title: CRISPR RNA-seq from K562 (ENCLB716LJJ)

description:
https://www.encodeproject.org/experiments/ENCSR519LZD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM28. (RBM28-BGKcLV30)
experiment encode accession: ENCSR519LZD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB716LJJ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3f7c1633-1e76-46d9-92c7-8d20b79f5ff4/@@download/attachment/L-RBM28-BGKcLV30-18.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM28. (RBM28-BGKcLV30-18)

value: female

value: adult

value: Brenton Graveley, UConn

value: ENCBS344KXS at ENCODE; https://www.encodeproject.org/ENCBS344KXS/


title: polyA plus RNA-seq from left cerebral cortex (ENCLB894RIO)

status: Public on Dec 04 2022

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR137GMB/
***************
biological replicate number: 1
technical replicate number: 1
description: Cortex from 6 mo C57BL/6 male
experiment encode accession: ENCSR137GMB
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2021-11-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB894RIO
fragmentation methods: chemical (Nextera tagmentation)
size range: <200
nucleic acid starting quantity: 20
nucleic acid starting quantity units: ng

library_source: transcriptomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: total RNA

organism: Mus musculus

source_name: Mus musculus strain B6NCrl adult (6 months) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

tag: description

value: Cortex from 6 mo C57BL/6 male

tag: biosample encode accession

tag: organism

value: Mus musculus

tag: Sex

value: not collected

tag: dev stage

tag: age

value: 6 month

tag: lab

value: Ali Mortazavi, UCI

tag: source

value: Andrea Tenner

tag: link

value: ENCBS668TCF at ENCODE; https://www.encodeproject.org/ENCBS668TCF/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: human_tonsil_organoid_06yrs_F_COVID_vaccine_TLR7NP_day04and09

status: Public on Nov 14 2022

city: Palo Alto

first: Meng

last: Sun

address: Biomedical Innovations Building 1300, 240 Pasteur Drive

institute: Stanford University

description: The reference fasta files were also uploaded here.

library_source: transcriptomic single cell

data_processing:
The Rhapsody raw data was first preprocessed by the Seven Bridges Genomics online platform (San Francisco, CA) using the BD Rhapsody Targeted Analysis Pipeline to align genes and calculate molecular counts with molecular index correction. After the preprocessing, the single cell Rhapsody count tables composing of 493 genes and 32 surface markers from the different timepoints and stimulants were imported in Seurat package of R for the following processing. Both the gene and abseq counts were log1p transformed.
Assembly: We used the BD Rhapsody customerized library. Please see the attached reference files for alignment.
Supplementary files format and content: tsv tables

molecule: polyA RNA

organism: Homo sapiens

source_name: tonsil

extract_protocol: Cell capture and library preparation were completed using the BD Rhapsody Targeted mRNA and AbSeq Reagent Kit (Cat. # 633774). Briefly, cells were captured with beads in  microwell plate, followed by cell lysis, bead retrieval, cDNA synthesis, template switching and Klenow extension, and library preparation following the BD Rhapsody protocol. Libraries were prepared for sample tags, targeted mRNA using the customized Immune Response panel, and AbSeq.

tag: tissue

value: tonsil

tag: cell line

value: primary

tag: cell type

value: immune cells

value: F

tag: genotype

value: RNA and proteins (cite-seq)

tag: treatment

value: SARS-CoV-2 subunit vaccine, toll-like receptor 7 agonist (TLR7)-nanoparticle adjuvant


title: Control_Hi-C

status: Public on Nov 03 2022

city: Philadelphia

first: Jennifer

middle: Mary

last: Luppino

state: Pennsylvania

address: 415 Curie Blvd., Room: 570

department: Genetics

institute: University of Pennsylvania

library_source: genomic

data_processing:
Hi-C:Raw reads for each Hi-C sample were processed with HiC-Pro (version 2.11.1) to obtain putative interactions with default parameters except LIGATION_SITE = GATCGATC and GENOME_FRAGMENT generated for MboI restriction enzyme. For downstream analyses, ValidPairs were converted to hic files using the “hicpro2juicebox.sh” in utils of HiC-Pro. We recovered the following number of contacts in each condition: Control (507359205), GSK3A KD (445835605).
Assembly: hg38
Supplementary files format and content: Hi-C: .hic file was generated using HiC-Pro (version 2.11.1)

molecule: genomic DNA

growth_protocol: We obtained the HCT-116 cell line from ATCC (RRID:CVCL_0291). All cells were cultured in McCoy’s 5A medium supplemented with 10% fetal bovine serum, 2 mM l-glutamine, 100 U ml−1 penicillin, and 100 μg ml−1 streptomycin at 37 °C with 5% CO2.

extract_protocol:
In situ Hi-C: Hi-C libraries were generated from 10e6 cells using the Arima-HiC+ kit (Arima Genomics) according to manufacturer's instructions
In situ Hi-C: Libraries were prepared using the Kapa Hyper Prep Kit with KAPA Library Amplification Primer Mix (KK8502), according to manufacturer’s recommendations. Libraries were validated for quality and size distribution using the Qubit dsDNA HS Assay Kit (Invitrogen, cat# Q32851), KAPA Library Quantification kit (Roche, Cat# KK4824) and TapeStation 2200 (Agilent).
In situ Hi-C: Paired-end sequenced (61bp+61bp) on a NovaSeq 6000 (Illumina).

treatment_protocol: RNAiMAX transfection reagent (Thermo Fisher Scientific) was diluted in Opti-MEM reduced serum medium (Thermo Fisher Scientific), and pipetted onto siRNA. Plates were incubated at room temperature for 20 minutes. HCT-116 cells were trypsinized and resuspended in antibiotic-free medium, then plated on siRNA duplexes to obtain a final siRNA concentration of 25 nM. After 72 h of RNAi treatment, cells were collected for experiments.

value: in situ Hi-C

value: Parental

value: Control siRNA

tag: molecule type

value: Crosslinked and sheared genomic DNA


title: Ctrl_4

status: Public on Oct 30 2022

city: Jinan

first: Ping

last: Mi

address: Wenhuaxi 44

country: China

institute: Shandong University

data_processing:
Raw data of fastq format were firstly fliterd to the low quality reads, reads with adapter sequences and reads with high levels of N base. In this step clean data were obtained.
Index of the reference genome was built using Bowtie2 and paired-edn reads werealigned to the reference genome.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GCF_000002035.6_GRCz11
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Danio rerio

source_name: heart

growth_protocol: zebrafish embryos were collected and exposure in different treatment from 2 hours postfertilization.

extract_protocol:
Total RNA was extracted by using Trizol (Invitrogen, USA) according to manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: zebrafish embryos were exposured in DMSO or TCDD from 2 hours postfertilization to 5 days postfertilization

value: heart

tag: time

value: DMSO


title: total RNA-seq from A549 (ENCLB490NEO)

description:
https://www.encodeproject.org/experiments/ENCSR018YHY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR018YHY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB490NEO
size range: 200-300

source_name: Homo sapiens A549 cell line treated with 1 uM CORT108297 (agonist) for 4 hours

extract_protocol:
extraction protocol: https://www.encodeproject.org/documents/e4e1b09a-8fe8-4212-9e76-a2fd6d0c8b49/@@download/attachment/supplemental%20PolyA%20plus%20RNA-seq%20library%20construction%20protocol.pdf
general protocol: https://www.encodeproject.org/documents/c2499c10-935d-4bc9-b374-5a40f69d4af9/@@download/attachment/Reddy_Lab_RNAseq_ENCODE_protocol.pdf
extraction method: Qiagen RNA extraction

tag: line

value: cell line

value: Homo sapiens

value: male

value: adult

value: 58 year

value: Tim Reddy, Duke

value: ATCC

tag: treatments

value: treatment_term_name:CORT108297; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS103UWX at ENCODE; https://www.encodeproject.org/ENCBS103UWX/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: Day 3 IgG CUT&RUN profiling in SMARCB1 +/+ G401 cell line

status: Public on Oct 17 2022

city: Lebanon

first: Xiaofeng

last: Wang

state: NH

address: 1 Medical Center Dr, Rubin Building

department: Molecular and Systems Biology

institute: Dartmouth College

data_processing:
Library strategy: CUT&RUN
Reads were deduplicated with the clumpify tool using flag -dedupe -subs=2, and subsequently trimmed with bbduk using parameters --ktrim=r --k=21 --mink=11 --hdist=1 --tpe --tbo.
The trimmed fastq files were then aligned to the Hg19 human genome using Bowtie2 aligner. Specifically, we used parameter “--end-to-end --very-sensitive --no-mixed --no-discordant -q -I 10 -X 700 --phred33” for the alignment.
Bam files were converted to bed files after removing chrM, chrUn, and reads containing “random” as chromosome position. Bed files were further cleaned by removing regions contained in the hg19 blacklist from ENCODE (v2)
Epic2 software (v.0.0.41) was used for calling histones and SWI/SNF peaks with parameters at default
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: CUT_RUN_peak.bed, which includes the peaks for all SWI/SNF subunits and AP-1 samples, is linked to the SuperSeries GSE175534 record.

source_name: G401 cell line

growth_protocol: G401 cell lines were purchased from American Type Culture Collection. Cell lines were cultured in DMEM with 10% FBS. SMARCB1 inducible re-expression stable G401 cell line was created previously and is maintained in media with Tet-free FBS (Gibco, Cat.# 16140071).

extract_protocol:
DNA was extracted using Phenol:Chloroform:Isoamyl Alcohol (Cat.# 15593031, ThermoFisher) and purified using ProNex Purification System (Cat.#NG2003, Promega).
CUT&RUN library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat.# E7645L, New England Labs). Libraries were paired-end sequenced with read lengths of 150 bp (PE 2X150 on the Illumina HiSeq Genome Analyzer). Average of 10 million reads per sample.

treatment_protocol: To induce SMARCB1 re-expression, cells were treated with doxycycline (1 μg/ml, EMD Millipore) for indicated time.

value: G401 cell line

value: SMARCB1 +/+

tag: cut&run antibody

value: IgG

tag: time point


title: Day 7 IgG CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 0 IgG CUT&RUN profiling in SMARCB1 -/- G401 cell line

value: SMARCB1 -/-


title: Day 1 IgG CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 7 PBRM1 CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 7 BRD9 CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 7 ARID1A CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Total gd T cells, sample tags 7-12

status: Public on Oct 31 2022

city: Chicago

first: Roshni

last: Roy Chowdhury

address: 924 E 57th Street

institute: University of Chicago

data_processing: Data were processed using the Seven Bridges Genomics online platform (San Francisco, CA) and BD Rhapsody Targeted Analysis Pipeline with V(D)J processing incorporated. After processing, data were imported into SeqGeq version 1.6.0 (BD, Ashland, OR).

