title: Liver, male, Deficient, ZT17, rep1

city: La Jolla

first: Laura

last: van Rosmalen

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description:
38_M_16H_LIVER_S7
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

data_processing:
Sequencing quality was assessed using FastQC, version 0.11.9
Cutadapt v4.1 was used to trim adapter sequences
Sequence reads were aligned to the Mus musculus (house mouse) genome GRCm38 (mm10) and counted per gene using STAR aligner v2.7.10a
Gene counts were filtered for low counts and normalized per tissue using DESeq2 v1.34.0
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes normalized counts for each sample

extract_protocol:
Total RNA was extracted from neural and peripheral tissues using TRIzol reagent according to the manufacturer’s instructions. 500ng of total RNA was used for the construction of sequencing libraries
Libraries were prepared using Illumina’s TruSeq Stranded mRNA (PolyA+) kit according to the manufacturer’s instructions

value: CBA/CaJ

value: Deficient


title: Day 5 iPSC IFNg_BS_OX

status: Public on Aug 07 2024

type: SRA

city: Barcelona

first: Mercedes

last: Barrero

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

library_source: genomic

data_processing:
Analysis of 5mC and 5hmC percentages was done independently for each CpG contained in the PCR amplicons. A customized pipeline was generated for this analysis. Amplicons which contained the SNP and at least a CpG in the same read were analyzed. First, reads were assigned to their corresponding genes by identification of the primer used for PCR. Then, a 15-20 nucleotides sequence upstream of the SNP was used to classify the reads in Mus or Cas. Then, a 15-20 nucleotides sequence upstream of the CpG was used to determine the presence of CG or TG. Percentages of CG were calculated independently for Mus and Cas, in control or IFNγ-treated samples, in BS or OxBS samples. 5mC percentages were calculated by analyzing the percentage of CG in OxBS samples, while 5hmC were calculated as %CG (BS) - %CG(OxBS). Finally, 5mC and 5hmC percentages for Mus and Cas CpGs were compared between control and IFNγ samples.
Assembly: mm10
Supplementary files format and content: txt: results of number of reads and percentages of CG and TG for X mus and X cas for each CpG. Contains 4 .txt files
Supplementary files format and content: Allele_specific_DNA_methylation_analysis.xlsx: final percentages of 5mC and 5hmC calculated for each CpG in each sample
Library strategy: PCR-amplicon sequencing

molecule: genomic DNA

organism: Mus musculus

source_name: embryonic stem cell

extract_protocol:
DNA was extracted using Wizard® Genomic DNA Purification Kit (Promega, A1120). After measuring DNA quantity by Qubit (ThermoFisher Scientific), 2µg of each sample was evenly splitted for the oxidation reaction (Oxidative Bisulfite -OxBS- treated samples) and the mock-oxidation reaction (Bisulfite -BS- treated samples) where the oxidant solution was replaced by water following the TrueMethyl oxBS Module manufacturer’s instructions (NuGEN-Tecan, 0414). Both aliquots were then processed in parallel for all stages of the protocol. After the oxidation reaction where 5-hydroxymethylcytosine is oxidized to 5-formylcytosine (5fC) and 5-methylcytosine (5mC) stays unchanged, the bisulfite treatment converts 5fC and all non-methylated cytosines to uracil, while 5mC is not altered.
Paired oxidative Bisulfite (OxBS) and the mock-oxidation reaction (Bisulfite BS) treated DNA from day 5 (control and IFNγ) reprogramming samples were used as templates for a two-step PCR amplification with the IMMOLASE™ DNA Polymerase (BIO-21046) with a custom program adapted to each primer pair annealing temperature and resulting amplicon size. In the first PCR, 0.5 ng of DNA were used to amplify the regions of interest to increase the specificity of the second PCR reaction and enrich the region of interest. In the second PCR, 1-3 µl of the first-step products were amplified using staggered primers to provide sequence variability for the sequencing. The sets of staggered forward and reverse primers were designed to contain partial P5 and P7 adaptor sequences, respectively, at the 5’ and 2-5 random nucleotides (N) before the gene-specific sequence. The amplicons from the different regions of interest were gel-purified, quantified, and pooled together for library preparation. 4 libraries corresponding to control and IFNγ samples (BS/BS-OX) at day 5 were prepared for sequencing, and subsequent steps were completed following the MiSeq System protocol (MiSeq Reagent Kit v3, Illumina). Next Generation Sequencing was performed using MiSeq (300bp, single-end).

treatment_protocol: Reprogramming was induced in the presence or absence of IFNγ at 10 ng/ml (from day 0 to 5) (R&D Systems, 485-MI-100). SSEA1+ day 5 iPSCs were sorted with a BD FACSAria II SORP.

