, applying in-house expertise in renal physiology with reference to the literature.
Fastq files was counted with cellranger v7.1.0 using GRCh38.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Kidney Biopsy

extract_protocol:
Single nuclei were isolated from fresh or liquid nitrogen flash frozen renal biopsies using the 10X Genomics Chromium Nuclei Isolation Kit with RNase Inhibitor 16 rxns (PN-1000494), with protocol modifications includingsupplementedRNase inhibitor and FACS sorting. The day prior to the nuclei isolation, polypropylene 1.5ml Eppendorf tubes were coated with 10% BSA (MACS BSA Stock Solution, Miltenyi Biotec, 130-091-376) overnight at 4°Cto be used during nuclear isolation experiment. Human renal biopsies (5-12mg) werehomogenized using kits pestle on ice in 200ul of chilled lysis buffer supplemented with additional 0.2U/ulRNase inhibitor.The samples were incubated on ice from 10 min in additional 300ul of lysis buffer with0.2U/ulRNase inhibitor. The homogenate was transfer to a Nuclei Isolation Column in a 10%BSA precoated collection tube and centrifuged at 16,000rcf for 20sec at4°C. Column was then discarded and the supernatant was resuspended with gentle mixing 15xtimeswith pipet,then centrifuged at 500 x for 3min at 4°C. The pellet was resuspended and washed with 500ul of the Debris Removal Buffer with.2U/ul of RNase inhibitorand mixed by gently pipetting 15x times. The resuspension was then centrifuged at 700 rcf for 10min at 4°C and supernatant was discarded. The pellet was resuspended in 200ul of Wash Buffer and filtered through a 40-μm FLOWMI cell strainer (SP Bel-Art, 136800040) and counted using a hemacytometer. Samples with more than 1 million nuclei were then FACS sorted to clean up the sample using Sytox-7AAD Live dead staining. Samples with below 1 million nuclei after washing were filtered a second time with the 40-μm FLOWMI cell strainer.
Gene libraries from isolated human renal single nuclei were constructed with droplet-based single-cell RNA sequencing using the Chromium Next Gen Single Cell 3’ Reagent v3.1 Dual Index Kit. Single nuclei were load at 1,000 nuclei/ul for a targeted 10,000 nuclei per sample depending on starting biopsy weight.

value: Kidney Biopsy

tag: Sex

value: Female

value: Multi-Cellular

value: CTL


title: PRP_37, Ctrl, week0

value: Patient skin biopsy

value: patient skin tisuse


title: PRP_01, Ctrl, week0


title: PRP_43, Ctrl, week0


title: PRP_30, Ctrl, week0


title: C3,control,replicate2,snRNA-seq

description: 10X Genomics

value: Male


title: PRP_15, Ctrl, week0


title: A1,control,replicate1,snRNA-seq

description: 10X Genomics


title: PRP_07, Ctrl, week0


title: PRP_25, Ctrl, week0


title: Control_2

city: Hwasun-eup

first: Hosouk

last: Joung

state: Jeollanam-do

address: 264, Seoyang-ro

institute: Chonnam National  University

data_processing:
High throughoutput sequencing was performed as paired-end 150 sequencing runs using NovaSeq 6000 (Illumina).
Raw reads were assembled and low-quality reads were filtered using Cutadapt (version 3.4).
Filtered reads were aligned on a reference genome downloaded from Ensembl (GRCh38 [Homo sapiens]) using STAR (version 2.7.8a)
Read counts were normalized for effective library size using DESeq2 package.
Assembly: GRCh38
Supplementary files format and content: Comma Separated Values (CSV) file includes raw counts for each sample
Supplementary files format and content: Comma Separated Values (CSV) file includes TPM values for each sample
Supplementary files format and content: Comma Separated Values (CSV) file includes DESeq2 normalized counts for each sample

growth_protocol: The cells were cultured in a humidified incubator maintained in MEM (LM007-07; Welgene) containing 10% fetal bovine serum (SH30919.03; Hyclone) and 1% streptomycin–penicillin (15140122; Gibco) at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted from SK-LMS-1 cells using NucleoSpin RNA/Protein (740933.50; MACHEREY-NAGEL) according to the manufacturer's instructions.
Libraries with total RNAs were constructed using the KAPA RNA HyperPrep Kit with RiboErase (Roche) according to the manufacturer’s instructions.

treatment_protocol: SK-LMS-1 cells were treated with 50 μM of 2-D08 for 48 hours.

value: uterine leiomyosarcoma

value: untreated


title: PRP_39, Ctrl, week0

value: Ctrl


title: 2-D08 treated for 48 hour_1

value: 2-D08 treated


title: 2-D08 treated for 48 hour_2


title: Control_1


title: H9 Cells, KPT-330 250 nM, 48 hours

city: Philadelphia

first: Nitin

last: Chakravarti

state: PA

address: 233 S Tenth St

department: Medical Oncology

institute: Thomas Jefferson University

data_processing:
Illumina's bcl2fastq 2.17
Assembly: human_hg38
Supplementary files format and content: Tab-delimited text fileincludesraw countsforeach sample

extract_protocol:
Total RNA was extracted using the Total RNA Purification Plus kit (Norgen Biotek, ON, Canada) as per the manufacturer's protocol.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA).

value: T-cells

value: WT


title: human fibroblasts,  hc5, pcnc-t [B18]

city: changsha

first: Liqing

last: Ding

address: xiangya street

country: China

institute: Central South University

description:
B18
multi_count_20231105.txt

data_processing:
Based on the human gene reference gene set GRCh38, HISAT2 (v2.2.1) was used for sequence alignment. The expression matrix was obtained by statistical distribution of reads of different genes through FeatureCounts.
Assembly: GRCh38
Supplementary files format and content: tab-delimited txt files include raw counts for samples

source_name: skin

extract_protocol:
Discard the culture bottle or culture dish, rinse the cells with PBS buffer once, add TRIzol lysate to lysate the cells, blow for 5-10 times, leave on ice for 1 minute, and then aspirate the lysate into the RNase-free tubes.
HFB collected by TRIzol was used to construct a library after RNA extraction and sequencing. The NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) was used for sequencing, generating a library as recommended by the manufacturer and adding an index code to the attribute sequence of each sample. PCR was performed with Phusion high-fidelity DNA polymerase, Universal PCR primer and Index (X) primer. Finally, the product was purified by AMPure XP system, the library quality was evaluated on Agilent 5400 system (Agilent,USA), and quantified by QPCR (1.5 nM). Based on the effective library concentration and the amount of data required, eligible libraries were pooled on the Illumina platform of Novo Geno Bioinformation Technology Co., LTD. (Beijing, China) for sequencing using the PE150 strategy. The above steps are performed at Novo Source Technology Co., LTD.

value: skin

value: fibroblasts

value: NC

value: in TGFβ stimulation


title: MyLa Cells, KPT-330 250 nM, 48 hours

source_name: MyLa

value: MyLa


title: H9 Cells, Control DMSO, 48 hours

value: DMSO


title: human fibroblasts,  hc5, pccrispld2-t [B20]

description:
B20
multi_count_20231105.txt

value: CRISPLD2 up-regulate


title: human fibroblasts,  hc5, pccrispld2-nt [B19]

description:
B19
multi_count_20231105.txt

value: not in TGFβ stimulation


title: human fibroblasts,  hc4, pccrispld2-t [B16]

description:
B16
multi_count_20231105.txt


title: MyLa Cells, Control DMSO, 48 hours


title: human fibroblasts,  hc4, pccrispld2-nt [B15]

description:
B15
multi_count_20231105.txt


title: C5,control,replicate4,snRNA-seq

description: 10X Genomics

value: Kidney Biopsy

value: Female

value: Multi-Cellular

value: CTL


title: MJ Cells, Control DMSO, 48 hours

source_name: MJ

value: MJ


title: A375 PIK3CA-H1047R overexpressing, dabrafenib/trametinib 7 day (chronic), replicate 3

city: Indianapolis

first: Steven

middle: P

last: Angus

state: IN

address: 1044 W Walnut St

department: Pediatrics

institute: Indiana University School of Medicine

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: GRCh38
Supplementary files format and content: raw_counts.csv

growth_protocol: A375 cells (parental and engineered) were grown in DMEM, supplemented with 100U/mL penicillin and 100 mcg/mL streptomycin

extract_protocol:
Qiagen RNeasy Plus Mini Kit with optional Dnase I treatment
NEBNext Ultra II RNA Library Prep with PolyA selection, 500 ng input, 10 PCR amplification cycles

treatment_protocol: Cells were treated with DMSO (vehicle) or 100nM dabrafenib/10nM trametinib for the indicated times

value: BRAFV600E melanoma

value: ectopic PIK3CA-H1047R overexpression

value: 100nM dabrafenib, 10nM trametinib, 7d ("chronic", C)


title: A375 PIK3CA-H1047R overexpressing, dabrafenib/trametinib 7 day (chronic), replicate 1


title: A375 PIK3CA-H1047R overexpressing, dabrafenib/trametinib 7 day (chronic), replicate 2


title: human fibroblasts,  hc3, pccrispld2-nt [B11]