source_name: gamma delta T cells

extract_protocol: Samples were stained with oligonucleotide-conjugated Sample Tags from the BD Human Single-Cell Multiplexing Kit in BD staining buffer following the manufacturer’s protocol. Barcoded samples were then washed and spun down at 350xg for 10 minutes and pooled. Cell capture and library preparation were completed using the BD Rhapsody Targeted mRNA and AbSeq Reagent kits

value: gamma delta T cells


title: Day 3 PBRM1 CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: total RNA-seq from middle frontal area 46 (ENCLB251AKV)

description:
https://www.encodeproject.org/experiments/ENCSR562ORH/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E1208017_BS171_ENC4_cDNA725
experiment encode accession: ENCSR562ORH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB251AKV
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (90 or above years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

tag: description

tag: biosample encode accession

tag: organism

tag: Sex

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS934UCP at ENCODE; https://www.encodeproject.org/ENCBS934UCP/

value: Derived from ENCODE donor ENCDO283GDX; https://www.encodeproject.org/ENCDO283GDX/


title: Day 3 BRD9 CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: polyA plus RNA-seq from left cerebral cortex (ENCLB671GZH)

description:
https://www.encodeproject.org/experiments/ENCSR137GMB/
***************
biological replicate number: 2
technical replicate number: 1
description: Cortex from 6 mo C57BL/6 male
experiment encode accession: ENCSR137GMB
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2021-11-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB671GZH
fragmentation methods: chemical (Nextera tagmentation)
size range: <200
nucleic acid starting quantity: 20
nucleic acid starting quantity units: ng

value: left cerebral cortex

value: Cortex from 6 mo C57BL/6 male

value: Mus musculus

value: not collected

tag: dev stage

value: adult

tag: age

value: 6 month

tag: lab

value: Ali Mortazavi, UCI

tag: source

value: Andrea Tenner

value: ENCBS191KAZ at ENCODE; https://www.encodeproject.org/ENCBS191KAZ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: Day 1 SMARCC1 CUT&RUN profiling in SMARCB1 +/+ G401 cell line

tag: cell line

value: G401 cell line

value: SMARCB1 +/+


title: Day 3 ARID1A CUT&RUN profiling in SMARCB1 +/+ G401 cell line

tag: genotype


title: DNase-seq from suppressor macrophage (ENCLB860FRP)

description:
https://www.encodeproject.org/experiments/ENCSR367FKP/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR367FKP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB860FRP
instrument models: Illumina HiSeq 4000,Illumina HiSeq 2000

source_name: Homo sapiens male adult (24 years) suppressor macrophage primary cell

value: suppressor macrophage

value: primary cell

value: male

value: 24 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

tag: link

value: ENCBS381YCP at ENCODE; https://www.encodeproject.org/ENCBS381YCP/

value: Derived from ENCODE donor ENCDO488BDS; https://www.encodeproject.org/ENCDO488BDS/


title: Day 1 BRD9 CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 1 ARID1A CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 1 PBRM1 CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 0 SMARCC1 CUT&RUN profiling in SMARCB1 -/- G401 cell line

value: SMARCB1 -/-


title: Day 0 BRD9 CUT&RUN profiling in SMARCB1 -/- G401 cell line


title: DNase-seq from T-helper 17 cell (ENCLB650FKX)

description:
https://www.encodeproject.org/experiments/ENCSR139KYP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR139KYP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB650FKX

source_name: Homo sapiens female adult (25 years) T-helper 17 primary cell

value: T-helper 17 cell

value: female

value: adult

value: 25 year

value: AllCells

value: ENCBS605VNU at ENCODE; https://www.encodeproject.org/ENCBS605VNU/

value: Derived from ENCODE donor ENCDO011KGM; https://www.encodeproject.org/ENCDO011KGM/


title: Day 0 PBRM1 CUT&RUN profiling in SMARCB1 -/- G401 cell line

value: G401 cell line


title: Day 0 ARID1A CUT&RUN profiling in SMARCB1 -/- G401 cell line


title: Day 7 SMARCC1 CUT&RUN profiling in SMARCB1 +/+ G401 cell line

value: SMARCB1 +/+


title: PRO-seq from HCT116 (ENCLB938FMI)

description:
https://www.encodeproject.org/experiments/ENCSR545PWV/
***************
biological replicate number: 1
technical replicate number: 1
description: PRO-seq in RAD21_T
experiment encode accession: ENCSR545PWV
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB938FMI
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: Homo sapiens

tag: health state

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS364ERK at ENCODE; https://www.encodeproject.org/ENCBS364ERK/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: Day 3 RNA-seq profiling in SMARCB1 +/+ G401 cell line Rep2

data_processing:
Raw fastq files were trimmed using the software Trimmomatic by setting the parameter “SLIDINGWINDOW: 4:15 LEADING: 3 TRAILING: 3 MINLEN: 36”.
The trimmed fastq files were than aligned to the human hg19 reference genome and normalized to obtain Transcripts Per Kilobase Million (TPM) for each RNA-seq sample using the software Salmon with the parameter “-l A”.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) and further purified using the Monarch RNA Cleanup Kit (New England Biolabs).
1 μg of total RNA was used to generate each RNA–seq library using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), and libraries were paired-end sequenced with the Illumina HiSeq Genome Analyzer.


title: Day 7 RNA-seq profiling in SMARCB1 +/+ G401 cell line Rep1


title: Day 3 SMARCC1 CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 7 RNA-seq profiling in SMARCB1 +/+ G401 cell line Rep2


title: Day 1 RNA-seq profiling in SMARCB1 +/+ G401 cell line Rep2


title: Day 3 RNA-seq profiling in SMARCB1 +/+ G401 cell line Rep1


title: Day 1 RNA-seq profiling in SMARCB1 +/+ G401 cell line Rep1


title: Day 0 RNA-seq profiling in SMARCB1 -/- G401 cell line Rep1

value: SMARCB1 -/-


title: Day 7 H3K27me3 CUT&RUN profiling in SMARCB1 +/+ G401 cell line

data_processing:
Library strategy: CUT&RUN
Reads were deduplicated with the clumpify tool using flag -dedupe -subs=2, and subsequently trimmed with bbduk using parameters --ktrim=r --k=21 --mink=11 --hdist=1 --tpe --tbo.
The trimmed fastq files were then aligned to the Hg19 human genome using Bowtie2 aligner. Specifically, we used parameter “--end-to-end --very-sensitive --no-mixed --no-discordant -q -I 10 -X 700 --phred33” for the alignment.
Bam files were converted to bed files after removing chrM, chrUn, and reads containing “random” as chromosome position. Bed files were further cleaned by removing regions contained in the hg19 blacklist from ENCODE (v2)
Epic2 software (v.0.0.41) was used for calling histones  peaks with parameters at default
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: CUT_RUN_histone_peak.bed includes peaks for all histone modifications.


title: Day 0 RNA-seq profiling in SMARCB1 -/- G401 cell line Rep2


title: Day 7 H3K4me3 CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 3 H3K27me3 CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 7 H3K4me CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 3 H3K4me3 CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 3 H3K4me CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 1 H3K4me3 CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 1 H3K27Ac CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 1 H3K4me CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 1 H3K27me3 CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 0 H3K27me3 CUT&RUN profiling in SMARCB1 -/- G401 cell line


title: Day 0 H3K27Ac CUT&RUN profiling in SMARCB1 -/- G401 cell line

address: 1 Medical Center Dr Rubin Building


title: Day 0 H3K4me CUT&RUN profiling in SMARCB1 -/- G401 cell line


title: Day 3 ARID1A HiChIP profiling in SMARCB1 +/+ G401 cell line Rep2

data_processing:
Library strategy: HiChIP
: Fastq files of the paired-end Hi-ChIP data were acquired from Illumina HiSeq. The annotation file of restriction fragments after digestion in Hg19 genome was generated using digest_genome.py function from HiC pro package (v.2.11.1). The chromosome size file was downloaded from UCSC genome browser.
The HiChIP interaction pairs were identified for each fastq sample by running HiC-Pro with parameters ” MIN_MAPQ = 10, BOWTIE2_GLOBAL_OPTIONS = --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder, BOWTIE2_LOCAL_OPTIONS =  --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder, LIGATION_SITE = GATCGATC, GET_ALL_INTERACTION_CLASSES = 1, GET_PROCESS_SAM = 0, RM_SINGLETON = 1, RM_MULTI = 1, RM_DUP = 1, BIN_SIZE = 20000 40000 150000 500000 1000000, MATRIX_FORMAT = upper, MAX_ITER = 100, FILTER_LOW_COUNT_PERC = 0.02, FILTER_HIGH_COUNT_PERC = 0, EPS = 0.1 “
Genome_build: hg19
Supplementary_files_format_and_content: Interaction loop mango file

extract_protocol:
DNA was purified using Monarch PCR & DNA Cleanup Kit (Cat.#T1030S, New England Biolabs).
Libraries were purified and sized selected using ProNex Purification System (Cat.#NG2003, Promega). Libraries were paired-end sequenced with read lengths of 150 bp (PE 2X150 on the Illumina HiSeq Genome Analyzer).

tag: hchip antibody


title: Day 3 ARID1A HiChIP profiling in SMARCB1 +/+ G401 cell line Rep1


title: Day 0 K27Ac HiChIP profiling in SMARCB1 -/- G401 cell line Rep2


title: Day 3 K27Ac HiChIP profiling in SMARCB1 +/+ G401 cell line Rep1


title: Day 7 JUND CUT&RUN profiling in SMARCB1 +/+ G401 cell line

data_processing:
Library strategy: CUT&RUN
Reads were deduplicated with the clumpify tool using flag -dedupe -subs=2, and subsequently trimmed with bbduk using parameters --ktrim=r --k=21 --mink=11 --hdist=1 --tpe --tbo.
The trimmed fastq files were then aligned to the Hg19 human genome using Bowtie2 aligner. Specifically, we used parameter “--end-to-end --very-sensitive --no-mixed --no-discordant -q -I 10 -X 700 --phred33” for the alignment.
Bam files were converted to bed files after removing chrM, chrUn, and reads containing “random” as chromosome position. Bed files were further cleaned by removing regions contained in the hg19 blacklist from ENCODE (v2)
MACS2 software (v.2.1.1.20160309) was used for calling TF peaks with parameters at default “callpeak -g hs -f BAMPE -q 0.05 -B”. Peaks were further cleaned by using a cutoff of signalValue greater than 5.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: CUT_RUN_peak.bed, which includes the peaks for all SWI/SNF subunits and AP-1 samples, is linked to the SuperSeries GSE175534 record.