tag: tissue

value: embryonic stem cell

tag: cell line

value: hybrid 129S1/SvImJ, CAST/EiJ

tag: cell type


title: Unstimulated human NK (24h)

city: Marseille

first: Eric

last: Vivier

state: PACA

address: 117 Avenue de Luminy BP 30191

country: France

institute: Innate Pharma

description: 10 X Genomics

library_source: transcriptomic single cell

data_processing:
Droplet-based sequencing data were aligned using Cell Ranger (version 6.0.0) against a combination of the human (GRCh38) and mouse (mm10) reference genomes. Gene expression was quantified as well by Cell Ranger using gene annotations from GENCODE (release 32 for the human genome and M23 for the mouse one).
Assembly: hg38
Supplementary files format and content: Tab-separated value files and matrix files

molecule: polyA RNA

organism: Homo sapiens

source_name: NK cell

extract_protocol:
After incubation (4 hours or 24 hours), plates were washed in complete RPMI medium and  centrifuged 400g for 5 minutes at +5 ± 3°C. Cells were washed once with PBS + 1% BSA and centrifuged at 400g for 5 minutes at +5 ± 3°C. Samples from the same conditions of all 4 donors were individually stained with barcoded lipids from 3’ CellPlex kit Set A (10X Genomics, #1000261).
After pooling, samples from the same conditions of all 4 Healthy Donors  were individually stained with barcoded lipids from 3’ CellPlex kit Set A (10X Genomics, #1000261): cells were centrifuged at 400g for 5 minutes at +5 ± 3°C, and resuspended in either 100 µL of individual barcode from 3’ CellPlex kit Set A reagent (10X Genomics, #1000261).
Following recommendations of 10X Genomics, cells were resuspended in 50 µl PBS 1% BSA. Libraries were prepared with Chromium Next GEM Single Cell 3’ v3.1 kit (10X Genomics). For each condition, 100 ng of Gene Expression Library were mixed with 25 ng of Cell Multiplexing Oligos Library.

treatment_protocol: Purified NK cells from four donors were co-incubated with huCD20B16-F10 cells at an Effector Target (ET) ratio of 10:1, with 100 000 NK cells for 10 000 huCD20B16-F10 cells per well, in a U-bottom 96 wells plate, for 4 or 24 hours at 37°C. Two conditions were tested: 1) Vehicle (US for Unstimulated), containing 100 000 NK cells, 10 000 huCD20B16-F10 cells, no antibody/molecule). 2) ANKET4, containing 100 000 NK cells, 10 000 huCD20B16-F10 cells, and ANKET4 (GA101-T5-3D9H1L1-IL2v) at a concentration of 0.1µg/ml.

value: NK cell

tag: treatment

value: Unstimulated (24h)

tag: library type

value: mRNA


title: 2234021080125

city: Guangzhou

first: Bingxue

last: Hu

state: China Mainland (PRC)

address: Guangzhou 510700

country: China

institute: Vision MedicalsCo., Ltd.

library_source: transcriptomic

data_processing:
high-quality data were aligned to the human genome hg38 using HISAT2 with default parameters. Gene-level quantification was performed using FeatureCounts. The gene counts were aggregated using the featureCounts program from the Subread package release 2.0.0.
Assembly: hg38
Supplementary files format and content: Tab-delimited text includes raw per-gene counts for each sample.

molecule: total RNA

source_name: BALF mNGS with Mycoplasma pneumoniae positive

extract_protocol:
total RNA from BALF samples was extracted using QIAamp® Viral RNA Kit (Qiagen, Valencia, CA, USA), then subjected to human rRNA depletion by application of Ribo-Zero rRNA Removal Kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions
Nextera XT DNA Library Prep Kit (Illumina) was then applied for the construction of cDNA library

value: BALF

tag: genotype


title: Liver, male, Deficient, ZT05, rep3

state: California

department: RBIO-P

country: USA

description:
53_M_4H_LIVER_S17
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Liver

tag: strain

value: Liver

tag: Sex

value: male

tag: zeitgeber time


title: 2234041261153


title: 2234041201555


title: Unstimulated human NK (4h)

description: 10 X Genomics

value: Unstimulated (4h)


title: 2180941212422


title: Human NK stimulated with IPH6501 (24h)

description: 10 X Genomics


title: Liver, male, Deficient, ZT05, rep1

description:
37_M_4H_LIVER_S265
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Liver, male, Deficient, ZT05, rep2

description:
45_M_4H_LIVER_S12
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2180942071783


title: Liver, male, Control, ZT17, rep3

description:
58_M_16L_LIVER_S20
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Control


title: 2180941234288


title: 2098311008561


title: Human NK stimulated with IPH6501 (4h)

description: 10 X Genomics


title: 2098311008813


title: 2234032281481


title: 2234041101114


title: Liver, male, Deficient, ZT17, rep2

description:
54_M_16H_LIVER_S18
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Liver, male, Control, ZT17, rep1

description:
34_M_16L_LIVER_S4
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2234041261290


title: E7

city: Nanjing

first: Jie

last: Mei

state: Jiangsu

address: No. 101, Longmian Road

institute: Nanjing Medical University

data_processing:
fastx (version:0.0.13)
Assembly: GRCh38
Supplementary files format and content: csv file include TPM values for each sample

source_name: circulating extracellular vesicles

extract_protocol:
Total RNA was extracted usingmirVana™ miRNA Isolation Kit following the manufacturer’s instructions.
RNA library for RNA-seq were perpared using QIAseq miRNA Library Kit following the manufacturer’s instructions.