description:
B11
multi_count_20231105.txt


title: A375 PIK3CA-H1047R overexpressing, dabrafenib/trametinib 1 day (acute), replicate 3

value: 100nM dabrafenib, 10nM trametinib, 24h ("acute", A)


title: A375 PIK3CA-H1047R overexpressing, dabrafenib/trametinib 1 day (acute), replicate 2


title: A375 PIK3CA-H1047R overexpressing, dabrafenib/trametinib 1 day (acute), replicate 1


title: human fibroblasts,  hc3, pcnc-nt [B9]

description:
B9
multi_count_20231105.txt

value: skin


title: human fibroblasts,  hc2, pccrispld2-t [B8]

description:
B8
multi_count_20231105.txt

value: fibroblasts


title: MJ Cells, KPT-330 250 nM, 48 hours

value: T-cells

value: WT


title: A375 PIK3CA-H1047R overexpressing, DMSO, replicate 3


title: A375 PIK3CA-H1047R overexpressing, DMSO, replicate 1


title: human fibroblasts,  hc2, pcnc-t [B6]

description:
B6
multi_count_20231105.txt

value: NC

value: in TGFβ stimulation


title: A375 PIK3CA-H1047R overexpressing, DMSO, replicate 2

value: DMSO


title: human fibroblasts,  hc5, pcnc-nt [B17]

description:
B17
multi_count_20231105.txt

value: not in TGFβ stimulation


title: human fibroblasts,  hc2, pcnc-nt [B5]

description:
B5
multi_count_20231105.txt


title: A375 PIK3CA overexpressing, dabrafenib/trametinib 7 day (chronic), replicate 1

value: ectopic PIK3CA overexpression


title: human fibroblasts,  hc2, pccrispld2-nt [B7]

description:
B7
multi_count_20231105.txt

value: CRISPLD2 up-regulate


title: human fibroblasts,  hc4, pcnc-t [B14]

description:
B14
multi_count_20231105.txt


title: human fibroblasts,  hc1, pccrispld2-t [B4]

description:
B4
multi_count_20231105.txt


title: human fibroblasts,  hc1, pccrispld2-nt [B3]

description:
B3
multi_count_20231105.txt


title: A375 PIK3CA overexpressing, dabrafenib/trametinib 7 day (chronic), replicate 3


title: human fibroblasts,  hc1, pcnc-t [B2]

description:
B2
multi_count_20231105.txt


title: A375 PIK3CA overexpressing, dabrafenib/trametinib 1 day (acute), replicate 3


title: A375 PIK3CA overexpressing, dabrafenib/trametinib 7 day (chronic), replicate 2


title: A375 PIK3CA overexpressing, DMSO, replicate 3


title: A375 PIK3CA overexpressing, dabrafenib/trametinib 1 day (acute), replicate 1


title: human fibroblasts,  hc3, pcnc-t [B10]

description:
B10
multi_count_20231105.txt


title: human fibroblasts,  hc3, pccrispld2-t [B12]

description:
B12
multi_count_20231105.txt


title: human fibroblasts,  hc5, sicrispld2-nt [A19]

description:
A19
multi_count_20230908.txt

value: CRISPLD2 knockdown


title: human fibroblasts,  hc5, sinc-t [A18]

description:
A18
multi_count_20230908.txt


title: A375 PIK3CA overexpressing, DMSO, replicate 2


title: human fibroblasts,  hc1, pcnc-nt [B1]

description:
B1
multi_count_20231105.txt


title: A375 PIK3CA overexpressing, dabrafenib/trametinib 1 day (acute), replicate 2


title: human fibroblasts,  hc4, pcnc-nt [B13]

description:
B13
multi_count_20231105.txt


title: human fibroblasts,  hc5, sinc-nt [A17]

description:
A17
multi_count_20230908.txt


title: A375 PTEN KO11, dabrafenib/trametinib 7 day (chronic), replicate 2

value: PTEN null (CRISPR/Cas9)

tag: clone


title: human fibroblasts,  hc5, sicrispld2-t [A20]

description:
A20
multi_count_20230908.txt


title: A375 PTEN KO11, dabrafenib/trametinib 7 day (chronic), replicate 3


title: A375 PTEN KO11, dabrafenib/trametinib 7 day (chronic), replicate 1


title: human fibroblasts,  hc4, sicrispld2-nt [A15]

description:
A15
multi_count_20230908.txt


title: human fibroblasts,  hc4, sicrispld2-t [A16]

description:
A16
multi_count_20230908.txt


title: human fibroblasts,  hc3, sicrispld2-nt [A11]

description:
A11
multi_count_20230908.txt


title: A375 PIK3CA overexpressing, DMSO, replicate 1


title: A375 PTEN KO11, DMSO, replicate 3


title: human fibroblasts,  hc4, sinc-t [A14]

description:
A14
multi_count_20230908.txt


title: A375 PTEN KO11, dabrafenib/trametinib 1 day (acute), replicate 3


title: human fibroblasts,  hc4, sinc-nt [A13]

description:
A13
multi_count_20230908.txt


title: human fibroblasts,  hc3, sicrispld2-t [A12]

description:
A12
multi_count_20230908.txt


title: A375 PTEN KO11, dabrafenib/trametinib 1 day (acute), replicate 1


title: human fibroblasts,  hc3, sinc-t [A10]

description:
A10
multi_count_20230908.txt


title: human fibroblasts,  hc2, sicrispld2-t [A8]

description:
A8
multi_count_20230908.txt


title: A375 PTEN KO11, DMSO, replicate 2


title: human fibroblasts,  hc3, sinc-nt [A9]

description:
A9
multi_count_20230908.txt


title: human fibroblasts,  hc2, sinc-t [A6]

description:
A6
multi_count_20230908.txt


title: A375 PTEN KO5, dabrafenib/trametinib 7 day (chronic), replicate 3


title: A375 PTEN KO5, dabrafenib/trametinib 1 day (acute), replicate 3


title: human fibroblasts,  hc2, sicrispld2-nt [A7]

description:
A7
multi_count_20230908.txt


title: A375 PTEN KO5, dabrafenib/trametinib 7 day (chronic), replicate 2


title: human fibroblasts,  hc1, sicrispld2-t [A4]

description:
A4
multi_count_20230908.txt


title: A375 PTEN KO5, dabrafenib/trametinib 7 day (chronic), replicate 1


title: human fibroblasts,  hc1, sinc-t [A2]

description:
A2
multi_count_20230908.txt


title: human fibroblasts,  hc1, sinc-nt [A1]

description:
A1
multi_count_20230908.txt


title: human fibroblasts,  hc2, sinc-nt [A5]

description:
A5
multi_count_20230908.txt


title: A375 PTEN KO5, DMSO, replicate 2

value: wild type


title: A375 PTEN KO5, dabrafenib/trametinib 1 day (acute), replicate 1

value: BRAFV600E melanoma


title: A375 PTEN KO5, DMSO, replicate 3


title: A375 PTEN KO5, dabrafenib/trametinib 1 day (acute), replicate 2


title: A375 PTEN KO11, dabrafenib/trametinib 1 day (acute), replicate 2


title: human fibroblasts,  hc1, sicrispld2-nt [A3]

description:
A3
multi_count_20230908.txt


title: A375 wild type, dabrafenib/trametinib 7 day (chronic), replicate 2


title: A375 PTEN KO5, DMSO, replicate 1


title: USC1504, LN229, siZFX, Input

first: Peggy

middle: J

last: Farnham

state: CA

address: 1450 Biggy St, NRT6514

department: Biochemistry and Molecular Medicine

institute: University of Southern California

description: genomic DNA

data_processing:
Data was analyzed using the ENCODE pipeline.
Reads were mapped to the genome using Bowtie2
Peaks were called using MACS2
Assembly: hg38
Supplementary files format and content: bigwig with total mapped reads

source_name: brain

growth_protocol: LN-229 was grown in DMEM supplemented with 10% FBS and pen/strep

extract_protocol:
Chromatin was prepared using the protocol previously published (PMID: 29429977). Briefly, cells were crosslinked using 1% formedelhyde for 10 mins and lysed. Chromatin was sonicated using a Bioruptor Pico.
Libraries were prepared using Roche KAPA Hyper Prep Kit (Roche# 07962347001) according to provided protocol

value: brain

value: glioblastoma

value: siZFX

tag: chip antibody


title: USC1588, LN229, siZFX, H4K12ac, rep2

description: genomic DNA

value: Active Motif; 39165


title: USC1592, LN229, siZFX, ZNF593, rep3

description: genomic DNA

value: ProteinTech #19426-1-AP


title: A375 wild type, dabrafenib/trametinib 1 day (acute), replicate 3

value: 100nM dabrafenib, 10nM trametinib, 24h ("acute", A)