value: JUND


title: Day 7 JUNB CUT&RUN profiling in SMARCB1 +/+ G401 cell line

value: JUNB


title: Day 0 K27Ac HiChIP profiling in SMARCB1 -/- G401 cell line Rep1


title: Day 7 H3K27Ac CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 3 H3K27Ac CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 3 JUNB CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 3 JUND CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 3 pJUN CUT&RUN profiling in SMARCB1 +/+ G401 cell line

value: pJUN


title: Day 1 JUNB CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 0 JUND CUT&RUN profiling in SMARCB1 -/- G401 cell line


title: Day 1 pJUN CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Day 0 JUNB CUT&RUN profiling in SMARCB1 -/- G401 cell line


title: Day 0 pJUN CUT&RUN profiling in SMARCB1 -/- G401 cell line


title: scProgenyProduction_lowMOI_secondInfection_NA_biolRep2

status: Public on Oct 08 2022

city: Seattle

first: Jesse

last: Bloom

state: WA

address: 1100 Fairview Ave N, room B3-123

institute: Fred Hutchinson Cancer Center

description:
Viral barcode sequencing: read1 file contains viral barcode and NA transcript
Second infection (infectious progeny) NA viral barcodes low MOI biological replicate 2
scProgenyProduction_trial3_filtered_progeny_viral_bc.csv.gz

library_source: other

data_processing:
All code for data processing as well as detailed explanations are at https://github.com/jbloomlab/barcoded_flu_pdmH1N1. The dms_variants package was used to parse viral barcodes from Illumina sequencing reads. Viral barcodes were corrected using UMItools directional adjacency method. Agregate counts of each viral barcode were generated for viral barcodes associated with sequenced infected cells and output in a CSV file.
Supplementary files format and content: CSV containing viral barcodes and barcode counts for each viral barcode associated with an infected cell
Library strategy: viral barcode

molecule: other

organism: Influenza A virus (A/California/04/2009(H1N1))

source_name: Influenza-infected MDCK, viral barcodes

extract_protocol:
All code for data processing as well as detailed explanations are at https://github.com/jbloomlab/barcoded_flu_pdmH1N1. RNA was isolated from the viral supernatant or infected cell pellets using the RNeasy Mini Kit. Lysis buffer was mixed with the viral supernatant sample and 70% ethanol was added. For the infected cell pellets, the sample was mixed with lysis buffer and homogenized by vortexing at high speed for 20 seconds. The homogenized sample was processed on a gDNA eliminator spin column to remove genomic DNA. The processed sample was combined with 70% ethanol. From this point, both the viral supernatant and infected cell pellets were treated identically and followed the standard RNA purification protocol specified by the manufacturer. The RNA for each sample was eluted in 50 ul of RNase-free water.   Reverse transcription was performed with a segment-specific primer targeted to the HA or NA vRNA. Two replicate reactions were performed using RNA from the viral supernatant sample, and two independent reactions were performed using RNA from the two infected cell pellet samples; these replicates provide technical duplicate measurements of both the physical progeny in the supernatant and the infectious progeny in the cell pellets.  Reverse transcription was performed using the SuperScript III First-Strand Synthesis SuperMix kit according to the manufacturer protocol [46]. For the viral supernatant samples, 12 ul of each RNA sample was used as template for each 40 ul reaction. For the infected cell pellet samples–which contain much larger amounts of total RNA, due to the host RNA present in the cell–1000 ng of RNA was used as template for each 40 ul reaction. The low-concentration cDNA generated from the viral supernatant samples was purified and concentrated using 2X Ampure SPRI beads and eluted into 22 ul of elution buffer.   Viral barcodes were amplified in 50 ul PCR reactions using KOD Hot-Start Master Mix. For the viral supernatant samples, 22 ul of concentrated cDNA was used as template. For the high-concentration infected cell pellet samples, 10 ul of unpurified cDNA was used as template. Segment-specific primers (Table S3) were used and reactions were run for 20 cycles. Amplicons were size-selected and purified using a double-sided AmpureXP bead cleanup. Samples were first combined with 0.8X AmpureXP beads and the supernatant was collected. The supernatant was then combined with 1.8X AmpureXP beads and the bound DNA was collected.   Sequencing indices and adapters were attached in a 50 ul PCR reaction using KOD Hot-Start Master Mix. For all samples, 2 ng of purified amplicon DNA was used as template. Sample-specific index primers (Table S3) were used and reactions were run for 20 cycles. The resulting amplicons were gel-purified and pooled for sequencing. Single-end sequencing was performed on an Illumina MiSeq.
At 12 hours post-infection, the supernatant was collected and cells and debris were removed by centrifugation at 300 RCF for 3 min. The supernatant was split into 2 aliquots of 220 ul each and frozen at -80C. The cells were collected by addition of 100 ul trypsin and a single-cell suspension was generated. The trypsin digestion was stopped by addition of 400 ul of D10 medium. The cells were washed 3 times with phosphate-buffered saline supplemented with 0.8% by volume non-acetylated bovine serum albumin. The cells were counted to confirm that approximately 10,000 cells were present per well and loaded into the 10X Chromium device.

tag: sequencing target

value: Infectious virus progeny

tag: cell or_virus_type

value: A/California/04/2009 (pdmH1N1)


title: scProgenyProduction_lowMOI_secondInfection_NA_biolRep1

description:
Viral barcode sequencing: read1 file contains viral barcode and NA transcript
Second infection (infectious progeny) NA viral barcodes low MOI biological replicate 1
scProgenyProduction_trial3_filtered_progeny_viral_bc.csv.gz


title: Day 0 H3K4me3 CUT&RUN profiling in SMARCB1 -/- G401 cell line

value: G401 cell line

tag: cut&run antibody


title: Day 3 K27Ac HiChIP profiling in SMARCB1 +/+ G401 cell line Rep2

value: SMARCB1 +/+

tag: time point


title: scProgenyProduction_lowMOI_secondInfection_HA_biolRep2

description:
Viral barcode sequencing: read1 file contains viral barcode and HA transcript
Second infection (infectious progeny) HA viral barcodes low MOI biological replicate 2
scProgenyProduction_trial3_filtered_progeny_viral_bc.csv.gz


title: scProgenyProduction_lowMOI_secondInfection_HA_biolRep1

description:
Viral barcode sequencing: read1 file contains viral barcode and HA transcript
Second infection (infectious progeny) HA viral barcodes biological replicate 1
scProgenyProduction_trial3_filtered_progeny_viral_bc.csv.gz


title: scProgenyProduction_lowMOI_supernatant_HA_biolRep2

description:
Viral barcode sequencing: read1 file contains viral barcode and HA transcript
Supernatant (physical progeny) HA viral barcodes low MOI biological replicate 2
scProgenyProduction_trial3_filtered_progeny_viral_bc.csv.gz

source_name: Influenza supernatant, viral barcodes

value: Physical virus progeny


title: scProgenyProduction_lowMOI_supernatant_NA_biolRep1

description:
Viral barcode sequencing: read1 file contains viral barcode and NA transcript
Supernatant (physical progeny) NA viral barcodes biological replicate 1
scProgenyProduction_trial3_filtered_progeny_viral_bc.csv.gz


title: scProgenyProduction_lowMOI_supernatant_NA_biolRep2

description:
Viral barcode sequencing: read1 file contains viral barcode and NA transcript
Supernatant (physical progeny) NA viral barcodes low MOI biological replicate 2
scProgenyProduction_trial3_filtered_progeny_viral_bc.csv.gz


title: scProgenyProduction_lowMOI_viralTranscripts

description:
Influenza transcripts enriched from low MOI single-cell 3' mRNA library: contain cell barcode, UMI, and transcript
Long-read sequencing of influenza poly A RNA on PacBio Sequel IIe instrument
This sample was not used for quantitative gene expression analysis. It was used to examine the viral sequences in infected cells.

data_processing:
All code for data processing as well as detailed explanations are at https://github.com/jbloomlab/barcoded_flu_pdmH1N1. The PacBio circular consensus sequencing data were processed using the PacBio's ccs program to build circular consensus sequences (CCSs). A custom script was used to remove duplicate sequences generated by circularization during library preparation. The dms_variants package was used to call consensus sequences for each infected cell's virus transcripts. The consensus sequences were output in a FASTQ file.
Assembly: A/California/04/2009 (pdmH1N1) with the G155E cell-culture adaptation mutation
Supplementary files format and content: no quantitative processed data for this sample.

source_name: Long-read influenza transcripts

extract_protocol:
All code for data processing as well as detailed explanations are at https://github.com/jbloomlab/barcoded_flu_pdmH1N1. Influenza transcripts were amplified from the 10X Genomics full-length single-cell cDNA library in a semi-specific PCR reaction. For semi-specific PCR, each segment was amplified with a primer annealing to the universal TruSeq primer site that is added to all cDNA molecules during the reverse transcription step of 10x Genomics protocol and a primer annealing to 5’ of viral mRNA (that also contains a flanking sequence that is complementary to the TrueSeq primer site). Semi-specific PCR reaction conditions were as follows: 12 ng cDNA, 0.5 µM of forward and reverse primer, 10 µl of KOD (EMD Millipore, 71842), 0.1 mg/ml BSA, and final volume adjusted to 20 µl with water. PCR was incubated for 120 s at 95°C followed by 10 cycles of 120 s at 95°C, 20 s at 55°C, 90 s at 70°C, and a final extension step at 70°C for 120 s. Semi-specific PCR reactions were purified using AMPure XP beads at 1.8x beads to sample ratio and eluted in 12 µl of water. Following purification, PCR products were circularized via complementary TrueSeq sequence. For circularization, 10 µl of purified PCR product were used in a 20 µl HiFi assembly reaction (NEB, E2621S). HiFi assembly was performed at 50°C for 1 hour.    Next, HiFi products were used in segment-specific PCR reactions. To amplify viral products of all lengths, primers that annealing to the ends of viral mRNA were used; to preferentially a+B75mplify full-length viral segments, primers that anneal to approximately the middle of each viral segment were used (Table S2). Segment-specific PCR conditions were as follows:  9 µl of Hifi reaction, 0.5 µM of forward and reverse primer, 25 µl of KOD, and final reaction volume adjusted to 50 µl with water. PCR was incubated for 120 s at 95°C followed by cycling for 120 s at 95°C, 20 s at 55°C and 90 s at 70°C, the final extension step was at 70°C for 120 s. For polymerase segments 14 cycles of segment-specific PCR were performed, for HA, NA and NP segments 10 cycles, and for M and NS segments 7 cycles. PCR reactions were purified using AMPure XP beads at 1.8x beads to sample ratio and eluted in 12 µl of water. All purified PCR products were pooled together and sequenced using PacBio Sequel II machine.
At 12 hours post-infection, the supernatant was collected and cells and debris were removed by centrifugation at 300 RCF for 3 min. The supernatant was split into 2 aliquots of 220 ul each and frozen at -80C. The cells were collected by addition of 100 ul trypsin and a single-cell suspension was generated. The trypsin digestion was stopped by addition of 400 ul of D10 medium. The cells were washed 3 times with phosphate-buffered saline supplemented with 0.8% by volume non-acetylated bovine serum albumin. The cells were counted to confirm that approximately 10,000 cells were present per well and loaded into the 10X Chromium device.

value: Virus transcripts


title: Day 7 pJUN CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Naive hiPSCs cultured on MEF, RSeT, SUSD2+, rep3 [15_2D_SUSD2+_3]

status: Public on Oct 01 2022

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk (bbmap suite 37.31)
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files including raw counts

source_name: human reprogrammed fibroblast (giulitti et al. 2019, Nature Cell Biology, DOI: 10.1038/s41556-018-0254-5)

growth_protocol: Naïve hiPSCs were cultured on a confluent layer of mitotically inactive MEFs (DR4, ATCC) in RSeT medium (Stemcell Technologies). Cells were passaged every 4-5 days with TrypLE™ Select Enzyme (Life Technologies) as previously described (Giulitti and Pellegrini, 2019). Naïve cells were switched from 2D to 3D culture by detaching naïve colonies from 2D MEF, dissociating the colonies as single cells with TrypLE and then embedding them in 100% Matrigel (Corning) drops as described below. Optimal cell density was defined as 2k cells/µl, and 25µl of this was spread on tissue culture treated multiwell plates (Falcon) for maintenance. Medium change was performed every 24 hours and cells were passaged every 4 - 5 days. After 2 passages in 3D, we confirmed the absence of MEF contamination.

extract_protocol:
Qiagen RNeasy Mini Kit.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostics srl).