value: circulating extracellular vesicles

value: NSCLC

value: WT

value: serum from NSCLC patients with exercise habit


title: Liver, male, Control, ZT17, rep2

description:
50_M_16L_LIVER_S16
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: E8


title: 2098341060775


title: 2180931107950


title: 2234041431358


title: 2180941432462


title: E5


title: Liver, male, Control, ZT05, rep3

description:
49_M_4L_LIVER_S15
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2180933045250


title: 2180913081995


title: Liver, male, Control, ZT05, rep1

description:
33_M_4L_LIVER_S3
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2098311008523


title: Liver, male, Control, ZT05, rep2

description:
41_M_4L_LIVER_S9
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2180941095124


title: NE8

value: serum from NSCLC patients without exercise habit


title: Liver, female, Deficient, ZT17, rep3

description:
60_F_16H_LIVER_S22
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: CBA/CaJ

value: female


title: NE7


title: BT594.T85C.RT-TMZ  [GBM_67]

city: Toronto

first: Jason

last: Moffat

state: Ontario

address: 686 Bay Street

department: Genetics and Genome Biology

country: Canada

institute: Hospital for Sick Children

description: sgRNA amplified from gDNA

library_source: other

data_processing:
FASTQ files were pre-processed to extract Cas9 guide sequence using a bespoke Perl script.
The Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'.
Trimmed FASTQ files were then aligned to the TKOv3 FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.
Assembly: hg19
Supplementary files format and content: tab-delimited read count matrix
Library strategy: CRISPRseq

molecule: other

growth_protocol: Cells were cultured in Neurocult Complete media supplemented with 1X antibiotic/antimycotic and serially passaged for up to 90 days in biological triplicates. Aliquots were pelleted at indicated timepoints for gDNA extraction and quantification by next-generation sequencing.

extract_protocol:
Genomic DNA was extracted using the Wizard Genomic DNA Purification kit (Promega) according to manufacturer’s instructions
For each sample, the gRNA cassette was amplified directly from genomic DNA using primers harboring Illumina TruSeq adaptors with i5 and i7 barcodes. The resulting sequencing libraries were pooled and gel-purified.

treatment_protocol: Cells were transduced with the genome-wide TKOv3 'all-in-one' CRISPR-Cas9 library, selected with puromycin, and cultured as indicated.

value: primary GBM

value: Temozolomide + Radiation (IC20-IC30)


title: Liver, female, Deficient, ZT17, rep2

description:
44_F_16H_LIVER_S11
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Deficient


title: 2098311003870


title: 2098313080718


title: E6


title: 2180912050848


title: Liver, female, Deficient, ZT17, rep1

description:
36_F_16H_LIVER_S6
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: BT594.T85A.RT-TMZ  [GBM_65]

description: sgRNA amplified from gDNA


title: 2098315010294


title: BT594.T85B.RT-TMZ  [GBM_66]

description: sgRNA amplified from gDNA


title: BT594.T85C.RT  [GBM_64]

description: sgRNA amplified from gDNA

value: Radiation (IC20-IC30)


title: 1957544013050


title: 2098311008820


title: Liver, female, Deficient, ZT05, rep2

description:
43_F_4H_LIVER_S10
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2098335031040


title: 2180931261508


title: Liver, female, Deficient, ZT05, rep3

description:
59_F_4H_LIVER_S21
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: BT594.T85B.RT  [GBM_63]

description: sgRNA amplified from gDNA


title: 2180941195961


title: 2180941240746


title: Liver, female, Deficient, ZT05, rep1

description:
35_F_4H_LIVER_S5
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2180942031213


title: 1956031026450


title: 2180942073275


title: Liver, female, Control, ZT17, rep3

description:
56_F_16L_LIVER_S19
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 1956044121180


title: 2180943020889


title: Liver, female, Control, ZT17, rep2

description:
48_F_16L_LIVER_S14
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: BT594.T85B.TMZ [GBM_60]

description: sgRNA amplified from gDNA

value: Temozolomide (IC20-IC30)


title: Liver, female, Control, ZT17, rep1

description:
32_F_16L_LIVER_S2
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Liver, female, Control, ZT05, rep3

description:
47_F_4L_LIVER_S13
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2234042070501

value: BALF


title: Giredestrant-treated, GPX4 guide 2, rep2

city: South San Francisco

first: Marc

last: Hafner

state: CA

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

data_processing:
RNA-Seq reads were first aligned to ribosomal RNA sequences to remove ribosomal reads
remaining reads were aligned to the human reference genome (GRCh38) using GSNAP version 2013-11-1, allowing a maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 —pairmax-rna=200000—clip-overlap)
To quantify gene expression levels, the number of reads mapped to the exons of each RefSeq gene was calculated.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file that include gene counts for each sample

source_name: Breast

growth_protocol: Cells were grown in RPMI (10% serum); on day 1, the cells were transfected with sgRNAs; after Puro slection; then on day 13, the cells were treated with DMSO and GDC-9545 for 10 days.