title: USC1591, LN229, siControl, ZNF593, rep3

description: genomic DNA

value: siControl


title: A375 PTEN KO11, DMSO, replicate 1


title: USC1582, LN229, siZFX, H4K12ac, rep1

description: genomic DNA


title: A375 wild type, dabrafenib/trametinib 1 day (acute), replicate 1


title: A375 wild type, DMSO, replicate 2


title: USC1585, LN229, siControl, H4K8ac, rep2

description: genomic DNA

value: Millipore; 07-328


title: A375 wild type, DMSO, replicate 3


title: USC1587, LN229, siControl, H4K12ac, rep2

description: genomic DNA


title: A375 wild type, dabrafenib/trametinib 1 day (acute), replicate 2


title: USC1581, LN229, siControl, H4K12ac, rep1

description: genomic DNA


title: USC1580, LN229, siZFX, H4K8ac, rep1

description: genomic DNA


title: USC1586, LN229, siZFX, H4K8ac, rep2

description: genomic DNA


title: USC1579, LN229, siControl, H4K8ac, rep1

description: genomic DNA


title: A375 wild type, DMSO, replicate 1


title: USC1584, LN229, siZFX, H4K5ac, rep2

description: genomic DNA

value: Millipore; 07-327


title: A375 wild type, dabrafenib/trametinib 7 day (chronic), replicate 3

value: 100nM dabrafenib, 10nM trametinib, 7d ("chronic", C)


title: JG06_patient7_distal

city: New York

first: Veronika

last: Horn

address: 413 East 69th Street

institute: Weill Cornell Medicine

data_processing:
Base calling and demultiplexing with Illumina Casava 1.8.2
Adapter trimming using FLEXBAR (v2.4)
Alignment to hg19/GRCh37 reference genome using STAR version 2.3.0 with default settings
Reads per gene counted using Rsubread R package
Prefiltering genes with 50 or more counts in at least two samples and DE with DESeq2 version 1.20.0
Assembly: GRCh37/hg19
Supplementary files format and content: tab-delimited text file giving raw number of counts mapped to each gene (identified by Entrez ID) for each sample

source_name: colon

extract_protocol:
Human ILC3s (CD45+CD3-CD4-CD8-CD19-CD94-CD14-CD123-FcεRIa-CD34-CD11c-CRTH2-CD127+CD117+) were sort-purified from surgical-resection samples from the colon of patients with Ulcerative Colitis or Crohn’s Disease.
Sorted cells were used to prepare RNA sequencing libraries by the Epigenomics Core at Weill Cornell Medicine, using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).
Sequencing was performed on an Illumina HiSeq 4000, yielding 50-bp single-end reads.

value: colon

value: sorted ILC3s

tag: disease type

value: Crohn’s Disease

tag: location

value: distal


title: JG05_patient7_affected

value: affected


title: JG34_patient6_distal


title: USC1583, LN229, siControl, H4K5ac, rep2

description: genomic DNA

value: wild type


title: JG33_patient6_affected


title: A375 wild type, dabrafenib/trametinib 7 day (chronic), replicate 1

value: BRAFV600E melanoma


title: USC1576, LN229, siZFX, H4Kac, Input

description: genomic DNA

value: brain


title: JG03_patient5_affected


title: JG04_patient5_distal


title: JG27_patient3_affected

value: Ulcerative Colitis


title: TE-2547-401-D37-A

city: Uppsala

first: Philipp

last: Pottmeier

state: Uppland

address: Kabovagen 4

department: Evolution and Development

country: Sweden

institute: Uppsala University

data_processing:
Sequenced reads were aligned to GRCh38_r96 with 'Hisat2' and assigned to genomic features using 'featureCounts'.
Quality control was performed with FastQC and MultiQC.
DEseq2 was used to normalize counts and perform differentially gene expression analysis.
Assembly: GRCh38_r96
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes DEseq2-normalized counts for each sample

source_name: cell line

growth_protocol: Cell were cultivated on Matrigel and provided with mTeSR1 plus medium for growth.

extract_protocol:
Before extraction cells were rinsed with PBS. TriZol reagent was used to extract the RNA phase, which was subsequently purified with RNA binding columns using the 'PureLink RNA Mini Kit'. DNA depletion of the samples was performed using the 'DNA-free DNA Removal Kit'.
Sequencing libraries were prepared from 600 ng total RNA using TruSeq  stranded total RNA library preparation kit with RiboZero Gold treatment (cat# 20020599, Illumina Inc.). Unique dual indexes (cat# 20022371, Illumina Inc.) were used. The  library preparation was performed according to the manufacturers’ protocol (# 1000000040499).

treatment_protocol: Neural induction was performed on a substrate of poly-L-ornithine (20 µg/ml) and laminin (20 µg/ml). Differentiation was induced by dual SMAD inhibition using KO-DMEM/F12 and 1X knockout stem replace (KSR) together with 10 µM SB-431542 and 0.1 µM LDN-193189  for 9 days. On day 3, an additional 3 µM CHIR 99021 and 1 µM cyclopamine was added and kept until day 17 of differentiation. On day 5, a transition from KSR medium to a N2 supplement based medium in DMEM/F12 was performed in 25% steps per day. On day 6 the cells were split 1:3 and reseeded on Matrigel coated plates. On day 18, medium was changed to neurobasal medium with 1X B27, 55µM β-mercaptoethanol, 10 µM cAMP, 200 µM ascorbic acid, 20 ng/ml GDNF, 20 ng/ml BDNF and 50 ng/ml β-NGF. Each medium also received 2 mM glutamax and 0.1 mM non-essential amminoacids. Medium was replenished every day until day 17 and afterwards every second day. For the start of the differentiation 150.000 cells were seeded into the coated dishes together with mTeSR1 plus medium. After 24 hours of incubation, medium was changed to KSR medium to start the differentiation.

value: cell line

value: Population of mixed neurons

value: Male

value: Small molecule-based neuronal differentiation


title: JG28_patient3_distal


title: USC1575, LN229, siControl, H4Kac, Input

description: genomic DNA

value: glioblastoma

value: siControl


title: JG25_patient2_affected


title: JG02_patient4_distal


title: USC1578, LN229, siZFX, H4K5ac, rep1

description: genomic DNA

value: siZFX

value: Millipore; 07-327


title: JG01_patient4_affected

value: colon


title: JG24_patient1_distal

value: sorted ILC3s


title: TE-2547-401-D37-B


title: TE-2547-401-D37-C


title: TE-2547-980-D37-C

value: Female


title: JG26_patient2_distal

value: distal


title: TE-2547-975-D37-C


title: TE-2547-980-D37-B


title: TE-2547-975-D37-B


title: JG23_patient1_affected

value: affected


title: USC1577, LN229, siControl, H4K5ac, rep1

description: genomic DNA

value: wild type


title: TE-2547-980-D37-A


title: AtSDR4L, rep2

city: VANCOUVER

first: Liang

last: Song

state: British Columbia

address: 2231-6270 UNIVERSITY BLVD

department: Botany

country: Canada

institute: University of British Columbia

data_processing:
Basecalling was performed on NovaSeq 6000 with the built-in software RTA3 and Demultiplexing was performed using bcl2fastq v2.19.
Low-quality reads were filtered, and adapters were trimmed by fastp version 0.23.4
Reads were aligned to the Arabidopsis genome (TAIR10) with Botiew2 version 2.2.5 with the default parameters. Subsequently, the aligned reads were converted to BAM format and filtered for mapping quality scores greater than 10 by Samtools version 1.6. Alignment files of mock IgG controls from wild-type and mutant backgrounds were concatenated to form a common control for peak calling of H3K27me3 libraries.
Peaks were called by MACS2 version 2.2.7.1 for H3K27me3 ChIP using the combined mock IP as a control and “--broad” argument to call broad peaks. For native promoter-driven AtSDR4L ChIP, peak calling was performed on MACS2 version 2.2.6 using Col-0 wildtype as control. For both peak callings, the argument “-f BAMPE” was used to specify the pair-end library as well as “-g 1.2e8 -q 0.1". The argument "--call-summits" was used for native promoter-driven AtSDR4L peak calling.
The TDFs were created from BAM by igvtools version 2.5.3 for native promoter-driven AtSDRL libraries and version 2.14.1 for H3K27me3 libraries, with the maximum zoom level of 5 for precomputing, window size of 10 bp for averaging coverage, and “includeDuplicates” option enabled.
Assembly: TAIR10
Supplementary files format and content: broadpeak and narrowPeak files (MACS2 output)
Supplementary files format and content: tiled data files,TDF (igvtools output)

organism: Arabidopsis thaliana

source_name: 1-day-old seedling

extract_protocol:
Chromatins were fixed and extracted according to a published protocol (Song et al., 2016). Then, cross-linked DNA molecules with all proteins were fragmented by sonication using a Bioruptor Plus (Diagenode, Denville, NJ, USA) for 15 cycles, with each cycle consisting of 30 seconds ON and 90 seconds OFF at the HIGH setting. Sonicated chromatin was diluted by ChIP Dilution Buffer and then incubated overnight with HA antibody (CST, Danvers, MA, USA, 3724, 1:100 v/v dilution) and H3K27me3 antibody (Active Motif, Carlsbad, CA, USA, 61018, 1:100 v/v dilution) for precipitation of 3xHA-AtSDR4L-3xFLAG and H3K27me3 bound chromatin fragments, respectively. The captured chromatin was eluted in 200 μl Elution Buffer and then reserve crosslinked at 65°C for 6 h, followed by treatment of 100 μg/mL proteinase K at 55°C for 2 h before the phenol: chloroform: IAA (25:24:1 v/v, pH 8.0) extraction. DNA was precipitated and double‐size selected using 0.6 vol. and 1.3 vol. AMPure XP beads (Beckman Coulter, Brea, CA, USA, A63881)
ChIP-seq libraries were constructed using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA, E7645S)

value: 1-day-old seedling

value: 5 uM ABA (5 hours)


title: Mock IgG, Atsdr4l_5, pooled

description: processed data on Series record

source_name: pooled from 1 and 3 DAI seedlings

value: pooled from 1 and 3 DAI seedlings

value: 1% sucrose


title: MKN_45_ACBP-S-Se

city: Huhehaote

first: Xiulan

last: Su

address: Jinshan street

institute: Inner Mongolia Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Genome_build: Homo sapiens ensmebl release90
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each isoforms

source_name: Human Gastric cancer cells

growth_protocol: MKN-45 after ACBP-S-Se treatments were assessed by the IncuCyte live cell analysis system