treatment_protocol: SUSD2+ cells were FACS sorted from respective bulk samples

tag: cell type

value: Naive human induced pluripotent stem cells


title: Naive hiPSCs cultured on MEF, RSeT, SUSD2+, rep4 [16_2D_SUSD2+_4]


title: Naive hiPSCs cultured on MEF, RSeT, SUSD2+, rep2 [14_2D_SUSD2+_2]


title: Naive hiPSCs cultured on MEF, RSeT, SUSD2+, rep1 [13_2D_SUSD2+_1]


title: Naive hiPSCs cultured on MEF, RSeT, rep4 [12_2D_bulk_4]


title: Day 1 JUND CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: Naive hiPSCs cultured on MEF, RSeT, rep1 [9_2D_bulk_1]


title: Naive hiPSCs cultured in 3D matrigel, RSeT, SUSD2+, rep4 [8_3D_SUSD2+_4]


title: Naive hiPSCs cultured in 3D matrigel, RSeT, SUSD2+, rep3 [7_3D_SUSD2+_3]


title: Naive hiPSCs cultured on MEF, RSeT, rep2 [10_2D_bulk_2]


title: Naive hiPSCs cultured in 3D matrigel, RSeT, rep2 [2_3D_bulk_2]


title: Naive hiPSCs cultured in 3D matrigel, RSeT, SUSD2+, rep1 [5_3D_SUSD2+_1]


title: Naive hiPSCs cultured in 3D matrigel, RSeT, rep3 [3_3D_bulk_3]


title: Naive hiPSCs cultured in 3D matrigel, RSeT, rep1 [1_3D_bulk_1]


title: Naive hiPSCs cultured in 3D matrigel, RSeT, SUSD2+, rep2 [6_3D_SUSD2+_2]


title: scProgenyProduction_lowMOI_supernatant_HA_biolRep1

description:
Viral barcode sequencing: read1 file contains viral barcode and HA transcript
Supernatant (physical progeny) HA viral barcodes low MOI biological replicate 1
scProgenyProduction_trial3_filtered_progeny_viral_bc.csv.gz


title: Naive hiPSCs cultured in 3D matrigel, RSeT, SUSD2+, rep3


title: Naive hiPSCs cultured in 3D matrigel, RSeT, SUSD2+, rep4


title: Naive hiPSCs cultured in 3D matrigel, RSeT, rep3


title: Naive hiPSCs cultured in 3D matrigel, RSeT, rep4


title: Naive hiPSCs cultured in 3D matrigel, RSeT, rep2


title: Naive hiPSCs cultured in 3D matrigel, RSeT, SUSD2+, rep2


title: scProgenyProduction_lowMOI_polyAseq

description:
Low MOI influenza-infected single-cell 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript and viral barcode
poly A RNA

data_processing:
All code for data processing as well as detailed explanations are at https://github.com/jbloomlab/barcoded_flu_pdmH1N1. The raw sequencing data from the single-cell RNA sequencing was aligned using STARsolo against a composite reference made up of the canine genome CanFam3.1.98 concatenated to the A/California/04/2009 influenza virus genome. Alignment produced a cell-gene matrix containing the gene expression of every canine and virus gene for each single cell.
Assembly: CanFam3.1.98, A/California/04/2009 (pdmH1N1) with the G155E cell-culture adaptation mutation
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

organism:
Canis lupus familiaris
Influenza A virus (A/California/04/2009(H1N1))

source_name: Single influenza-infected MDCK cell cDNA

extract_protocol:
All code for data processing as well as detailed explanations are at https://github.com/jbloomlab/barcoded_flu_pdmH1N1. Single-cell RNA sequencing was performed with the 10X Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1. The manufacturer’s standard protocol was used with the following modifications. The template-switching oligo was replaced with a modified single-stranded DNA oligo with the sequence 5’-AGAGTGTTTGGGTAGAGCAGCGTGTTGGCATGTrGrGrG-3’ at a final concentration of 45 uM in the reaction mix. This change was made to accommodate some of the barcoded influenza segments’ exogenous sequence which shares homology with the standard 10X template-switching oligo. The cDNA amplification primer mix was replaced with a pair of primers with the sequences 5’-AGAGTGTTTGGGTAGAGCAGCG-3’ (binding to the custom template-switch oligo mentioned above) and 5’-CTACACGACGCTCTTCCGATCT-3’ (binding to the standard 10X adapter sequence) at a final concentration of 1 uM in the reaction mix. The cDNA amplification PCR reaction extension time was increased to 20 seconds to encourage the formation of full-length cDNA products. The amplified cDNA product was split in half; one half was used for fragmentation and preparation of the transcriptome sequencing library while the other half was used as template for long-read sequencing of viral transcripts.
At 12 hours post-infection, the supernatant was collected and cells and debris were removed by centrifugation at 300 RCF for 3 min. The supernatant was split into 2 aliquots of 220 ul each and frozen at -80C. The cells were collected by addition of 100 ul trypsin and a single-cell suspension was generated. The trypsin digestion was stopped by addition of 400 ul of D10 medium. The cells were washed 3 times with phosphate-buffered saline supplemented with 0.8% by volume non-acetylated bovine serum albumin. The cells were counted to confirm that approximately 10,000 cells were present per well and loaded into the 10X Chromium device.

value: Host and virus

value: Madin-Darby canine kidney cells (MDCK)-SIAT1-TMPRSS2; A/California/04/2009 (pdmH1N1)


title: Naive hiPSCs cultured on MEF, RSeT, rep4


title: Naive hiPSCs cultured on MEF, RSeT, rep3


title: Naive hiPSCs cultured on MEF, RSeT, SUSD2+, rep3


title: Naive hiPSCs cultured on MEF, RSeT, rep2


title: Naive hiPSCs cultured on MEF, RSeT, SUSD2+, rep2


title: Naive hiPSCs cultured on MEF, RSeT, SUSD2+, rep1


title: Syk_LPS_4h_replicate2 [SYKL4H2]

status: Public on Sep 26 2022

city: Bethesda

first: Iain

last: Fraser

state: MD

address: 9000 Rockville Pike, Bldg. 4, Rm. 109A, MSC-0421

department: NIAID

institute: NIH

data_processing:
RNA-seq data was processed using the Pipeliner workflow (https://github.com/CCBR/Pipeliner).
Reads were trimmed using cutadapt v1.18 (MARTIN, 2011). and aligned to the human hg38 reference genome and Gencode release28 using STAR v2.5.2b (Dobin et al., 2013).  RSEM v1.3.0 (Li and Dewey, 2011) was used for gene-level expression quantification
Assembly: hg38
Supplementary files format and content: RawCountFile_RSEM_genes.txt

source_name: primary macrophage cells

growth_protocol: Differentiated primary macrophage cells (4.5×105 per well) were plated in 12-well plates.

extract_protocol:
RNA was isolated with an RNeasy Mini Kit (QIAGEN) following the manufacturer’s protocol and eluted in RNase free TE buffer.
RNAseq libraries were created in triplicate for all cell types using Illumina TruSeq Stranded mRNA Library Prep, pooled, and sequenced on a NextSeq producing paired-end 75 base-pair reads.

treatment_protocol: Cells were treated with SYKi IV, RUT, or DMSO for 24h, rested for 3d, and stimulated with 100ng/mL LPS for designated amount of time. For RUT samples without LPS, cells were treated with RUT for the designated amount of time.

value: primary macrophage cells

tag: treatment

value: Syk inhibitor IV for 24h, washed and rested for 3 days, followed by LPS for 4h


title: Naive hiPSCs cultured on MEF, RSeT, rep1


title: Syk_LPS_4h_replicate3 [SYKL4H3]


title: Syk_LPS_24h_replicate2 [SYKL24H2]

value: Syk inhibitor IV for 24h, washed and rested for 3 days, followed by LPS for 24h


title: Syk_LPS_24h_replicate3 [SYKL24H3]


title: Syk_LPS_24h_replicate1 [SYKL24H1]


title: Syk_LPS_0h_replicate3 [SYKL0H3]

value: Syk inhibitor IV for 24h,  washed and rested for 3 days, followed by LPS for 0h


title: Rut_LPS_4h_replicate3 [RUTL4H3]

value: rutaecarpine for 24h washed and rested for 3 days, followed by LPS for 4h


title: Rut_LPS_4h_replicate2 [RUTL4H2]


title: Rut_LPS_24h_replicate3 [RUTL24H3]

value: rutaecarpine for 24h, washed and rested for 3 days, followed by LPS for 24h


title: Syk_LPS_0h_replicate1 [SYKL0H1]


title: Rut_LPS_24h_replicate2 [RUTL24H2]


title: Naive hiPSCs cultured in 3D matrigel, RSeT, rep1


title: Naive hiPSCs cultured on MEF, RSeT, SUSD2+, rep4


title: Rut_LPS_24h_replicate1 [RUTL24H1]


title: Rut_LPS_0hr_replicate3 [RUTL0H3]

value: rutaecarpine for 24h, washed and rested for 3 days, followed by LPS for 0h


title: Rut_LPS_0hr_replicate1 [RUTL0H1]


title: Rut_4h_replicate3 [RUT4H3]

value: rutaecarpine for 4h


title: Rut_4h_replicate1 [RUT4H1]


title: Rut_24h_replicate3 [RUT24H3]

value: rutaecarpine for 24h


title: Rut_24h_replicate1 [RUT24H1]


title: Syk_LPS_4h_replicate1 [SYKL4H1]


title: Rut_4h_replicate2 [RUT4H2]


title: Rut_0h_replicate3 [RUT0H3]

value: rutaecarpine for 0h


title: DMSO_LPS_4hr_ Replicate3 [DMSOL4H3]

value: DMSO, for 24h, washed and rested for 3 days, followed by LPS for 4h


title: Rut_0h_replicate2 [RUT0H2]


title: DMSO_LPS_4hr_ Replicate1 [DMSOL4H2]

value: DMSO for 24h, washed and rested for 3 days, followed by LPS for 4h


title: DMSO_LPS_4hr_ Replicate1 [DMSOL4H1]


title: Rut_0h_replicate1 [RUT0H1]


title: DMSO_LPS_24hr_replicate3 [DMSOL24H3]

value: DMSO for 24h, washed and rested for 3 days, followed by LPS for 24h


title: DMSO_LPS_24hr_replicate1 [DMSOL24H1]


title: DMSO_LPS_24hr_replicate2 [DMSOL24H2]


title: Rut_LPS_4h_replicate1 [RUTL4H1]

value: rutaecarpine for 24h, washed and rested for 3 days, followed by LPS for 4h


title: DMSO_LPS_0hr_ Replicate3 [DMSOL0H3]

value: DMSO for 24h, washed and rested for 3 days, followed by LPS for 0h


title: DMSO_LPS_0hr_ Replicate1 [DMSOL0H1]

value: DMSO for 24h, washed and rested for 3 days ,followed by LPS for 0h


title: Rut_LPS_0hr_replicate2 [RUTL0H2]


title: DMSO_LPS_0hr_ Replicate2 [DMSOL0H2]


title: Syk_LPS_0h_replicate2 [SYKL0H2]


title: Rut_24h_replicate2 [RUT24H2]


title: C1219

status: Public on Aug 16 2022

city: Kiel

first: Simonas

last: Juzenas

address: Am Botanischen Garten 11

department: Institute of Clinical Molecular Biology

country: Germany

institute: Christian-Albrechts-University of Kiel

data_processing:
Trimming of adapter sequences: cutadapt -b TGGAATTCTCGGGTGCCAAGG -m 18 -q 30 –discard-untrimmed (cutadapt)
Quantification of miRNAs: miraligner -sub 1 -trim 3 -add 3 -s hsa -db miRBase_v22 -freq (SeqBuster)
Genome_build: miRBase v22 (gemome build GRCh38)
Supplementary_files_format_and_content: tab-delimited text files include miRNA and iso-miRNA counts for each sample