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus Mini kit (Cat. No. 74134),
For sequencing library generation, the Truseq Stranded mRNA kit (Illumina) was used with an input of 100-1000 nanograms of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 million single-end 50-base pair reads for each sample.

value: Breast

value: Epithelial cell

value: Giredestrant, GPX4_h


title: Liver, female, Control, ZT05, rep2

description:
39_F_4L_LIVER_S8
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Liver

value: Control


title: BT594.T85A.RT  [GBM_62]

description: sgRNA amplified from gDNA


title: Giredestrant-treated, GPX4 guide 2, rep1


title: 2098311005522


title: Liver, female, Control, ZT05, rep1

description:
31_F_4L_LIVER_S1
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2180941263417


title: 1957544016822


title: 2234041250171


title: 2180935090098


title: 2180941550029


title: Brown adipose tissue, male, Deficient, ZT17, rep3

description:
74_M_H_ZT17_BAT_S297
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Brown adipose tissue

value: Brown adipose tissue

value: male


title: 2180941207176


title: 2098311008738


title: BT594.T85C.TMZ [GBM_61]

description: sgRNA amplified from gDNA


title: 2180941207756


title: Brown adipose tissue, male, Deficient, ZT17, rep2

description:
62_M_16H_BAT_S46
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Giredestrant-treated, control guide 2, rep2

value: Giredestrant, OR5M9_neg


title: 2180941540013


title: BT594.T85A.TMZ [GBM_59]

description: sgRNA amplified from gDNA


title: 1958611003745


title: Brown adipose tissue, male, Deficient, ZT17, rep1

description:
54_M_16H_BAT_S41
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Giredestrant-treated, control guide 2, rep1


title: 2234041091187


title: 2180937122810


title: Brown adipose tissue, male, Deficient, ZT05, rep3

description:
53_M_4H_BAT_S40
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2234041090043


title: 2234042070464


title: 1957511001240


title: Giredestrant-treated, control guide 1, rep2

value: Giredestrant, OR51Q1_b


title: 1958611004018


title: Giredestrant-treated, GPX4 guide 1, rep2

value: Giredestrant, GPX4_f


title: Brown adipose tissue, male, Deficient, ZT05, rep2

description:
45_M_4H_BAT_S35
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: CBA/CaJ


title: Giredestrant-treated, control guide 1, rep1


title: Brown adipose tissue, male, Control, ZT17, rep3

description:
58_M_16L_BAT_S43
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2180912080197


title: DMSO-treated, GPX4 guide 2, rep2

value: DMSO, GPX4_h


title: 2234011050121


title: Giredestrant-treated, GPX4 guide 1, rep1


title: 1956031013191


title: Brown adipose tissue, male, Deficient, ZT05, rep1

description:
37_M_4H_BAT_S30
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2180941095728


title: Brown adipose tissue, male, Control, ZT17, rep2

description:
50_M_16L_BAT_S39
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 1958611005077


title: DMSO-treated, GPX4 guide 2, rep1


title: DMSO-treated, GPX4 guide 1, rep2

value: DMSO, GPX4_f


title: 2098311008790


title: Brown adipose tissue, male, Control, ZT17, rep1

description:
34_M_16L_BAT_S27
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2180941234073


title: DMSO-treated, GPX4 guide 1, rep1


title: 2078111003287


title: 2234042072185


title: Brown adipose tissue, male, Control, ZT05, rep3

description:
49_M_4L_BAT_S38
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2098311003771


title: 2234032150411


title: Brown adipose tissue, male, Control, ZT05, rep2

description:
41_M_4L_BAT_S32
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 1957544084739


title: 2098311008868


title: 2098311008127


title: 1965611004443


title: DMSO-treated, control guide 1, rep2

value: DMSO, OR51Q1_b


title: Brown adipose tissue, male, Control, ZT05, rep1

description:
33_M_4L_BAT_S26
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: DMSO-treated, control guide 1, rep1


title: 2098332001213


title: Brown adipose tissue, female, Deficient, ZT17, rep2

description:
44_F_16H_BAT_S34
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: female

value: Deficient


title: FCPN, Layer5, DS, h311_Layer5

city: Orangeburg

first: Stephen

middle: D.