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA removal kit (Illumina, San Diego, USA).Then the left RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the Truseq Stranded Total RNA HT Sample Prep Kit (Illumina, San Diego, USA).

treatment_protocol: MKN-45 cells was cultured in RPMI 1640 growth medium (61870036, Invitrogen, Thermo Fisher Scientific, Shanghai, China) supplemented with 10% FBS (16000-044, Gibco, Shanghai, China) and 100 U/ml P/S (15140-122, Gibco, Shanghai, China) at 37°C in a humidified chamber containing 5% CO2.

value: treated with ACBP-S-Se


title: TE-2547-LT2e-D37-B

value: cell line

value: Population of mixed neurons


title: TE-2547-983a-D37-C

value: Male

value: Small molecule-based neuronal differentiation


title: TE-2547-WA14-D37-C


title: Mock IgG, Atsdr4l_4, pooled

description: processed data on Series record


title: TE-2547-983a-D37-B


title: TE-2547-LT2e-D37-A


title: MKN_45

value: untreated


title: AtSDR4L, rep 1


title: TE-2547-LT2e-D37-C


title: WT, mock


title: TE-2547-975-D37-A


title: TE-2547-983a-D37-A


title: Mock IgG, WT, pooled

description: processed data on Series record


title: TE-2547-WA14-D37-A


title: H3K27me3, Atsdr4l_5, 3 DAI, rep2

source_name: 3-day-old seedling

value: 3-day-old seedling


title: H3K27me3, Atsdr4l_5, 3 DAI, rep1


title: TE-2547-401-D9-C

value: Neuronal induction D9


title: H3K27me3, Atsdr4l_4, 3 DAI, rep1


title: TE-2547-WA14-D37-B


title: TE-2547-401-D9-B


title: TE-2547-975-D9-C


title: TE-2547-401-D9-A


title: H3K27me3, Atsdr4l_4, 3 DAI, rep2


title: H3K27me3, WT, 3 DAI, rep2


title: TE-2547-975-D9-B


title: H3K27me3, WT, 3 DAI, rep1


title: TE-2547-975-D9-A


title: H3K27me3, Atsdr4l_5, 1 DAI, rep1


title: H3K27me3, Atsdr4l_4, 1 DAI, rep2


title: TE-2547-980-D9-C


title: Hela, 180min, cytosol, rep2

first: Achim

last: Tresch

state: North Rhine-Westphalia

address: Paul-Schallueck-Str. 10

department: Institute of Medical Statistics and Computational Biology

institute: University of Cologne

data_processing:
Reads were mapped with slamdunk (version 0.3.0), settings: -n 100, -m. Count statistics for each 3’UTR were obtained by aggregating all mapped reads overlapping with a given 3’UTR. To prevent double counting, overlapping 3’UTRs on the same DNA strand were merged. We additionally defined and identified peak regions, genomic regions in which 3’ ends of mapped reads pile up, and calculated separate count statistics for each such peak.
We excluded all known potential SNP sites reported in the hg19 NCBI dbSNP database. Additionally, all T sites with an observed conversion rate higher than 5% in the nuclear or cytosolic fraction of the unlabeled control sample were considered putative SNPs or A>I editing sites and masked. SNP and RNA editing site correction was then applied to all samples of the two labeling time series.
Assembly: hg19
Supplementary files format and content: comma-delimited text file including counts for each UTR
Library strategy: SLAM-seq

molecule: cytoplasmic RNA

growth_protocol: Hela-S3 cells were cultured in DMEM supplemented with 10% heat inactivated FBS without antibiotics and incubated at 37°C and 5% CO2. Cells were tested regularly for mycoplasma with the PlasmoTest kit (InvivoGen) and are mycoplasma negative.

extract_protocol:
45 million cells were used per sample. The medium was supplemented with 500 μM for either 0, 15, 30, 45, 60, 90, 120 or 180 min immediately  followed by subcellular fractionation as described in Nojima et al. (2016) with modifications as follows: the cells were rinsed on the cell culture plates twice with 20 ml of ice-cold DPBS twice and scraped in 10ml ice-cold DPBS and transfered into a 15-ml tube. The cells were pelleted at 400 x g or 5 min at 4°C, resuspended in 4 ml of ice-cold HLB+N buffer (10mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2 and 0.5% (vol/vol) NP-40) followed by an incubation on ice for 5 min. The cell pellet was underlaid with 1 ml of ice-cold HLB+NS buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2, 0.5 % (vol/vol) NP-40 and 10 % (wt/vol) sucrose). The nuclei were pelleted by centrifugation at 400 x g for 5 min at 4 °C. The supernatant was the collected and lysed with 3 volumes of Trizol LS for cytoplasmic fraction. The nuclei were washed with 15 ml ice-cold DPBS and lysed in Qiazol. For the total fractions we lysed the metabolically labeled cells directly in Qiazol.
Synthetic spike-ins were produced and purified. The preparation protocol was modified to include in vitro poly(A) tailing with E. coli Poly(A) Polymerase (NEB) to make the spike-ins compatible with the NGS library preparation. We added equal amounts of synthetic spike-ins to all the RNA fraction lysates prior to RNA isolation. RNA was isolated according to the manufacturer’s protocol and then dissolved in nuclease-free water with 1 mM DTT. The carboxyamidomethylation reactions of 4sU were set up as described by Herzog et al. Briefly described here, we set up the reaction with 5 μg RNA in nuclease-free water with 1 mM DTT; 50% DMSO; 50 mM sodium phosphate buffer pH 8.0; and 10 mM iodoacetamide. The reactions were incubated at 50°C for 15 min and then quenched by 100 mM DTT. The RNA was then precipitated with ethanol to clean up and concentrate. Next generation sequencing libraries were prepared from 500 ng RNA with the QuantSeq 3’ mRNA-Seq Library Prep Kit REV for Illumina according to the manufacturer’s instructions, but with two modifications. In brief, the reverse transcription reaction temperature was increased to 50°C and the incubation was extended to 60 min. The NGS libraries were pooled and sequenced as single-read with the custom sequencing primer provided with the QuantSeq NGS library preparation kit with 100 cycles on a HiSeq2000 sequencer.

treatment_protocol: Asynchronously proliferating cells were metabolically labeled with 4-thiouracil (4sU) before subcellular fractionation to obtain the nuclear and cytoplasmic RNA fractions or total cellular RNA fraction.

tag: timepoint

tag: fraction

value: cytosol

tag: experiment


title: Hela, 180min, cytosol, rep1

tag: cell line


title: H3K27me3, Atsdr4l_5, 1 DAI, rep2

tag: tissue

tag: genotype


title: TE-2547-983a-D9-C

tag: cell type

tag: treatment


title: TE-2547-980-D9-A

value: Female


title: TE-2547-983a-D9-A


title: TE-2547-983a-D9-B


title: H3K27me3, WT, 1 DAI, rep2


title: Hela, 180min, nucleus, rep1

value: nucleus


title: Hela, 180min, nucleus, rep2


title: TE-2547-LT2e-D9-B


title: TE-2547-980-D9-B


title: TE-2547-WA14-D9-C


title: TE-2547-WA14-D9-A


title: Hela, 120min, cytosol, rep1


title: H3K27me3, WT, 1 DAI, rep1


title: TE-2547-401-D4-C

value: Neuronal induction D4


title: Hela, 120min, nucleus, rep2


title: Hela, 120min, cytosol, rep2


title: TE-2547-WA14-D9-B


title: csu6 rep 3

city: Beijing

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

data_processing:
We mapped RNA-seq reads to the TAIR10 genome using HISAT2. Only uniquely mapped reads were retained for subsequent analyses.  Differential expression between samples was statistically assessed using the R/Bioconductor package edgeR (V3.0.8) [65], and normalization was performed by trimmed mean of M values (TMM). Genes with pvalue < 0.05 and he absolute foldchange  more than 1.5 by edgeR were identified as differentially expressed.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Col-0 and csu6-2 mutant seedlings were grown in white light for 5 d

extract_protocol:
Total RNA was isolated from the whole Arabidopsis seedlings using RNeasy plant mini kits (Qiagen). mRNA was extracted from total RNA using Dynabeads oligo (dT) (Invitrogen Dynal).
First- and second-strand cDNAs were generated using SuperScript II reverse transcriptase (Invitrogen) and random hexamer primers. Double-stranded cDNAs were fragmented by nebulization and used for RNA-seq library construction following the NovaSeq protocol.