source_name: peripheral blood

extract_protocol:
Standard protocol of miRNeasy Mini Kit (Qiagen)
Standard protocol of TruSeq Small RNA Sample Preparation Kit (Illumina)

value: male

tag: diagnosis

value: Healthy control


title: C1138

tag: Sex

value: female


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title: C0261


title: C0239


title: C0234


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title: C0233


title: C0251


title: C0231


title: C0232


title: C0230


title: C0229


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title: C0224


title: C0246


title: C0220


title: C0222


title: C0223


title: C0226


title: C0257


title: C0219


title: C0225


title: C0217


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title: C0215


title: C0214


title: C0213


title: C0212


title: C0211


title: C0210


title: C0228


title: C0203


title: C0206


title: C0204


title: C0205


title: C0218


title: C0200


title: C0193


title: C0195


title: C0201


title: C0198


title: C0194


title: C0192


title: C0196


title: C0197


title: C0199


title: D5593


title: D5592

value: Symptomatic control


title: C0209


title: C0208


title: C0207


title: D5591


title: C0202


title: D5589


title: D5586


title: D5585


title: D5584


title: D5590

type: RNA

description: SAMPLE 202

hyb_protocol: Human HT-12 v4 BeadChip array (Illumina)

scan_protocol: iScan system (Illumina)

data_processing: Probes which were flagged as “bad” or having “No match” (without match to coding sequences or to any genomic region) by illuminaHumanv4PROBEQUALITY mapping were discarded. Non-expressed probes (in at least 10% of samples) were detected by limma’s detectionPValues() function and removed from further analyses. Probes that were unannotated by illuminaHumanv4SYMBOL or mapped to mitochondrial and ribosomal genes (those beginning with MRP, RPL, and RPS) were also discarded from further analysis. The findLargest() function from the genefilter was used to remove probes that mapped to the same gene symbol, while retaining the probe with the highest median intensity value.

label: biotin

label_protocol: TargetAmp-Nano Labeling Kit (Epicentre)

extract_protocol: PAXgene Blood RNA Kit (Qiagen)

tag: annotation file


title: C0357

tag: age


title: D5591

description: SAMPLE 203


title: C0350


title: D5590


title: D5587

description: SAMPLE 200


title: D5582

description: SAMPLE 196


title: D5592

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description: SAMPLE 188


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title: D5580

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description: SAMPLE 185


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description: SAMPLE 182


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title: D5650

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description: SAMPLE 178


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description: SAMPLE 177


title: E04828

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description: SAMPLE 176


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title: D5570


title: E04826

description: SAMPLE 166


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title: E04825

description: SAMPLE 165


title: D5573


title: E04824

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title: E04821

description: SAMPLE 161


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title: E04820

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title: E04823

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title: D5648


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title: E04814

description: SAMPLE 155


title: E04818

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title: D5643


title: D5559

description: SAMPLE 145


title: D5560

description: SAMPLE 146


title: D5563

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title: D5568

description: SAMPLE 153


title: D5567

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title: D5564

description: SAMPLE 149


title: E04831


title: D5561

description: SAMPLE 147


title: D5555

description: SAMPLE 142


title: D5556

description: SAMPLE 143


title: D5642


title: E04830


title: D5553

description: SAMPLE 140


title: E04829


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description: SAMPLE 141


title: D5569

description: SAMPLE 154


title: E04828


title: D5566

description: SAMPLE 151


title: D5551

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title: E04825


title: D5552

description: SAMPLE 139


title: E04824


title: D5640

description: SAMPLE 134


title: D5549

description: SAMPLE 136


title: D5638

description: SAMPLE 132


title: D5637

description: SAMPLE 131


title: E04823


title: D5635

description: SAMPLE 129


title: D5639

description: SAMPLE 133


title: D5634

description: SAMPLE 128


title: D5550

description: SAMPLE 137


title: D5627

description: SAMPLE 123


title: D5641

description: SAMPLE 135


title: D5636

description: SAMPLE 130


title: D5629

description: SAMPLE 125


title: D5633

description: SAMPLE 127


title: E04822


title: D5628

description: SAMPLE 124


title: E04827


title: D5624

description: SAMPLE 120


title: D5626

description: SAMPLE 122


title: E04821


title: D5557

description: SAMPLE 144


title: D5623

description: SAMPLE 119


title: D5632

description: SAMPLE 126


title: D5622

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title: D5625

description: SAMPLE 121


title: E04820


title: E04819


title: E04818


title: E04815


title: E04817


title: D5618

description: SAMPLE 114


title: D5620

description: SAMPLE 116


title: D5619

description: SAMPLE 115


title: D5569


title: D5568


title: D5567


title: D5496

description: SAMPLE 112


title: D5485

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title: D5488

description: SAMPLE 108


title: D5497

description: SAMPLE 113


title: D5484

description: SAMPLE 106


title: D5566


title: D5491

description: SAMPLE 111


title: D5481

description: SAMPLE 104


title: D5489

description: SAMPLE 109


title: D5479

description: SAMPLE 102


title: D5480

description: SAMPLE 103


title: D5490

description: SAMPLE 110


title: E04814


title: D5478

description: SAMPLE 101


title: D5475

description: SAMPLE 98


title: D5474

description: SAMPLE 97


title: D5477

description: SAMPLE 100


title: D5565


title: D5472

description: SAMPLE 95


title: D5483

description: SAMPLE 105


title: D5564


title: D5563


title: D5470

description: SAMPLE 94


title: D5476

description: SAMPLE 99


title: D5473

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title: D5467

description: SAMPLE 93


title: D5466

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title: D5561


title: D5556


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title: D5557


title: D5465

description: SAMPLE 91


title: D5463

description: SAMPLE 89


title: D5464

description: SAMPLE 90


title: D5555


title: D5460

description: SAMPLE 86


title: D5458

description: SAMPLE 85


title: D5554


title: D5461

description: SAMPLE 87


title: D5451

description: SAMPLE 79


title: D5462

description: SAMPLE 88


title: D5621

description: SAMPLE 117


title: D5452

description: SAMPLE 80


title: D5553


title: D5560


title: D5450

description: SAMPLE 78


title: D5456

description: SAMPLE 83


title: D5455

description: SAMPLE 82


title: D5552


title: D5454

description: SAMPLE 81


title: E04812

description: SAMPLE 77


title: E04811

description: SAMPLE 76


title: D5551


title: D5550


title: D5457

description: SAMPLE 84


title: E04807

description: SAMPLE 72


title: E04809

description: SAMPLE 74


title: E04808

description: SAMPLE 73


title: D5549


title: E04810

description: SAMPLE 75


title: E04804

description: SAMPLE 69


title: E04806

description: SAMPLE 71


title: E04803

description: SAMPLE 68


title: E04802

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title: D5665

description: SAMPLE 66


title: D5641


title: D5640


title: D5664

description: SAMPLE 65


title: D5639


title: D5637


title: D5636


title: D5659

description: SAMPLE 60


title: D5661

description: SAMPLE 62


title: D5660

description: SAMPLE 61


title: E04805

description: SAMPLE 70


title: D5662

description: SAMPLE 63


title: D5634


title: D5658

description: SAMPLE 59


title: D5635


title: D5663

description: SAMPLE 64


title: D5633


title: D5656

description: SAMPLE 57


title: D5655

description: SAMPLE 56


title: D5657

description: SAMPLE 58


title: D5632


title: D5545

description: SAMPLE 54


title: D5638


title: D5538

description: SAMPLE 50


title: D5542

description: SAMPLE 51


title: D5654

description: SAMPLE 55


title: D5629


title: D5544

description: SAMPLE 53


title: D5531

description: SAMPLE 48


title: D5528

description: SAMPLE 45


title: D5529

description: SAMPLE 46


title: D5530

description: SAMPLE 47


title: D5543

description: SAMPLE 52


title: D5627


title: D5527

description: SAMPLE 44


title: D5626


title: D5525

description: SAMPLE 42


title: D5628


title: D5625


title: D5624


title: D5623


title: D5522

description: SAMPLE 39


title: D5537

description: SAMPLE 49


title: D5521

description: SAMPLE 38


title: D5518

description: SAMPLE 36


title: D5524

description: SAMPLE 41


title: D5514

description: SAMPLE 35


title: D5621


title: D5622


title: D5620


title: D5509

description: SAMPLE 31


title: D5523

description: SAMPLE 40


title: D5511

description: SAMPLE 33


title: D5526

description: SAMPLE 43


title: D5510

description: SAMPLE 32


title: D5618


title: D5508

description: SAMPLE 30


title: D5506

description: SAMPLE 29


title: D5513

description: SAMPLE 34


title: D5497


title: D5500

description: SAMPLE 24


title: D5502

description: SAMPLE 26


title: D5501

description: SAMPLE 25


title: D5496


title: D5499

description: SAMPLE 23


title: D5505

description: SAMPLE 28


title: D5503

description: SAMPLE 27


title: D5491


title: D5619


title: D5490


title: D5498

description: SAMPLE 22


title: D5614

description: SAMPLE 19


title: D5616

description: SAMPLE 20


title: D5611

description: SAMPLE 17


title: D5609

description: SAMPLE 15


title: D5617

description: SAMPLE 21


title: D5488


title: D5485


title: D5484


title: D5613

description: SAMPLE 18


title: D5604

description: SAMPLE 10


title: D5519

description: SAMPLE 37


title: D5606

description: SAMPLE 12


title: D5489


title: D5479


title: D5478


title: D5476


title: D5603

description: SAMPLE 9


title: D5600

description: SAMPLE 6


title: D5605

description: SAMPLE 11


title: D5610

description: SAMPLE 16


title: D5597

description: SAMPLE 3


title: D5599

description: SAMPLE 5


title: D5483


title: D5602

description: SAMPLE 8


title: D5608

description: SAMPLE 14


title: D5601

description: SAMPLE 7


title: D5598

description: SAMPLE 4


title: D5595

description: SAMPLE 2


title: D5474


title: D5594

description: SAMPLE 1


title: D5480


title: D5481


title: D5467


title: D5477


title: D5472


title: D5473


title: D5466


title: D5464


title: D5470


title: D5463


title: D5475


title: D5458


title: D5456


title: D5455


title: D5462


title: D5465


title: D5454


title: D5450


title: D5451


title: D5452


title: E04812


title: E04810


title: E04809


title: E04807


title: E04805


title: E04811


title: E04804


title: E04803


title: D5461


title: D5460


title: D5457


title: E04808


title: D5664


title: D5661


title: D5663


title: D5660


title: D5607

description: SAMPLE 13


title: D5662


title: D5659


title: E04802


title: D5658


title: D5665


title: D5656


title: D5654


title: D5545


title: E04806


title: D5657


title: D5655


title: D5542


title: D5544


title: D5538


title: D5531


title: D5537


title: D5543


title: D5529


title: D5530


title: D5528


title: D5526


title: D5524


title: D5523


title: D5525


title: D5527


title: D5518


title: D5514


title: D5521


title: D5513


title: D5510


title: D5509


title: D5511


title: D5508


title: D5506


title: D5500


title: D5503


title: D5501


title: D5498


title: D5499


title: D5502


title: D5613


title: D5505


title: D5616


title: D5614


title: D5610


title: D5609


title: D5608


title: D5611


title: D5522


title: D5519


title: D5606


title: D5602


title: D5604


title: D5601


title: D5603


title: D5605


title: D5607


title: D5598


title: D5595


title: D5597


title: D5599


title: D5617


title: H3K9me3_Panob_2

status: Public on Aug 04 2022

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

description: Neuroblastoma cells, treated with Panobinostat, antibody H3K9me3 (Abcam ab8898)

data_processing:
Reads were aligned to the human genome version GRCh38 using the program subread v. 1.6.4
Peaks were called using the program MACS2 v. 2.26 using the input samples as controls
Differential peak binding was determined separately for each probe with R package DiffBind v. 2.10.0 with the following settings: minOverlap=3, summits=50, filterFun=max (and otherwise default options)
For peak annotation, R packages ChIPSeeker v. 1.18.0 and TxDb.Hsapiens.UCSC.hg38.knownGene v. 3.4.0 were used
Genome_build: GRCh38
Supplementary_files_format_and_content: BED files: position of peaks identified with MACS2

source_name: Neuroblastoma cells

growth_protocol: Cells were grown under standard conditions in a humidified atmosphere at 37°C and 5% CO2

extract_protocol:
Lysates were clarified from sonicated samples and histone-DNA complexes were isolated with antibody. Genomic DNA was extracted and purified using Qiagen PCR Purification Kit according to standard instructions
Libraries were prepared with the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina (10 ng input) following the manufacturers’ instructions. A size selection step for fragments of 300 bp length was performed after library preparation. Pools of six to seven libraries were sequenced on one lane HiSeq 4000 in 50 single read mode.