last: Ginsberg

state: New York

address: 140 Old Orangeburg Road

department: Centre for Dementia Research

institute: Research Foundation for Mental Hygiene

data_processing:
The samples with 2 technical replicates were merged to reduce the variability of the data and increase the accuracy in gene expression. The merged FastQ files with adapter contamination/ low quality were trimmed using Trimmomatic 0.39.
Trimmed sequence reads were aligned to the reference  genome (GRCh38) using STAR Aligner. Gene counts were extracted using RSEM.
Downstream Analysis was performed using R with the gene counts obtained from the RSEM. Genes with over 0.1 counts per million were retained followed by TMM normalization.
Assembly: hg38
Supplementary files format and content: tab delimited text files with gene counts of all samples per column
Supplementary files format and content: tab delimited text files with gene counts of one sample per one file

source_name: frontal cortex pyramidal neurons from Layer 5

extract_protocol:
Human brain specimens for Down Syndrome were procured in part as a gift of Dr. Jerzy Weigel at the Institute for Basic Research (Staten Island, NY) and in part from the NIH NeuroBiobank.  Non cognitively impaired (NCI) control human brain tissue was obtained from the NIH NeuroBioBank. Human brain tissue arrived frozen on dry ice, blocked for the BA9 frontal cortex region.  Tissue blocks were kept frozen to preserve tissue and RNA quality, and were cryostat cut (-25 0C) at 20 μm-thick tissue sections in the coronal plane to identify the cortical layers (CM1860UV, Leica, Buffalo Grove, IL) and mounted on polyethylene naphthalate (PEN) membrane slides (Leica).  Slides were kept under desiccant at -80 0C until used for immunohistochemistry. RNase-free precautions were employed, and solutions were made with 18.2 mega Ohm RNase-free water.  Slides were equilibrated to room temperature under dessicant to reduce condensation. Nissl (thionin) stained and air dried before proceeding directly to laser capture microscopy.  Semi-automated detection was used to identify layer III and layer V pyramidal neurons for isolation via LCM. Once cells were confirmed as pyramidal neurons by morphology, cutting was performed, dropping cells directly into lysis buffer (Qiazol).  Max LCM time was 1 hour per slide to preserve RNA quality.   RNA from ~500 L3 and L5 BA9 neurons from each brain specimen were combined and purified using miRNeasy Micro kit (Qiagen) according to manufacturers’ specifications, along with two rounds of the optional DNase digestion before the final washes.
Each RNA Sample was split into two technical replicates before library preparation using SMARTer Stranded Total RNA-Seq kit-Pico input Mammalian. Dual Index primers and UMIs were unique to each technical replicate.  Fragmentation was performed as needed based on RIN/DV200 values according to manufacturers' recommendation.
RNA-seq samples were quantified (Agilent Tapestation, D1000 DNA Assay), and samples below 2 nM of the library were excluded. Samples were pooled in equimolar concentrations and assayed on Illumina NovaSeq 6000 S1 and S2 flow cells using the 100-cycle paired-end read protocol at the NYUGSOM Genome Technology Center.

tag: diagnosis

value: DS

tag: layer


title: 2234041090340

value: BALF


title: Brown adipose tissue, female, Deficient, ZT17, rep3

description:
60_F_16H_BAT_S45
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2234041190187


title: 2098311005546


title: Brown adipose tissue, female, Deficient, ZT17, rep1

description:
36_F_16H_BAT_S29
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 1958611004292


title: 2078111006813


title: FCPN, Layer5, CTR, h309R_Layer5

value: frontal cortex pyramidal neurons from Layer 5

value: CTR


title: 1958611002533


title: Brown adipose tissue, female, Deficient, ZT05, rep3

description:
59_F_4H_BAT_S44
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer5, CTR, h308_Layer5


title: 2234033060793


title: 2234041190828


title: DMSO-treated, control guide 2, rep2

value: Breast

value: Epithelial cell

value: DMSO, OR5M9_neg4


title: FCPN, Layer5, CTR, h307R_Layer5


title: DMSO-treated, control guide 2, rep1


title: 2234041190385


title: Brown adipose tissue, female, Deficient, ZT05, rep1

description:
35_F_4H_BAT_S28
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Brown adipose tissue


title: 2180941104512


title: 1958611004483


title: FCPN, Layer5, CTR, h307_Layer5


title: 1997811002479


title: Brown adipose tissue, female, Control, ZT17, rep3

description:
56_F_16L_BAT_S42
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Control


title: FCPN, Layer5, CTR, h306R_Layer5


title: 2180941195688


title: 2180942031169


title: 2098344035619


title: Brown adipose tissue, female, Control, ZT17, rep2

description:
48_F_16L_BAT_S37
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer5, CTR, h305R_Layer5


title: 1997811002615


title: FCPN, Layer5, CTR, h306_Layer5


title: Brown adipose tissue, female, Control, ZT17, rep1

description:
32_F_16L_BAT_S25
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2098311008837