value: seedlings

value: csu6 mutant

value: white light 5 days

tag: time

value: Day 5


title: H3K27me3, Atsdr4l_4, 1 DAI, rep1

value: 1-day-old seedling

value: 1% sucrose


title: TE-2547-401-D4-B

value: cell line


title: csu6 rep 1


title: Col-0 rep 3

value: WT


title: TE-2547-401-D4-A

value: Male


title: Hela, 120min, nucleus, rep1


title: TE-2547-975-D4-C

value: Small molecule-based neuronal differentiation


title: Col-0 rep 2


title: TE-2547-LT2e-D9-C


title: TE-2547-975-D4-B


title: Col-0 rep 1


title: TE-2547-980-D4-B


title: TE-2547-980-D4-C


title: TE-2547-975-D4-A


title: TE-2547-980-D4-A


title: Hela, 90min, cytosol, rep1


title: TE-2547-LT2e-D9-A


title: WT_D9_pM_NFIAp_rep3

city: London

first: M Joaquina

last: Delas

address: 1 Midland Road

department: Briscoe Lab

institute: The Francis Crick Institute

data_processing:
Data was processed using the nf-core atacseq pipeline (https://nf-co.re/atacseq) with the following options: --genome mm10  --skip_diff_analysis --min_reps_consensus 2 -r 1.2.1.
Assembly: mm10
Supplementary files format and content: normalised vsd values, columns are samples and rows are genomic intervals.

source_name: neural progenitor differentiation

growth_protocol: 60-80,000 mouse ES cells were plated onto the pre-coated CellBIND dishes (Corning) in N2B27 medium (Advanced DMEM - F12 (Gibco, Cat. No. 21331-020) and Neurobasal medium (Gibco, Cat. No. A35829-01) (1:1), supplemented with 1xN2 (Gibco Cat no. 17502001), 1xB27 (Gibco Cat no. 17504001), 2 mM L-glutamine (Gibco, Cat No. 25030024), 40 μg/ml BSA (Sigma-Aldrich, Cat No. A7979-50ML), and 0.1 mM 2-mercaptoethanol) supplemented with 10 ng/ml bFGF (R&D, Cat. No. 100-18B). On day 2, the media was changed to N2B27 supplemented with 5 μM CHIR99021 (GSK3β inhibitor; Axon, 1386). 20-21 h later, on day 3, the media was changed to N2B27 with 100 nM RA and 10 nM of Smoothened Agonist (SAG; Calbiochem, 566660). From day 5 onwards, cells were kept in N2B27 supplemented with 10 nM SAG. From day 3 onwards, media changes were performed daily.

extract_protocol:
CaTS-ATAC was performed as previously described (Delás et al., 2023) with in-house produced Tn5. A dead cell removal step was introduced to enrich for live cells prior to fixation and transposition. The details are as follows: at the differentiation timepoint of collection, cells were washed once with PBS and dissociated with Accutase (Gibco, A1110501) for 5 min at 37°C. Cells were collected in 1.5 ml LoBind Eppendorf tubes (Eppendorf cat. #Z666548) and spun down at 400xg for 4 min. Cell suspensions were supplemented with LIVE/DEADTM Fixable Dead Cell Stain Near-IR fluorescent reactive dye (Thermo Fisher, L34976), according to the manufacturer's instructions (1 µl dye/1 ml PBS for 1x106 cells) and incubated for 30 min on ice protected from light. During the incubation, the autoMACS® Pro Separator (Miltenyi Biotec) was set-up according to the manufacturer’s instructions. After the 30 min cell suspensions were divided into 15 ml falcon tubes and spun down for 10 min at 400xg at 4°C. Cells were resuspended, pooled into one tube, and counted. Cells were magnetically labelled with Dead Cell Removal Microbeads from the Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101). For 1.0x107 cells, 100 µl beads were used. Cells and microbeads were mixed and incubated for 15 min at room temperature. If necessary, 1x Binding Buffer provided by the kit was added to the cell suspension to reach a minimum volume of 500 μl for separation. The samples were run through the autoMACS® Pro Separator (Miltenyi Biotec) using the ‘Depl05’ programme. The microbeads label dead cells, which are retained in the separation columns. Unlabelled live cells run through the column and were collected in a 15 ml falcon tube in PBS. Live cells were count and spun down for 4 min at 400xg at 4°C. Cell pellet was resuspended in 300 µl of PBS in 1.5 ml LoBind Eppendorf tubes. Cells were then fixed, transposed, stained for viability and intracellular markers (anti-SOX2-V450, anti-Nkx6.1-PE, goat anti-Olig2, rabbit anti-Nfia) and sorted. DNA of samples was isolated using the DNA Clean & Concentrator-5 kit (Zymo; D4013) as per manufacturer’s instructions.
Transposed DNA was first amplified with 2X PCR Master Mix NEB (Cat. No. M0541S), and 1 µl of constant forward primer and indexed reversed primer (Table S1) (both at 25 µM) in a total reaction volume of 50 ul. The program was as follows: 5 min at 72ºC, 30 s at 98ºC, followed by 7 cycles of 30 s at 98ºC, 30 s at 63 ºC and 60 s at 72 ºC, with a final extension of 5 min at 72 ºC. DNA was cleaned up with 1.8x volumes of AMPureXP beads (Beckman Coulter, Cat. No. A63882) and eluted in 18 µl of EB buffer. qPCR was carried out to determine the number of extra cycles using 2 µl of the amplified DNA in technical duplicates. Each 20 µl reaction contained 20 µl of 2X SYBR Green PCR assay, using PowerUP SYBR Green Master Mix (Thermo Fisher, Cat. No. A25742) and 2.5 µl of each primer (at 25 µM each). The qPCR program was as follows: initial activation for 2 min at 50ºC, 30 s at 98ºC, followed by 40 cycles of 10 s at 98ºC, 30 s at 63ºC and 60 s at 72ºC. The number of additional cycles was calculated as ¼ of the maximum amplification 86. The second amplification was done using 12.5 µl of amplified DNA, 2X PCR Master Mix NEB and 2.5 µl of each primer (at 25 uM) in a total volume of 50 ul. The program was the same as the first amplification without the initial extension and for the calculated number of cycles. Finally, re-amplified DNA was cleaned up using 1.8x volumes AMPureXP beads and eluted in 30 ul. Samples were quantified in the QuBit, size profiles examined in the Bioanalyzer using the DNA High Sensitivity DNA Kit (Agilent, Part No. 5067-4626).

value: neural progenitor differentiation

tag: cell population

value: pMN


title: WT_D9_pM_NFIAp_rep2


title: csu6 rep 2


title: TE-2547-983a-D4-C


title: TE-2547-983a-D4-A


title: TE-2547-LT2e-D4-C


title: TE-2547-LT2e-D4-B


title: WT_D9_pM_NFIAn_rep2


title: WT_D9_pM_NFIAn_rep1


title: TE-2547-LT2e-D4-A


title: Hela, 90min, cytosol, rep2


title: Hela, 90min, nucleus, rep1


title: Hela, 60min, nucleus, rep2


title: TE-2547-WA14-D4-A


title: Hela, 60min, cytosol, rep2


title: WT_D9_p2_NFIAp_rep3


title: Hela, 60min, cytosol, rep1


title: TE-2547-WA14-D4-C


title: WT_D9_p2_NFIAp_rep2


title: TE-2547-401-T0-B

value: hESC


title: Hela, 90min, nucleus, rep2


title: TE-2547-401-T0-C


title: TE-2547-983a-D4-B


title: TE-2547-WA14-D4-B


title: TE-2547-401-T0-A


title: Hela, 45min, cytosol, rep2

value: cytosol


title: Hela, 60min, nucleus, rep1


title: Hela, 45min, cytosol, rep1


title: WT_D9_pM_NFIAp_rep1


title: WT_D9_p2_NFIAn_rep3


title: TE-2547-980-T0-C

value: Female


title: WT_D9_p2_NFIAp_rep1


title: Hela, 45min, nucleus, rep2

value: nucleus


title: TE-2547-975-T0-A


title: WT_D9_p2_NFIAn_rep2


title: TE-2547-980-T0-B


title: Hela, 45min, nucleus, rep1


title: TE-2547-980-T0-A


title: TE-2547-983a-T0-C


title: WT_D9_p2_NFIAn_rep1


title: Hela, 30min, cytosol, rep2


title: TE-2547-LT2e-T0-C


title: WT_D9_p1_NFIAn_rep3


title: Hela, 30min, cytosol, rep1


title: TE-2547-975-T0-C


title: WT_D9_p1_NFIAn_rep2


title: TE-2547-LT2e-T0-A


title: TE-2547-LT2e-T0-B


title: Hela, 30min, nucleus, rep2


title: WT_D9_p1_NFIAn_rep1


title: TE-2547-975-T0-B


title: TE-2547-WA14-T0-B


title: WT_D7_pM_NFIAn_rep3


title: DKO, ZFX[12-13]-FLAG siControl FLAG ChIP

data_processing:
Data was analyzed using the ENCODE pipeline.
Reads were mapped to the genome using BWA
Peaks were called using MACS2
Assembly: hg38
Supplementary files format and content: bigwig with total mapped reads

source_name: kidney

growth_protocol: LN-229 & HEK293T (DKO) was grown in DMEM supplemented with 10% FBS and pen/strep

treatment_protocol: For studies of ZFX and ZNF593 cooperation, HEK293T DKO cells were first transfected with siRNA using RNAiMax. 24h later, the same cells were subsequently transfected with plasmids containing ZFX[11-13]-FLAG using Lipofectamine 3000.