treatment_protocol: 24h after seeding, adherent cells were treated with solvent (DMSO) or 30 nM panobinostat for 18 h.

value: Neuroblastoma cells

value: Panobinostat

tag: chip antibody

value: H3K9me3 (Abcam ab8898)

value: GI-ME-N


title: H3K9me3_Panob_3


title: H3K9me3_Solv_3

description: Neuroblastoma cells, treated with Solvent, antibody H3K9me3 (Abcam ab8898)

value: Solvent


title: H3K9me3_Panob_1


title: H3K4me3_Panob_3

description: Neuroblastoma cells, treated with Panobinostat, antibody H3K4me3 (Abcam ab8580)

value: H3K4me3 (Abcam ab8580)


title: H3K9me3_Solv_2


title: H3K9me3_Solv_1


title: H3K4me3_Solv_2

description: Neuroblastoma cells, treated with Solvent, antibody H3K4me3 (Abcam ab8580)


title: H3K4me3_Solv_3


title: H3K36me3_Panob_3

description: Neuroblastoma cells, treated with Panobinostat, antibody H3K36me3 (Abcam ab9050)

value: H3K36me3 (Abcam ab9050)


title: H3K4me3_Panob_1


title: H3K4me3_Solv_1


title: H3K4me3_Panob_2


title: H3K36me3_Solv_2

description: Neuroblastoma cells, treated with Solvent, antibody H3K36me3 (Abcam ab9050)


title: H3K36me3_Panob_2


title: H3K36me3_Solv_1


title: H3K36me3_Solv_3


title: D5600


title: H3K36me3_Panob_1


title: H3K27me3_Panob_2

description: Neuroblastoma cells, treated with Panobinostat, antibody H3K27me3 (Active Motif 39155)

value: H3K27me3 (Active Motif 39155)


title: H3K27me3_Panob_1


title: H3K27me3_Solv_4

description: Neuroblastoma cells, treated with Solvent, antibody H3K27me3 (Active Motif 39155)


title: H3K27me3_Panob_4


title: H3K27me3_Solv_2


title: H3K27me3_Solv_3


title: H3K27me3_Panob_3


title: D5594


title: H3K27me3_Solv_1


title: H3K27ac_Panob_2

description: Neuroblastoma cells, treated with Panobinostat, antibody H3K27ac (Abcam ab4729)

value: H3K27ac (Abcam ab4729)


title: H3K27ac_Panob_3


title: H3K27ac_Panob_1


title: Input_Panob_3

description: Neuroblastoma cells, treated with Panobinostat, antibody none


title: H3K27ac_Solv_1

description: Neuroblastoma cells, treated with Solvent, antibody H3K27ac (Abcam ab4729)


title: Input_Panob_4


title: Input_Panob_2


title: H3K27ac_Solv_2


title: Input_Solv_4

description: Neuroblastoma cells, treated with Solvent, antibody none


title: Input_Panob_1


title: Input_Solv_3


title: Input_Solv_2


title: Input_Solv_1


title: Spleen_Chronic_D21_CD8_PD1Pos_rep2_atac

status: Public on Jul 25 2022

first: Ansuman

middle: T

last: Satpathy

address: 300 Pasteur Drive

department: Pathology

description: Single cell ATAC-seq library (10X Genomics)

data_processing:
Processed with cellranger-atac count pipeline, version 1.2.0.
Genome_build: mm10
Supplementary_files_format_and_content: *_fragments.tsv, scATAC_LCMV_metadata.tsv

source_name: CD8+ PD1+ T cells from spleen 21 dpi with LCMV-c13

extract_protocol: 10X Genomics Next GEM Single Cell ATAC Library & Gel Bead Kit (v1.1 Chemistry).

value: CD8+ PD1+ T cells


title: Spleen_Chronic_D21_CD8_PD1Pos_rep1_atac


title: Spleen_Chronic_D21_CD8_TetNeg_atac

source_name: CD8+ gp33- T cells from spleen 21 dpi with LCMV-c13

value: CD8+ gp33- T cells


title: Spleen_Chronic_D8_CD8_TetNeg_atac

source_name: CD8+ gp33- T cells from spleen 8 dpi with LCMV-c13


title: Spleen_Acute_D8_CD8_TetPos_atac

source_name: CD8+ gp33+ T cells from spleen 8 dpi with LCMV-Armstrong

value: CD8+ gp33+ T cells


title: Spleen_Chronic_D8_CD8_TetPos_atac

source_name: CD8+ gp33+ T cells from spleen 8 dpi with LCMV-c13


title: RPE1_ETS1_CutTag

status: Public on Jul 28 2022

city: Zhanjiang

first: Yun-Miao

last: Guo

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

institute: Central People's Hospital of Zhanjiang

data_processing:
For CUT&Tag data processing, FASTQC was used to measure the date quality distribution.
The clean reads were then aligned to reference genome sequences using the bwa program.
Peaks were called using MACS2 peak caller with q-value < 0.05.
Genome-wide normalized signal coverage tracks were visualized in the IGV.
Assembly: hg38
Supplementary files format and content: bigWig files include peaks for each sample, respectively.
Library strategy: CUT&Tag

growth_protocol: hTERT RPE-1 cells (ATCC, CRL-4000) were cultured in F12/DMEM (1:1) supplemented with 10% fetal bovine serum (FBS, Gemini, 900-108) and 0.01mg/ml hygromycin B under 5% CO2 at 37°C.

extract_protocol:
10,000 fresh cells were counted and processed according to Hyperactive® Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) instructions. Briefly, ConA beads were added to the cell pellet and incubation at room temperature for 10 min. Subsequently, the mixed complexes were incubated overnight at 4°C with primary antibody. The following day, the cells were washed and incubated with diluted secondary antibody at room temperature for 2 h. Antibody-protein-DNA complexes were then linked by pA/G-Tnp by incubation at room temperature for 1 h. After washing, the eluted complexes were subsequently sheared by adding 5 × TTBL. The proteinase K and DNA extract beads were used for obtaining eluted DNA.
Sequencing libraries were established after 11 cycles of PCR amplification. Selected size-selected were proceeded using AMPure XP beads and the DNA were sequenced on the Illumina Hiseq-PE150 platform to a depth of 2.5 × 107 reads.

value: Retinal pigment epithelial cells

tag: antibody


title: Spleen_Chronic_D21_CD8_CX3CR1Pos_atac

source_name: CD8+ CX3CR1+ T cells from spleen 21 dpi with LCMV-c13

value: CD8+ CX3CR1+ T cells


title: Spleen_Chronic_D21_CD8_CX3CR1Neg_atac

source_name: CD8+ CX3CR1- T cells from spleen 21 dpi with LCMV-c13

value: CD8+ CX3CR1- T cells


title: H3K27ac_Solv_3

tag: cell line


title: Spleen_Chronic_D21_CD8_CX3CR1Neg_Slamf6Pos_atac

source_name: CD8+ CX3CR1- SLAMF6+ T cells from spleen 21 dpi with LCMV-c13

value: CD8+ CX3CR1- SLAMF6+ T cells


title: H-sh103-2

status: Public on Jul 11 2022

city: Farmington

first: Sabriya

last: Syed

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory for Genomic Medicine

data_processing:
Basecalling performed by BGI
Sequenced reads were processed using the SOAPnuke software.  Reads were trimmed for the adaptor sequence and filtered for low quality reads and stored in FASTQ format.
HISAT2 was used for genome mapping to GRCh38/hg38 after which a complete reference transcriptome was generated using StringTie, Cufflinks and CPC.
The SOAPnuke output was then mapped to the reference transcriptome using Bowtie2 and RSEM was used to calculate gene expression levels.
Differential gene expression was calculated using DESeq2
Assembly: GRCh38/hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: HeLa  cells obtained from American Type Culture Collection were cultured in DMEM media (Sigma-Aldrich) supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics (penicillin G/Streptomycin, Gibco) in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol:
TRIzol was used to harvest total RNA from proliferating HeLa cells transduced with lentivirus for scr and ZIP11 shRNA
RNA libraries were prepared by the Beijing Genomics Institute (BGI) for sequencing on a BGISEQ-500

treatment_protocol: Mission plasmids encoding for two different shRNA against human ZIP11 and the control scrambled (Scr) construct with a puromycin resistance cassette ere used to tranduce HeLa cells. Stable cell lines were geenrated, and cells plated at 1x10^5 cells cm2 were allowed to proliferate for 48 h.