title: 2180937135582


title: Brown adipose tissue, female, Control, ZT05, rep3

description:
47_F_4L_BAT_S36
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Brown adipose tissue, female, Deficient, ZT05, rep2

description:
43_F_4H_BAT_S33
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer5, CTR, h305_Layer5


title: 1958611004742


title: Brown adipose tissue, female, Control, ZT05, rep2

description:
39_F_4L_BAT_S31
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Brown adipose tissue, female, Control, ZT05, rep1

description:
31_F_4L_BAT_S24
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2180953040945


title: 2098311008363


title: FCPN, Layer5, CTR, h302_Layer5


title: 1956051020551


title: FCPN, Layer5, CTR, h301_Layer5


title: Lung, male, Deficient, ZT17, rep3

description:
62_M_16_5H_LUNG_S248
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Lung

value: Lung

value: male


title: Lung, male, Deficient, ZT17, rep2

description:
54_M_16_5H_LUNG_S243
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: CBA/CaJ


title: 2234042071256


title: 2180941102853


title: 2180943140075


title: 2180941206988


title: Lung, male, Deficient, ZT17, rep1

description:
38_M_16_5H_LUNG_S232
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2098341020465


title: 1958611005176


title: 2098311008110


title: 2098341220025


title: 2098311007960


title: FCPN, Layer5, CTR, h298_Layer5


title: FCPN, Layer5, CTR, h299_Layer5


title: Lung, male, Deficient, ZT05, rep3

description:
53_M_4_5H_LUNG_S242
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer5, CTR, h300_Layer5


title: FCPN, Layer5, CTR, h302R_Layer5


title: FCPN, Layer5, CTR, h297_Layer5


title: Lung, male, Deficient, ZT05, rep2

description:
45_M_4_5H_LUNG_S237
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2180943020254


title: 2234041190705


title: Lung, male, Deficient, ZT05, rep1

description:
37_M_4_5H_LUNG_S231
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2234041530143


title: FCPN, Layer5, CTR, h296_Layer5


title: 2098350060292


title: Lung, male, Control, ZT17, rep3

description:
58_M_16_5L_LUNG_S245
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2098311007366


title: 1958611003769


title: 2234041260934


title: Lung, male, Control, ZT17, rep2

description:
50_M_16_5L_LUNG_S241
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Lung, male, Control, ZT17, rep1

description:
34_M_16_5L_LUNG_S228
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer5, CTR, h294_Layer5


title: 2234041061074


title: 2126145002667


title: FCPN, Layer5, CTR, h293R_Layer5


title: FCPN, Layer5, CTR, h293_Layer5


title: Lung, male, Control, ZT05, rep3

description:
49_M_4_5L_LUNG_S240
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Lung, male, Control, ZT05, rep2

description:
41_M_4_5L_LUNG_S234
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 1958611003080


title: 2098311007915


title: 1965611005884


title: 2180941194841


title: 2180941207169


title: FCPN, Layer5, CTR, h292_Layer5


title: 2180941234158


title: 1958611002465


title: FCPN, Layer5, CTR, h295_Layer5


title: FCPN, Layer5, DS, h287R_Layer5


title: Lung, male, Control, ZT05, rep1

description:
33_M_4_5L_LUNG_S227
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2234041190347


title: 2180941263394


title: 1965611004405


title: Lung, female, Deficient, ZT17, rep3

description:
60_F_16_5H_LUNG_S247
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 1957544013296


title: Lung, female, Deficient, ZT17, rep2

description:
44_F_16_5H_LUNG_S236
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Lung, female, Deficient, ZT17, rep1

description:
36_F_16_5H_LUNG_S230
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2180942073374


title: FCPN, Layer5, DS, h286R_Layer5


title: Lung, female, Deficient, ZT05, rep3

description:
59_F_4_5H_LUNG_S246
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer5, DS, h284_Layer5


title: 2234041191535


title: 1956044160400


title: 2098311008592


title: FCPN, Layer5, DS, h285_Layer5


title: 1958611003660


title: Lung, female, Deficient, ZT05, rep2

description:
43_F_4_5H_LUNG_S235
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer5, DS, h283R_Layer5


title: 1958611005640


title: FCPN, Layer5, DS, h287_Layer5


title: Lung, female, Control, ZT17, rep3

description:
56_F_16_5L_LUNG_S244
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 1958611005084


title: 2234032150695


title: Lung, female, Deficient, ZT05, rep1

description:
35_F_4_5H_LUNG_S229
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer5, DS, h283_Layer5


title: 2234043100092


title: FCPN, Layer5, DS, h282_Layer5


title: 119032000617


title: 2098311007908


title: Lung, female, Control, ZT17, rep2

description:
48_F_16_5L_LUNG_S239
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Lung, female, Control, ZT17, rep1

description:
32_F_16_5L_LUNG_S226
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer5, DS, h281_Layer5