value: kidney

value: human embryonic kidney

value: ZFX/ZNF711 knockout

value: ZFX[12-13], siControl

tag: antibody

value: FLAG (Sigma #F3165)


title: TE-2547-WA14-T0-A


title: TE-2547-WA14-T0-C


title: Hela, 15min, cytosol, rep2


title: TE-2547-983a-T0-B


title: DKO, wt ZFX-FLAG siControl FLAG ChIP

value: wt ZFX, siControl


title: WT_D7_pM_NFIAn_rep2


title: DKO, wt ZFX-FLAG siControl Input


title: mESCs, netrin1 treated samples (condition 3), rep1

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description:
Exp4-D9-BMP-NetLow-Rep1
ProcessedData.xlsx

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with GRCm38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: mm10
Supplementary files format and content: Counts

source_name: mESCs, day 9 (RA+BMP4-patterned progenitors)- with netrin 1 extended (0.125ug/ml)

growth_protocol: mESCs were differentiated as adherant cultures in triplicates with RA+BMP4. Differentiations were terminated at day 5, day 6 and day 9 depending on the conditions analyzed.

extract_protocol:
At each timepoints, cells were washed with 1X PBS and then cell lysate was collected with RLT buffer (Qiagen). Total RNA was extracted using Rneasy mini kit (Qiagen)
Libraries were constructed with Universal plus mRNA sequencing kit (NuGEN) and sequenced onto NovaseqS1 to generate 30-50 million reads/sample.

treatment_protocol: differentiating dIs were treated with three conditions- (1) RA+BMP4+/- netrin1 (o.125ug/ml) between day 4-day5 (condition 1) (2) RA+ BMP4-patterned progenitors were treated with +/- netrin1 between day 5-day6 (condition2), and (3) RA+BMP4-patterned progenitors were treated with +/- netrin1 for extended duration between day 5-day9 (condition3).

value: mESCs

value: day 9

tag: condition

value: netrin1 treated samples (condition 3)


title: mESCs, netrin1 treated samples (condition 3), rep2

description:
Exp4-D9-BMP-NetLow-Rep2
ProcessedData.xlsx


title: WT_D7_p2_NFIAn_rep3

value: WT


title: WT_D7_p2_NFIAn_rep2


title: mESCs, no netrin1 control (condition 3), rep2

description:
Exp4-D9-BMPcont-Rep2
ProcessedData.xlsx

source_name: mESCs, day 9 (RA+BMP4-patterned progenitors)- no netrin1

value: no netrin1 control (condition 3)


title: Hela, 15min, nucleus, rep1


title: mESCs, netrin1 treated samples (condition 2), rep2

description:
D6-BMP-NetLow-Rep2
ProcessedData.xlsx

source_name: mESCs, day 6 (RA+BMP4-patterned progenitors)- with netrin 1 (0.125ug/ml)

value: day 6

value: netrin1 treated samples (condition 2)


title: TE-2547-983a-T0-A

value: cell line

value: hESC

tag: Sex

value: Male


title: mESCs, no netrin1 control (condition 3), rep1

description:
Exp4-D9-BMPcont-Rep1
ProcessedData.xlsx


title: Hela, 15min, cytosol, rep1

value: cytosol


title: mESCs, netrin1 treated samples (condition 2), rep3

description:
D6-BMP-NetLow-Rep3
ProcessedData.xlsx


title: Hela, 0min, cytosol, rep2


title: Hela, 0min, nucleus, rep2

value: nucleus


title: WT_D7_p2_NFIAn_rep1

value: neural progenitor differentiation


title: mESCs, no netrin1 control (condition 2), rep2

description:
D6-BMP-NoNet-Rep2
ProcessedData.xlsx

source_name: mESCs, day 6 (RA+BMP4-patterned progenitors)- no netrin1

value: no netrin1 control (condition 2)


title: mESCs, netrin1 treated samples (condition 2), rep1

description:
D6-BMP-NetLow-Rep1
ProcessedData.xlsx


title: Hela, 30min, nucleus, rep1


title: Hela, 0min, cytosol, rep1


title: mESCs, netrin1 treated samples (condition 1), rep3

description:
D5-R-plus-B-NetLow-Rep3
ProcessedData.xlsx

source_name: mESCs, day 5 (RA+BMP4)- with netrin 1 (0.125ug/ml)

value: day 5

value: netrin1 treated samples (condition 1)


title: Hela, 0min, nucleus, rep1


title: mESCs, no netrin1 control (condition 2), rep1

description:
D6-BMP-NoNet-Rep1
ProcessedData.xlsx


title: WT_D7_p1_NFIAn_rep3


title: DKO, ZFX[12-13]-FLAG siControl Input

value: kidney

value: human embryonic kidney

value: ZFX/ZNF711 knockout

value: ZFX[12-13], siControl


title: WT_D7_p1_NFIAn_rep1

value: WT


title: mESCs, netrin1 treated samples (condition 1), rep1

description:
D5-R-plus-B-NetLow-Rep1
ProcessedData.xlsx

value: mESCs


title: mESCs, no netrin1 control (condition 2), rep3

description:
D6-BMP-NoNet-Rep3
ProcessedData.xlsx

value: day 6


title: WT_D5_pM_NFIAn_rep2

value: pMN


title: WT_D7_p1_NFIAn_rep2


title: WT_D7_pM_NFIAn_rep1


title: mESCs, netrin1 treated samples (condition 1), rep2

description:
D5-R-plus-B-NetLow-Rep2
ProcessedData.xlsx


title: mESCs, no netrin1 control (condition 1), rep1

description:
D5-R-plus-B-cont-Rep1
ProcessedData.xlsx

source_name: mESCs, day 5 (RA+BMP4)- no netrin1

value: no netrin1 control (condition 1)


title: mESCs, no netrin1 control (condition 1), rep2

description:
D5-R-plus-B-cont-Rep2
ProcessedData.xlsx


title: mESCs, no netrin1 control (condition 1), rep3

description:
D5-R-plus-B-cont-Rep3
ProcessedData.xlsx


title: Hela, 0min, total, rep1

value: total


title: Hela, 15min, nucleus, rep2


title: Hela, 0min, total, rep2


title: FD5, scRNAseq

city: Seongnam-si

first: Chan Yeong

last: Heo

state: Gyeonggi-do

address: 82, Gumi-ro 173 Beon-gil, Bundang-gu

institute: Seoul National University Bundang Hospital

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: transcriptome GRCh38 (Ensembl-GENCODE 2020-A build)
Supplementary files format and content: Tab-separated values files and matrix file

source_name: Fibrous dysplasia bone tissue

extract_protocol:
Fresh lesion specimens were finely minced into small particles until they reached the consistency of sand and digested with 2mg/ml collagenase D solution (Roche, Mannheim, Germany) in basal medium Dulbecco’s Modified Eagle medium (DMEM; Gibco Life Technologies, Carlsbad, CA, USA) supplemented with 1% antibiotic-antimycotic solution, containing 10,000U/mL penicillin and 10,000U/mL streptomycin) (Life Technologies) for 4h at 37°C with gentle agitation. Digestion was terminated with fetal bovine serum (FBS; Life Technologies) and washed three times and resuspended in freshly prepared growth medium (DMEM supplemented with 10% FBS and 1% antibiotic-antimycotic solution). The resulting cell suspension was passed through a 70-mm cell strainer, pelleted by centrifugation at 300 x g, resuspended with 5ml of 1x RBC Lysis Buffer (Invitrogen, San Diego, CA), washed with DMEM, and pelleted for cryopreservation in cryopreservative medium (Nippon Zenyaku Kogyo, Fukushima, Japan) or culture in a 75cm2 T-flask containing growth medium at a density of 3x105 cells per flask in an atmosphere of 37°C, 5% CO2, and 95% humidity. Any undigested residues were transferred to a 75cm2 T-flask and maintained in growth medium for primary explant culture under normal culturing conditions. Approximately 2 weeks after explantation when outgrown cells reached near confluence, cells and tissue fragments were detached using 0.25% trypsin-EDTA (Gibco, Paisly, Scotland), washed, and resuspended in culture medium. Cells were collected from the suspension using a 70-mm cell strainer (PluriSelect, San Diego, CA) and either cryopreserved or replated in fresh culture dishes. Normal bone specimens consisted of marrow which was used to isolate bone marrow mesenchymal stromal cells (BMSCs). The marrow was scraped into the basal medium prepared as described above, followed by pipetting and serial passages through needles of decreasing diameter. Cells were treated with RBC Lysis Buffer prior to being either cryopreserved or plated into 75cm2 T-flask at a density of 3x105 cells per flask containing growth medium (DMEM supplemented with 10% FBS and 1% antibiotic-antimyotic) and cultured until near confluence. Cryopreserved cells dissociated from specimen digestion and cells obtained after two weeks of explant culture (2x106 cells each) were used for scRNAseq analysis.
The cell concentration of the single-cell suspension was maintained at500cells/ul(Total 1 * 10^5 cells)and loadedontoChromium Next GEM Chip G Single Cell Kit(10X genomics, cat no.1000120). Single-cell RNA-seq (scRNA-seq) libraries were constructed usingChromium Next GEM Single Cell 3' Kit v3.1(10X genomics, cat no.1000268).Individual libraries were diluted to250-500 pMand sequencing was completed on the IlluminaNextSeq 500sequencing platform,using S2ReagenttKit(200cyc)paired-end mode.