value: HeLa cells (CCL2, ATCC)

value: ZIP11 sh103


title: H-sh103-1


title: H-CONT-2

source_name: Scr control 2

value: Scr control


title: H-CONT-1

source_name: Scr control 1


title: H-sh67-2

value: ZIP11 sh67


title: H-sh67-1


title: MPM10_sn

status: Public on Jul 06 2022

city: New York

first: Jana

last: Biermann

state: New York

address: 622 W168th Street

institute: Columbia University

description: Single-nuclei RNA sequencing

data_processing:
Raw sc/snRNA-seq data were analyzed using Cell Ranger (v6.1.1). Transcripts were aligned to the human GRCh38 reference genome.
Ambient RNA was removed using CellBender (v0.2.0). Gene expression matrices were processed individually in R (v4.1.1) using Seurat (v4.1.0).
Filters were applied to keep cells with 500–10,000 genes, 1,000–60,000 UMIs, and <10% of mitochondrial reads in each individual sample.
Scrublet v0.2.1 (Wolock et al., 2019) and DoubletFinder v2.0.3 (McGinnis et al., 2019) were applied to identify and remove doublets with an expected doublet rate ranging from 2.8–6.4% based on the loading rate.
Assembly: GRCh38
Supplementary files format and content: mtx file (MatrixMarket format) of combined gene expression count matrix
Supplementary files format and content: csv file of gene names corresponding to the combined gene expression count matrix
Supplementary files format and content: csv file of integrated gene expression matrix
Supplementary files format and content: csv file with metadata
Supplementary files format and content: h5 file of CellBender output
Supplementary files format and content: csv file of SCENIC matrix (tumor cells snRNA-seq)
Supplementary files format and content: csv file of VIPER matrix (tumor cells snRNA-seq)

source_name: Melanoma subcutaneous metastasis

extract_protocol:
Single-cell samples: Melanoma brain metastases from surgical resections were dissociated using the human tumor dissociation kit from Miltenyi and viable CD45- and CD45+/CD15-/CD66b- populations were sorted. Of each sorting population 15,000 cells were loaded for droplet-based RNA capture and reverse transcription using 10x Genomics 5’ reagentsand a Chromium controller. Single-nuclei samples: Single-nuclei suspension from frozen melanoma metastases were generated using methods published in Slyper et al. (Nature Medicine, 2020) with modifications. The tissue was first cut in 20 µm sections using a cryostat and stored on dry ice until the next step. Then the tissue was put on wet ice and washed once with 5 ml PBS to remove OCT. After this step nuclei were extracted by vigorous pipetting in salt-tris buffer with Tween-20 (TST)  followed by a high-volume wash in salt-tris buffer (ST). Nuclei were counted and 15,000 nuclei were separated for droplet-based RNA capture and reverse transcription using 10x Genomics  3' v3.0 reagents and a Chromium controller.
Single-cell RNA sequencing (scRNA-seq) libraries were generated using Chromium 5’ reagents and T cell enrichment kit according to the manufacturer protocol. SingleSingle-nuclei RNAseq (snRNA-seq) libraries were generated using Chromium 3' v3.0 reagents according to the manufacturer protocol with one additional cycle during library amplification to account for lower material input from nuclei compared to whole cells.

tag: metastatic site

value: ECM

tag: patient id

tag: mutation status

value: BRAF/NRAS WT

tag: sequencing technique

value: snRNA-seq

tag: tcr-seq

value: no


title: MPM09_sn

description: Single-nuclei RNA sequencing

source_name: Axillary LN

value: NRAS mutated


title: MPM08_sn

description: Single-nuclei RNA sequencing

value: BRAF V600E


title: Spleen_Chronic_D21_CD8_TetPos_atac

source_name: CD8+ gp33+ T cells from spleen 21 dpi with LCMV-c13


title: MPM07_sn

description: Single-nuclei RNA sequencing


title: MPM06_sn

description: Single-nuclei RNA sequencing

value: BRAF WT, JAK  P429S


title: MPM04_sn

description: Single-nuclei RNA sequencing


title: MPM02_sn

description: Single-nuclei RNA sequencing


title: MPM01_sn

description: Single-nuclei RNA sequencing

value: ECM01_rep1_slide and ECM01_rep2_slide


title: MPM05_sn

description: Single-nuclei RNA sequencing


title: MBM21_sn

description: Single-nuclei RNA sequencing

source_name: Melanoma brain metastasis

value: MBM


title: Spleen_Acute_D8_CD8_TetNeg_atac

source_name: CD8+ gp33- T cells from spleen 8 dpi with LCMV-Armstrong

value: CD8+ gp33- T cells


title: MBM20_sn

description: Single-nuclei RNA sequencing


title: MBM18_sn

description: Single-nuclei RNA sequencing

value: BRAF WT


title: MBM17_sn

description: Single-nuclei RNA sequencing


title: MPM11_sn

description: Single-nuclei RNA sequencing


title: MBM13_sn

description: Single-nuclei RNA sequencing


title: MBM11_sn

description: Single-nuclei RNA sequencing

value: MBM11_rep1_slide, MBM11_rep2_slide and MBM11_rep3_slid


title: MBM14_sn

description: Single-nuclei RNA sequencing


title: MBM10_sn

description: Single-nuclei RNA sequencing


title: MBM08_sn

description: Single-nuclei RNA sequencing


title: MBM09_sn

description: Single-nuclei RNA sequencing


title: MBM12_sn

description: Single-nuclei RNA sequencing


title: MBM07_sn

description: Single-nuclei RNA sequencing

value: BRAF WT/NRAS WT


title: MBM05_sn

description: Single-nuclei RNA sequencing

value: MBM05_rep1_slide, MBM05_rep2_slide and MBM05_rep3_slide


title: MBM06_sn

description: Single-nuclei RNA sequencing

value: NRAS Q61R


title: MBM19_sn

description: Single-nuclei RNA sequencing


title: MBM01_sc

description: Single-cell RNA sequencing

value: scRNA-seq

value: yes


title: MBM02_sc

description: Single-cell RNA sequencing

value: HRAS T58I


title: MBM03_sc

description: Single-cell RNA sequencing


title: MBM05_sc

description: Single-cell RNA sequencing


title: MBM04_sc

description: Single-cell RNA sequencing


title: liver, high-content tumor, Day12 [HT_3]

status: Public on Jun 18 2022

city: ShenZhen

first: Huan

last: Ren

address: 1088 Xueyuan Avenue

institute: Southern university of science and technology

data_processing:
CASAVA base recognition.
Clean data were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data through in-house perl scripts.
Paired-end clean reads were aligned to the reference genome (GRCm38/mm10) using Hisat2 (v2.0.5).
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Assembly: GRCm38/mm10
Supplementary files format and content: gene_count.txt: Tab-delimited text file includes raw counts of sequencing reads as a matrix table for each sample.

source_name: liver

extract_protocol:
RNA was harvested using TRIzol Reagent (Life Technologies), total amounts and integrity of RNA were assessed using the Agilent 5400.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols, the effective concentration of the library is higher than that of 2nM.

tag: tissue

value: liver

value: male

tag: genotype

value: WT

tag: time

value: Day 12


title: liver, high-content tumor, Day12 [HT_1]


title: MBM16_sn

description: Single-nuclei RNA sequencing

value: NRAS mutated

value: snRNA-seq

value: no


title: liver, high-content tumor, Day12 [HT_2]


title: liver, medium-content tumor, Day11 [MT1_2]

value: Day 11


title: liver, medium-content tumor, Day11 [MT1_1]


title: MBM15_sn

description: Single-nuclei RNA sequencing

value: MBM


title: liver, medium-content tumor, Day11 [MT2_2]


title: liver, medium-content tumor, Day11 [MT2_1]


title: liver, medium-content tumor, Day9 [MT3_2]

value: Day 9


title: liver, low-content tumor, Day9 [LT_2]


title: liver, tumor-free liver tissue, remote from tumor Day12 [FC_1]


title: liver, low-content tumor, Day9 [LT_1]


title: liver, medium-content tumor, Day9 [MT3_1]


title: liver, control, Day0 [C_1]

value: normal saline

value: Day 0


title: liver, control, Day0 [C_2]


title: SmaC9P

status: Public on May 31 2022

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

data_processing:
Quality control of raw reads by FastQC and AfterQC
STAR version2.5.3  for reads alignment and counts summary
Reads count data were processed using R/Bioconductor "limma" package for RPKM and 'voom' normalization
Batch effect resulted from two library preps were adjusted using "combat" function implemented in R/Bioconductor "sva" package
Assembly: GenCode GRCh38
Supplementary files format and content: counts data and TPM ormalized data in .txt

source_name: lung

extract_protocol:
IPF patients were diagnosed based on multidisciplinary review and published criteria. Non-IPF donor lungs not suitable for transplantation were obtained from the Regional Organ Bank of Illinois.
IPF lungs were grossly examined within 6-12 hours from the time of explant, and multiple 1cm3 biopsies were obtained from visibly non-fibrotic central (IPF.C) and fibrotic peripheral (IPF.P) areas. Non-IPF donor lung biopsies of central (CTR.C) and peripheral (CTR.P) were similarly obtained. H&E-stained biopsies were reviewed and confirmed by two clinical pathologists
Total RNA was isolated using TRIzol (Invitrogen) following manufacturer’s protocol. All RNA samples displayed RNA Integrity Number (RIN) >7.
RNAseq including cDNA library preparation was processed at the Genomics Core Facility of University of Chicago (https://fgf.uchicago.edu/). Total RNA in the amount of 100-500μg per sample was depleted of ribosomal RNA using the Ribo-Zero kit (Epicentre, Madison, WI). The directional (first strand) cDNA libraries were prepared following the guide of TruSeq Stranded Total RNA Sample Preparation kit.

tag: subject

tag: site

value: peripheral

value: Donor


title: SmaC9C

value: central

tag: diagnosis


title: SmaC3P

tag: Sex


title: SmaC3C


title: SmaC5C


title: SmaC6C

value: female


title: SmaC4P


title: SmaC4C


title: SmaC8P


title: SmaC5P


title: SmaC2C


title: SmaC2P


title: SmaC8C


title: SmaC6P


title: SmaC1P


title: Sma14P

value: IPF


title: Sma14C


title: Sma12C


title: Sma6P


title: Sma8C


title: Sma13C


title: Sma12P


title: Sma9C


title: SmaC1C


title: Sma11P


title: Sma6C


title: Sma11C


title: Sma5C


title: Sma9P


title: Sma10C


title: Sma5P


title: Sma13P


title: Sma4P


title: Sma4C


title: Sma3P


title: Sma10P


title: Sma8P


title: Sma3C


title: 35nt size marker_rep2

status: Public on Apr 27 2022

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

data_processing:
Raw counts were calculated by HTSeq
Supplementary files format and content: Excel sheet with raw counts and norrmcounts of 20 and more.

organism: synthetic construct

source_name: Oligonucleotides synthesized by IDT

extract_protocol:
In the A samples all four oligos were mixed before library preparation and sequencing.
In the B and C samples two libraries were prepared, one with the B and one with the C samples and the sequenced together
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. RNA-SEQ libraries were generated using Illumina TruSEQ TotalRNA kits using the Illumina provided protocol.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

tag: sample type

value: Oligonucleotides


title: Sma2C

value: male

tag: age


title: Sma1P


title: Sma2P


title: 19nt size marker_rep2


title: 19nt size marker_rep1


title: 12xCAG_rep1


title: 35nt size marker_rep1


title: 12xCAG_rep2


title: Sma1C


title: 7xCAG_rep2


title: PSA Lesional Patient 5

status: Public on May 12 2022

first: Shruti

last: Naik

state: NY

address: 435 East 30th Street

institute: NYU Langone Health

description:
st_images.gz
Sample name: PSA_LES_P5
sample id v2: ST-L-RP2

data_processing:
Sequencing output and the histology images were processed using space ranger software (10X Genomics).  The space ranger mkfastq function was used for sample demultiplexing and to converting spatial barcodes and reads into FASTQ format.
The space ranger count function was used to align reads from FASTQ files to human genome (hg38) and then align microscopic slide image and transcriptome to generate barcode/UMI counts, feature spot matrices, cluster data, and perform gene expression analysis.
Assembly: hg38
Supplementary files format and content: Filtered feature-barcode matrices (filtered_feature_bc_matrix) containing only spot barcodes in MEX format for each sample. Spatial folder output from space ranger count function containing QC images for aligned fiducials and detetected tissue in jpg format, scalefactors_json.json, high and low resolution versions of the input image in png format, and tissue_positions_list.csv.  All spatial outputs (Spatial image data) are stored in st_images.tar.gz.
Library strategy: spatial transcriptomics

source_name: Skin

growth_protocol: Three to four millimeter skin punch biopsies were obtained from lesional and non-lesional skin of healthy controls and subjects with psoriatic disease.