title: 2180941432325


title: Lung, female, Control, ZT05, rep3

description:
47_F_4_5L_LUNG_S238
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2234011090196


title: 1965611004474


title: FCPN, Layer5, DS, h280_Layer5


title: FCPN, Layer5, DS, h279_Layer5


title: FCPN, Layer5, DS, h278_Layer5


title: 1997811002417


title: 2180932070581


title: 2180942073534


title: Lung, female, Control, ZT05, rep1

description:
31_F_4_5L_LUNG_S225
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 1997811002509


title: FCPN, Layer5, DS, h277_Layer5


title: 1957544018253


title: 1957532004459


title: Heart, male, Deficient, ZT17, rep3

description:
62_M_16_5H_HEART_S224
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Heart

value: Heart


title: 2098311008646


title: Heart, male, Deficient, ZT17, rep2

description:
54_M_16_5H_HEART_S219
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2234014020084


title: 2180943020582


title: FCPN, Layer3, CTR, h309AR_Layer3

source_name: frontal cortex pyramidal neurons from Layer 3


title: 2098311008844


title: Heart, male, Deficient, ZT17, rep1

description:
38_M_16_5H_HEART_S208
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer3, DS, h311R_Layer3

value: frontal cortex pyramidal neurons from Layer 3


title: 1958611003028


title: Heart, male, Deficient, ZT05, rep3

description:
53_M_4_5H_HEART_S218
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2180942040482


title: 1951611003685


title: Lung, female, Control, ZT05, rep2

description:
39_F_4_5L_LUNG_S233
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer3, CTR, h308B_Layer3


title: Heart, male, Deficient, ZT05, rep2

description:
45_M_4_5H_HEART_S213
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2234041101527


title: 2180941194858


title: 2180932070574


title: Heart, male, Deficient, ZT05, rep1

description:
37_M_4_5H_HEART_S207
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer3, CTR, h308AR_Layer3


title: 1957544082155


title: Heart, male, Control, ZT17, rep3

description:
58_M_16_5L_HEART_S221
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2180943140099


title: 2234032300410


title: 2180944164070


title: FCPN, Layer3, CTR, h307B_Layer3


title: FCPN, Layer5, CTR, h270_Layer5


title: Heart, male, Control, ZT17, rep2

description:
50_M_16_5L_HEART_S217
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2098311007557


title: FCPN, Layer3, CTR, h306R_Layer3


title: 1956032008790


title: FCPN, Layer3, CTR, h307R_Layer3


title: FCPN, Layer3, CTR, h306B_Layer3


title: Heart, male, Control, ZT05, rep2

description:
41_M_4_5L_HEART_S210
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2180941095131


title: 1956035020423


title: 1958611002557


title: 1965611004450


title: FCPN, Layer3, CTR, h305R_Layer3


title: Heart, male, Control, ZT05, rep3

description:
49_M_4_5L_HEART_S216
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2180943020902


title: FCPN, Layer3, CTR, h305B_Layer3


title: 2098311008691


title: 2180944282736


title: FCPN, Layer3, CTR, h302_Layer3


title: FCPN, Layer3, CTR, h301A_Layer3


title: 2180941068937


title: 2180932280652


title: 2234041190545


title: Heart, female, Deficient, ZT17, rep2

description:
44_F_16_5H_HEART_S212
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 1956044151019


title: Heart, female, Deficient, ZT17, rep1

description:
36_F_16_5H_HEART_S206
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer3, CTR, h300A_Layer3


title: FCPN, Layer3, CTR, h300BR_Layer3


title: 2098353033439


title: 2098311006093


title: 2180944124326


title: Heart, female, Deficient, ZT05, rep3

description:
59_F_4_5H_HEART_S222
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 1958611003943


title: FCPN, Layer3, CTR, h299B_Layer3


title: 2180951131416


title: 2180961061598


title: Heart, female, Deficient, ZT05, rep1

description:
35_F_4_5H_HEART_S205
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Heart, male, Control, ZT17, rep1

description:
34_M_16_5L_HEART_S204
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: 2098311008707


title: FCPN, Layer3, CTR, h299AR_Layer3


title: Heart, female, Deficient, ZT05, rep2

description:
43_F_4_5H_HEART_S211
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer3, CTR, h298B_Layer3