value: Fibrous dysplasia bone tissue

tag: site

value: Forehead / upper orbit

tag: mutation

tag: age

value: M


title: WT_D5_pM_NFIAn_rep1

value: neural progenitor differentiation


title: FD4, scRNAseq

description: 10X Genomics

value: Mandible


title: WT_D5_p1_NFIAn_rep2


title: PML knockdown, RCC4 [shPML_rep1]

city: Milan

first: Rosa

last: Bernardi

address: via Olgettina 60

country: Italy

institute: San Raffaele Scientific Institute

data_processing:
Base-calling was performed on NovaSeq 6000 Illumina machine.
Sequencing adapters were removed using trimmomatic v0.39.
Trimmed sequence reads were mapped to the human genome assembly GRCh38 (hg38) using the STAR aligner.
Annotation of genomic features was performed using the featureCounts tool v1.6.4 using the last GENCODE release for RNA-seq. Differential gene expression was evaluated in R/BioConductor using the DESeq2 package vs 1.30.1
Assembly: hg38
Supplementary files format and content: tab delimited text of normalized counts

growth_protocol: Cells were cultured in DMEM supplemented with 1% penicillin/streptomycin and 10% 10% tetracycline-free FBS.

extract_protocol:
RNA was isolated with QIAGEN RNeasy Plus Micro Kit
RNA libraries were prepared using the TruSeq stranded mRNA protocol (Illumina).

treatment_protocol: Silencing of PML was performed via lentiviral shRNA

value: Human kidney cancer

value: PML knockdown

value: shPML


title: control, RCC4 [shCTRL_rep1]

value: control

value: shCTRL


title: HSC3_DOX_PLUS_R3

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description:
HSC3_DOX_PLUS_R3
RawCounts_ByGene_HSC3.csv

data_processing:
Pre-alignment quality control was performed using FASTQC v0.11.9.
Sequenced reads (fastq files) were alinged to the human genome GRCh38.74 (Gencode) using STAR v2.7.9a.
counts at the gene level were quantified using subread v2.0.1 featureCounts
Assembly: GRCh38
Supplementary files format and content: raw counts (featureCounts) at the gene level for all samples

source_name: HSC3 HNSCC cell line

growth_protocol: HPV-negative CAL27 cells (ATCC) were cultured in DMEM medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS; GEMINI Bio-Products, West Sacramento, CA, USA). HPV-negative HSC3 cells (ATCC) were cultured in MEM medium (Corning, Corning, NY, USA) supplemented with 10% FBS. MUC1shRNA#1 (MISSION shRNA TRCN0000122938; Sigma, St. Louis, MO, USA) and a control scrambled shRNA (CshRNA; Sigma) were inserted into the pLKO-tet-puro vector (Plasmid #21915; Addgene, Cambridge, MA, USA) as described [Morimoto, 2023, #12670]. The MUC1shRNA#2 (MISSION shRNA TRCN0000430218) was produced in HEK293T cells (RRID:CVCL_HA7) as described [Morimoto, 2023, #12670]. Flag-tagged MUC1-C/CD was inserted into the empty control pLenti CMV Blast DEST(706-1) vector (Plasmid #17451; Addgene) as described [Yamashita, 2023, #12527]. Vector-transduced cells were selected for growth in 1–2 μg/ml puromycin. Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline (DOX; Millipore Sigma).

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using Trizol reagent (Invitrogen).
One microgram total RNA was used for library preparation using the TruSeq Stranded mRNA kit (Illumina Inc) following manufacturer's instructions.

value: doxycycline

tag: concentration

value: 500 ng/ml

tag: treatment duration

value: 7 days


title: WT_D5_p2_NFIAn_rep1

value: WT

tag: timepoint


title: WT_D5_p2_NFIAn_rep2


title: control, RCC4 [shCTRL_rep2]


title: WT_D5_p1_NFIAn_rep1


title: UN_dC_1

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description: Matrix column 23

data_processing:
Raw fastq reads were processed by: 1) trimming adapters and low-quality ends with Cutadapt (v. 2.5); 2) removing ribosomal RNA sequences with fastq_screen (v. 0.11.1) and 3) filtering out low complexity reads using reaper (v. 15-065)
Next, reads were aligned against Homo sapiens genome (build GRCh38) using STAR (v. 2.5.3a).
Gene counts were obtained with htseq-count (v. 0.9.1) using Human Ensembl 102 gene annotation.
Assembly: Reads were aligned against Homo sapiens genome build GRCh38
Supplementary files format and content: tab-delimited text file including raw gene counts per sample.

source_name: Peripheral blood neutrophils

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions.
RNA-seq libraries were prepared with the SMART-seq v4 PLUS kit (Takara Bio Inc.) from 9.5ng of total RNA (for sample 2_UN_dB_3 only 3.6 ng were available)

treatment_protocol: Purified human neutrophils were cultured in RPMI-1640 medium (Gibco) supplemented with 2% HI human AB serum (Sigma) (2.5 × 106 cells/mL) in the presence or absence of L. (V.) panamensis parasites at a multiplicity of infection (MOI) of 2 for 6 h.

value: Peripheral blood neutrophils

value: uninfected

tag: donor

value: DonorC


title: HSC3_DOX_PLUS_R2

description:
HSC3_DOX_PLUS_R2
RawCounts_ByGene_HSC3.csv

tag: cell line


title: UN_dC_2

description: Matrix column 24


title: FD3, scRNAseq

description: 10X Genomics

tag: tissue

value: Fibrous dysplasia bone tissue

value: Hemiface / mandible

value: F


title: UN_dB_1

description: Matrix column 20

value: DonorB


title: UN_dB_2

description: Matrix column 21


title: UN_dA_3

description: Matrix column 19

value: DonorA


title: WT_D11_pM_NFIAp_rep3

value: neural progenitor differentiation

value: pMN

tag: genotype


title: UN_dB_3

description: Matrix column 22

tag: cell type


title: HSC3_DOX_PLUS_R1

description:
HSC3_DOX_PLUS_R1
RawCounts_ByGene_HSC3.csv

tag: treatment


title: UN_dA_2

description: Matrix column 18


title: UN_dA_1

description: Matrix column 17


title: S_dC_2

description: Matrix column 16

value: infected with drug-susceptible parasites


title: WT_D11_pM_NFIAp_rep1


title: S_dB_3

description: Matrix column 14


title: HSC3_DOX_NEG_R2

description:
HSC3_DOX_NEG_R2
RawCounts_ByGene_HSC3.csv

value: DMSO


title: S_dB_2

description: Matrix column 13


title: WT_D11_p2_NFIAp_rep3


title: S_dB_1

description: Matrix column 12


title: HSC3_DOX_NEG_R1

description:
HSC3_DOX_NEG_R1
RawCounts_ByGene_HSC3.csv


title: WT_D11_p2_NFIAp_rep2


title: S_dA_2

description: Matrix column 10


title: CAL27_DOX_PLUS_R2

description:
CAL27_DOX_PLUS_R2
RawCounts_ByGene_CAL27.csv

source_name: CAL27 HNSCC cell line


title: R_dC_1

description: Matrix column 7

value: infected with drug-resistant parasites


title: CAL27_DOX_PLUS_R3

description:
CAL27_DOX_PLUS_R3
RawCounts_ByGene_CAL27.csv

value: doxycycline


title: WT_D11_p2_NFIAp_rep1


title: WT_D11_p1_NFIAp_rep3


title: R_dB_2

description: Matrix column 5


title: CAL27_DOX_PLUS_R1

description:
CAL27_DOX_PLUS_R1
RawCounts_ByGene_CAL27.csv

value: 500 ng/ml


title: WT_D11_pM_NFIAp_rep2


title: R_dB_3

description: Matrix column 6


title: CAL27_DOX_NEG_R3

description:
CAL27_DOX_NEG_R3
RawCounts_ByGene_CAL27.csv

value: 7 days


title: R_dB_1

description: Matrix column 4


title: WT_D11_p1_NFIAp_rep2

value: WT


title: S_dC_1

description: Matrix column 15

value: Peripheral blood neutrophils


title: R_dA_3

description: Matrix column 3


title: WT_D11_p1_NFIAp_rep1


title: HSC3_DOX_NEG_R3

description:
HSC3_DOX_NEG_R3
RawCounts_ByGene_HSC3.csv


title: R_dA_1

description: Matrix column 1


title: CAL27_DOX_NEG_R2

description:
CAL27_DOX_NEG_R2
RawCounts_ByGene_CAL27.csv


title: R_dA_2

description: Matrix column 2


title: LN-229, siZFX, groseq, Rep2

city: Los Angeles

data_processing:
Reads with Illumina small RNA adapter sequences were trimmed using Trimgalore
Reads were aligned to hg38 using Tophat
Normalization was done across samples using an equal number of uniquely mapped reads
Assembly: hg38
Supplementary files format and content: bigwig file with total mapped reads
Library strategy: GRO-seq

source_name: brain

growth_protocol: LN-229 and HEK293T were grown using DMEM supplemented with 10% FBS and pen/strep.