extract_protocol: Tissues were embedded in OCT and frozen in liquid nitrogen-chilled isopentane within 5 minutes of devascularization. 10-µm cryosections were mounted onto the ST arrays (10X Visium)  where reverse transcription of cellular transcripts took place in situ after tissue permeabilization.

treatment_protocol: Subjects were biologic-naïve (untreated)

tag: individual

value: patient 5

value: Skin punch biopsy

tag: sequencing run / batch

tag: disease state

value: Psoriatic Arthritis (PsA)

tag: disease status

value: Lesional

tag: pasi score


title: 7xCAG_rep1


title: NB7 HP-shSCR rep2

description: Single Read

data_processing:
Processing was done with the SPOROS pipeline: https://github.com/ebartom/SPOROS
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Reads were demultiplexed according to adaptor barcodes to separate into the individual samples listed below.
6 bp UMIs were removed with Trim_galore (4N before pull-down sequence and 2N after).  This resulted in the deposited fastq files.
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Reads with hits against artificial and adapter sequences are removed from the table, as well as reads with a summed count < total number of samples
Raw counts were calculated by HTSeq
Assembly: NA
Supplementary files format and content: Excel sheet with raw reads

source_name: Teitz et al., 2000, Nat Med, 5:529

extract_protocol:
Cells were subjected to pull down with a GW182 peptide bound to anti-FLAG M2 Magnetic beads RNA at a size of 19-35 nt was gel extracted and used to generate library
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol containing library fragments 140-160 bp in size.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol:
NB7 cells were plated in 6-well plates and transfected with 2.5 nM of siRNAs/HPs using RNAiMax. Total RNA was isolated after 24hrs.
Cells were subjected to Ago pull down and smRNA Seq

tag: cell line

value: Brain

tag: treatment/infection

value: Transfected with 2.5 nM shScr for 24hrs

value: wt


title: NB7 HP-HTT-loss of inhibition rep1

description: Single Read

value: Transfected with 2.5 nM mHTT LOI for 24hrs


title: NB7 HP-HTT-loss of inhibition rep2

description: Single Read


title: NB7 siNT1 rep2

description: Single Read

value: Transfected with 2.5 nM siNT1 for 24hrs


title: NB7 HP-HTT-ref seq rep2

description: Single Read

value: Transfected with 2.5 nM mHTT Ref for 24hrs


title: NB7 HP-HTT-ref seq rep1

description: Single Read


title: NB7 ssCAG rep2

description: Single Read

value: Transfected with 2.5 nM ssCAG for 24hrs


title: NB7 HP-shSCR rep1

description: Single Read


title: NB7 ssCAG rep1

description: Single Read


title: BRF20985-R6/2 250-3-19W

description: Single Read

data_processing:
Processing was done with the SPOROS pipeline: https://github.com/ebartom/SPOROS
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Reads were demultiplexed according to adaptor barcodes to separate into the individual samples listed below.
6 bp UMIs were removed with Trim_galore (4N before pull-down sequence and 2N after).  This resulted in the deposited fastq files.
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Reads with hits against artificial and adapter sequences are removed from the table, as well as reads with a summed count < total number of samples
Raw counts were calculated by HTSeq
Assembly: NA
Supplementary files format and content: Excel sheet with reads normalized to 1 million reads

source_name: Jennifer Morton, University of Cambridge

extract_protocol:
Lysates of 250 mg brain tissue were subjected to pull down with a GW182 peptide bound to anti-FLAG M2 Magnetic beads RNA at a size of 19-35 nt was gel extracted and used to generate library
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol containing library fragments 140-160 bp in size.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

value: Brain striatum


title: BRF22484-WT1-19W

description: Single Read


title: BRF20965-R6/2 250-1-19W

description: Single Read


title: BRF22534-WT3-18W

description: Single Read


title: BRF26940-R6/2 450-1-85W

description: Single Read


title: NB7 siNT1 rep1

description: Single Read


title: BRF26367-R6/2 450-2-90W

description: Single Read


title: pBAD_yffP300_mutCS, 300 bp insert, mut SceI site

status: Public on Apr 17 2022

city: Moscow

first: Anastasiia

last: Okhtienko

address: Akademika Kurchatova square 2

country: Russia

institute: Institute of Molecular Genetics, Russian Academy of Sciences

data_processing:
All libraries were quality checked before further processing using FastQC (v0.11.9).
Trimmomatik (v0.36) was used to remove adapters, eliminate reads shorter than 14 bp and to cut reads longer than 24 bp.
Reads were aligned onto the reference genome E.coli (MG1655 Refseq: NC_000913.3 or BW25113 Refseq: CP009273.1) and plasmid (pBAD_CbAgo_lacI_full, pBAD_CbAgo_lacI_dec or pBAD_CS_yffP) via bowtie (v1.3.1) allowing zero mismatches and unique alignment
Alligned .sam files were converted to binary .bam, sorted using samtools (v. 1.15)
The E. coli  genome was divided into intervals of length 1 kb using custom Python script. bedtools (v2.30.0) was used to intersect the resulted bed file with the bam file. smDNA counts were expressed in terms of RPKM. Reads from “+” and “-” strands were selected with samtools view –F/ -f 16. For them, the coverage was calculated separately according to the method described above.
Assembly: NC_000913.3 / CP009273.1 with manually added CbAgo gene (802798-810180)
Supplementary files format and content: tsv files include count values for 1kb genome intervals (both strands and + / - separately)
Library strategy: DNA-seq (smDNA)

organism: Escherichia coli

growth_protocol: Cells from plate were grown in LB media supplemented with antibiotics and the  inducing agent (0.1% L-arabinose or/and anhydrotetracycline, 200 ng/ml)  at 18˚C until OD 600 = 1.0

extract_protocol:
Cells were collected by centrifugation (6000 g, 6 min at 4 °C) and pellets were frozen at -20 °C. Pellets were defrosted at room temperature and diluted with 30 ml lysis buffer (40 mM tris HCl pH 7.9, 150 mM NaCl) in the presence of ½ tb of protease inhibitor cocktail EDTA-free (Roche). After filtration using 170 mkm nylon filters samples were lysed using high-pressure homogenizer cell disruptor PEC at 30 kpsi twice and then centrifugated (17000 rpm R21A rotor Hitachi, 15 min at 4 °C twice). Clarified lysate was incubated with 0.3 ml prewashed Co2+beads (Clontech) for 140 min at +4 °C with rotation in top-bottom direction. Suspension was centrifugated 3 min 500 g at +4 °C, supernatant (flowthrough) was removed. Beads were washed twice with 25 ml ice-cold lysis buffer for 5 min, 4 times with 1 ml  lysis buffer 10 mM imidazole and CbAgo was eluted with lysis buffer contained 200 mM imidazole 0.33 ml 3 times. Fractions were analyzed using protein PAGE, 0.3 ml of each elution fraction was Proteinase K treated (100 μg, 1 h 37 °C) and elution fractions with CbAgo were combined. Deproteinazed samples were treated with 0.5 ml phenol-chloroform-isoamyl alcohol (25:24:1) pH 7.5-8, vortex for 10 seconds, centrifugated 2 min at 21000 g. Supernatant was washed twice with 0.5 ml chloroform. Nucleic acids from final aqueous phase were ethanol precipitated in the presence of PINK coprecipitant and 30 mM sodium acetate pH 5.0 for 1h in liquid nitrogen or overnight at -70 °C. Samples were centrifugated for 30 min, 21000 g at +4 °C and pellets were washed with 70% ice-cold EtOH. Air-dried pellets were diluted in nuclease-free water (40 mkl per sample). 10% of each sample was dephosphorylate using rSAP (NEB) in 1x PNK buffer for 30 min at 37 °C, rSAP was inactivated for 10 min at 75 °C. Dephosphorylated samples were subsequently radiolabelled with γ-P32-ATP using T4 polynucleotide kinase (NEB), oligos ladder (12-70 nt) was also radiolabelled at this point. Radiolabelled samples were mixed with correspondent 20 μl of nontreated samples and resolved on 19% PAGE gel with 8M urea in 1x TBE and visualized on a Typhoon FLA 9500 imager (GE Healthcare) with position labels. Gel slices corresponding to 14–22 nt were cut from gel and crushed in 0.4 M NaCl overnight at 20 °C with constant shaking 1000 rpm on bench tube shaker. Gel slices were removed and solution with nucleic acids was ethanol precipitated as described, DNA was resuspended in 20 μl nuclease-free water.
Small DNAs were ligated with Illumina-compatible adaptors. Samples (20 μl) were mixed with 8 μl of 5x Rapid Ligation buffer (ThermoFisher), 2 μl of 100 μM 5′-adaptor, 2 μl of 100 μM of 3′-linker, 2 μl of 100 μM bridge 1, 2 μl of 100 μM bridge 2 and 800 units of T4-ligase (NEB) and incubated 16 h at room temperature. Ligated DNA fragments were sliced from 19% urea PAGE and eluted from gel slices as described. The libraries were PCR amplified with RP1 and indexing primers (TrueSeq) and NEBNext Ultra II Q5 Master Mix with adjusting number of cycles using product visualization on 6% native PAGE gel with SYBR Gold staining. Amplified libraries were also cut from native 6% PAGE in blue light, and PCR products were extracted in 0.4 M NaCl and precipitated as described. smDNA libraries were sequenced using the HiSeq2500 platform (Illumina) in the rapid run mode (50-nucleotide single-end reads)

tag: strain

value: BW27784 araB::PBAD-I-SceI lacIq lacZc- lacZ+

tag: plasmid


title: BRF20976-R6/2 250-2-19W

description: Single Read

tag: tissue

tag: genotype


title: pBAD_CbAgo_lacI_rec, recoded gene

value: F-, lambda-, rph-1


title: pBAD_CbAgo_lacI_0.45, 450 bp


title: pBAD_CbAgo_lacI_0.6, 600 bp


title: pBAD_CbAgo_lacI_0.05, 50 bp


title: pBAD_CbAgo_lacI_0.2, 200 bp


title: pBAD_CbAgo_lacI_0.3, 300 bp


title: BRF22485-WT2-19W

description: Single Read


title: pBAD_CbAgo_lacI_0, no gene


title: GI-ME-N_Solv_1

type: genomic

description: Solvent-treated

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

scan_protocol: Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol.

data_processing: Illumina files were read and processed using the R package minfi (v. 1.28.4). The arrays were normalized using the quantile algorithm. Probes with detection p.value above 0.1 were discarded.

label: Cy3, Cy5

source_name: Neuroblastoma cell line

label_protocol: 350-500 ng genomic DNA from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo Research Corporation, Orange, US) according to the manufacturer recommendations. Each sample was whole genome amplified and enzymatically fragmented following the instructions in the Illumina Infinium HD Assay Methylation Protocol Guide .

growth_protocol: Cells were grown under standard conditions in a humidified atmosphere at 37°C and 5% CO2.

extract_protocol: Genomic DNA was extracted and purified from cell samples using Qiagen QIAamp DNA Mini Kit according to standard instructions.

tag: gender

value: female

value: GI-ME-N

tag: treatment

value: Solvent-treated


title: pBAD_CbAgo_lacI_0.1, 100 bp


title: pBAD_yffP300_noCS, 300 bp insert, no SceI site


title: pBAD_CbAgo_lacI_full, full gene (1083 bp)