extract_protocol:
5x106 cells per nuclear run-on reaction were harvested and incubated in swelling buffer (10 µM Tris-HCl, 2 mM MgCl2, 3 mM CaCl2). Nuclei were isolated with lysis buffer (10 µM Tris-HCl, 2 mM MgCl2, 3 mM CaCl2, 10% glycerol, 1% NP-40). Nuclear run-on was performed at 30°C for 5 min in 10 mM Tris-HCl pH 8, 5 mM MgCl2, 300 mM KCl, 1 mM DTT, 500 µM ATP, 500 µM GTP, 500 µM Br-UTP, 2 µM CTP, 200 U/mL Superase In RNase Inhibitor (Invitrogen #AM2696), and 1% sarkosyl. Nuclear RNA was isolated with Trizol (Invitrogen #15596026). RNA was purified with Micro Bio-Spin P-30 Gel Columns (Bio-Rad # 7326250), fragmented with RNA Fragmentation Kit (Invitrogen # AM8740), and treated with 15 units mRNA decapping enzyme (NEB # M0608S) and 30 units T4 PNK (NEB # M0201S). RNA immunoprecipitation was performed 3 times with anti-BrdU-conjugated agarose beads (Santa Cruz Biotechnologies # sc-32323 AC).
Library preparation was performed with TruSeq Small RNA Library Preparation Kit (Illumina # RS-200-0012 following the manufacturer’s protocol.

treatment_protocol: LN-229 cells were transfected in triplicate with 100nM of siRNA oligonucleotides targeting human ZFX (Horizon #L006572000005) or control oligonucleotides (Horizon #D0018101005) using Lipofectamine RNAiMAX (Thermo Fisher #13778150) for 72 hours.

value: brain

value: glioblastoma

value: wild type

value: siZFX

tag: fraction

value: nascent RNA


title: MUT_D9_pM_NFIAn_rep2

tag: cell population

value: MUT


title: S_dA_3

description: Matrix column 11

value: DonorA


title: CAL27_DOX_NEG_R1

description:
CAL27_DOX_NEG_R1
RawCounts_ByGene_CAL27.csv


title: R_dC_2

description: Matrix column 8

value: DonorC


title: MUT_D9_pM_NFIAn_rep1

value: neural progenitor differentiation

value: pMN


title: S_dA_1

description: Matrix column 9

value: infected with drug-susceptible parasites


title: LN-229, siZFX, groseq, Rep1


title: LN-229, siControl, groseq, Rep2

value: siControl


title: HEK293T, DKO, groseq, Rep2

value: kidney

value: human embryonic kidney

value: ZFX & ZNF711 knockout


title: MUT_D9_p2_NFIAn_rep2


title: Uninfected_BEC_I_R3_total_RNA

city: Cologne

first: Till

last: Sauerwein

address: Gleueler Str. 60

institute: ZB MED - Information Centre for Life Sciences

description: IPSC-BECs only replicate 3

data_processing:
Adapter filtering: Illumina’s TruSeq “Read 1” adapter sequence using cutadapt version: 1.15
Trimming of reads with a Phred score below 20 using cutadapt version 1.15
Poly(A) clipping reads using READemption 0.4.3
Discarding of reads with a length below 20 using READemption version 0.4.3
Aligning of reads to both genomes using segemehl version 0.2.0
Gene quantification using READemption version 0.4.3
Differential gene expression analysis using DESeq2 version: 1.18.1, R version: 3.4.4
Genome_build: Human: GENCODE version: 26, NCBI assembly name: GRCh38.p10 / Streptococcus: accession number: HG939456.1, Genbank assembly accession number: GCA_000689235.1
Supplementary_files_format_and_content: csv files containing DESeq2 results

source_name: Brain-like endothelial cells generated from induced pluripotent stem cells (iPSC-BECs)

extract_protocol:
Total RNA was collected using the MirVana RNA (Thermo Scientific) isolation kit
Sequencing was performed on a NextSeq500 platform (Illumina) in single-end mode for 75 cycles

tag: disease state

value: uninfected


title: Uninfected_BEC_I_R2_total_RNA

description: IPSC-BECs only replicate 2


title: LN-229, siControl, groseq, Rep1


title: HEK293T, WT, groseq, Rep2


title: MUT_D9_p2_NFIAn_rep1


title: Uninfected_BEC_I_R1_total_RNA

description: IPSC-BECs only replicate 1


title: HEK293T, WT, groseq, Rep1


title: 293T, DKO, ZFX12_13_rep3

data_processing:
RNA-seq results were aligned to the human genome GRCh38 using STAR
Counts quantified using HTseq and Rsem
Differentially expressed genes with absolute log2 fold change >0.5 and q-value cut-off of 0.05 were determined using DEseq2
Assembly: hg38
Supplementary files format and content: txt files containing output for reads per gene

growth_protocol: LN-229 was grown using DMEM supplemented with 10% FBS and pen/strep.

extract_protocol:
Total RNA was extracted using trizol.
Libraries were constructed by Novogene using NEBNext Ultra™ II RNA Library Prep Kit for Illumina

value: ZFX/ZNF711 knockout

value: ZFX FLAG


title: 293T, DKO, ZFX12_13_rep2


title: PC9, PSAT1 silenced, Replicate 3 [BC-06-PC9-PSAT1sh-3_S6]

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1)
The fastq sequences were directly aligned to the hg38 reference genome assembly using STAR (version 2.6).
Raw counts were obtained from the STAR aligned bam format files using HTSeq version 0.10.0 and the ENSEMBL human gene gtf file.
Genome_build: hg38
Supplementary_files_format_and_content: HTSeq raw counts

source_name: PC9, PSAT1 silenced

growth_protocol: PC9 Control and shPSAT1 cells were maintained into 10% FBS supplemented RPMI media

extract_protocol:
RNA was extracted using Rneasy Mini Kit ( Qiagen)
Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit- Set A (Cat# RS-122-2101) and Set B (Cat# RS-122-2102) with poly-A enrichment.

treatment_protocol: PC9 Control and shPSAT1 cells at 70% confluency were  serum-starved for 24 hours before RNA extraction

value: PSAT1 silenced


title: MUT_D9_p1_NFIAn_rep2


title: PML knockdown, RCC4 [shPML_rep2]

value: Human kidney cancer

value: PML knockdown

value: shPML


title: MUT_D9_p1_NFIAn_rep1

value: MUT


title: PC9, PSAT1 silenced, Replicate 2 [BC-05-PC9-PSAT1sh-2_S5]


title: 293T, DKO, pCMV6_rep3


title: 293T, DKO, ZFX12_13_rep1


title: MUT_D7_pM_NFIAn_rep3


title: PC9, PSAT1 silenced, Replicate 1 [BC-04-PC9-PSAT1sh-1_S4]


title: MUT_D7_pM_NFIAn_rep2


title: 293T, DKO, pCMV6_rep1


title: PC9, Control, Replicate 3 [BC-03-PC9-Cntsh-3_S3]

source_name: PC9, Control

value: control


title: MUT_D7_pM_NFIAn_rep1


title: 293T, DKO, wtZFX_rep3

value: wt ZFX FLAG


title: 293T, DKO, wtZFX_rep1


title: PC9, Control, Replicate 2 [BC-02-PC9-Cntsh-2_S2]


title: HEK293T, DKO, groseq, Rep1

value: nascent RNA


title: PC9, Control, Replicate 1 [BC-01-PC9-Cntsh-1_S1]


title: MUT_D7_p2_NFIAn_rep3

value: neural progenitor differentiation


title: MUT_D7_p2_NFIAn_rep2


title: LN-229, siControl_2_rep3

value: brain

value: glioblastoma

value: wild type


title: 293T, DKO, wtZFX_rep2

value: kidney

value: human embryonic kidney


title: LN-229, siZFX siZNF593_rep3

value: siZFX siZNF593