title: MCF10Ca1a, rep3

city: Oslo

first: Roberto

last: Rossini

address: Blindernveien 31

country: Norway

institute: University of Oslo

data_processing:
nf-core/rnaseq v3.12.0
Samples were processed using nf-core/rnaseq.
hg38 and Gencode v43 were used as reference genome assemby and gene annotation, respectively.
The pipeline was run using Salmon as pseudo-aligner, passing --seqBias and --gcBias as optional parameters.
Please refer to nf-core/rnaseq documentation for a complete list of the analysis steps performed by the pipeline: https://nf-co.re/rnaseq/3.12.0
Assembly: hg38
Supplementary files format and content: bigWig with read coverage (reverse)
Supplementary files format and content: bigWig with read coverage (forward)
Supplementary files format and content: BAM containing reads aligned to the reference genome
Supplementary files format and content: BAI indexing BAM files
Supplementary files format and content: TAR file containing the quantification files produced by Salmon
Supplementary files format and content: TSV file containing the matrix of gene-level length-scaled counts across all samples
Supplementary files format and content: TSV file containing the matrix of gene-level library size-scaled counts across all samples
Supplementary files format and content: TSV file containing the matrix of gene-level raw counts across all samples
Supplementary files format and content: TSV file containing the matrix of gene-level TPM values across all samples
Supplementary files format and content: TSV file containing the matrix of isoform-level raw counts across all samples
Supplementary files format and content: TSV file containing the matrix of isoform-level TPM values across all samples

source_name: mammary gland

growth_protocol: MCF10A, MCF10AT1, and MCF10Ca1a cell lines were grown in DMEM/Nutrient F12 (DMEM/F12) media supplemented with 5% horse serum (MCF10A and MCF10Ca1a) or 2.5% horse serum (MCF10AT1), 14 mM NaHCO3, 10 µg/mL insulin, 2 mM L-glutamine, 20 ng/mL human epidermal growth factor, 500 ng/mL Hydrocortisone and 100 ng/mL cholera Toxin

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy kit following manufacturer’s instructions
Stranded mRNAseq libraries were constructed using Illumina mRNA Prep kit, following vendors protocol with poly-A enrichment (Illumina)

value: mammary gland

value: epithelial cell


title: Heart, female, Deficient, ZT17, rep3

description:
60_F_16_5H_HEART_S223
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: female

value: Deficient


title: Heart, female, Control, ZT17, rep3

description:
56_F_16_5L_HEART_S220
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer3, CTR, h298AR_Layer3


title: MCF10AT1, rep2


title: HFK H3K36me3 2

city: Chicago

first: Conor

last: Templeton

address: 300 E Superior Street

institute: Northwestern University

data_processing:
FastQC (v0.11.8) was used to check the quality of raw and trimmed reads. Trimmomatic (v0.38) was used to cut adapters and trim low-quality bases with a default setting. BWA (v0.7.10-r789) was used to map the trimmed reads to the reference genome* using the Burrows-Wheeler Alignment algorithm (BWA-MEM). Mapped reads that have low-quality MAPQ score (MAPQ < 10), not-properly-paired, or duplicated (assessed with Picard tools (v 2.20.4)) were removed. BAM was used to generate BW format (normalized by RPKM) for visualization. MACS (v2.2.4) was chosen to call peaks.
Agreement between biological replicates was assessed using multiBAMSummary (Galaxy Version 3.5.4+galaxy0), and then plotting principal component analyses using plotPCA (Galaxy Version 3.5.4+galaxy0) and plotting Pearson coefficients as a heatmap using plotCorrelation (Galaxy Version 3.5.4+galaxy0) (Supp Fig 8). From the BAM files, BAM Compare (Galaxy Version 3.5.4+galaxy0) was used to normalize log2 IP to input ratios for both biological replicates of H3K36me3, H3K9me3, and gH2AX ChIPs from HFK and CIN 612 cells.  ComputeMatrix was used to prepare files for visualization via plotProfile and plotHeatmap. CHIPseeker (Galaxy Version 1.28.3+galaxy0) was used on the BED files generated by Admera Biosciences or NUseq to determine the genomic distribution of each modified histone. MACS (v2.2.4) was used to call peaks. HOMER (Galaxy Version 4.11+galaxy0) was used to annotate where peaks occurred relative to their genomic location (intron, exon, etc.) and the corresponding gene name.
Assembly: Hg38
Supplementary files format and content: bigWig

source_name: Foreskin

growth_protocol: HFK and CIN 612 cells were maintained in E-media containing 10% FBS DMEM

extract_protocol:
1 × 107 cells were harvested and collected in Southern lysis buffer before being treated with RNase A (5 ng/mL) and Proteinase K (7.5 ng/mL) at 37 °C overnight. DNA was purified from these samples using phenol-chloroform extractions, and 25 to 50 mg of DNA was used for each sample. DNA was sheared using a Bioruptor (Diagenode) on high power, 30 s on/90 s off cycles for 20 min. Input DNA was removed before loading the samples into preblocked magnetic beads in IP buffer containing 2 ug of the H3K36me3 antibody. Immunoprecipitations were allowed to incubate overnight at 4 °C while rotating. The next day, samples were washed 8 times with RIPA buffer for 5 min while rotating. One wash in TE buffer was performed before samples were eluted for 10 min at 65 °C in 10% sodium dodecyl sulfate (SDS), 10 mM Tris pH 7.4, 50 mM ethylenediaminetetraacetic acid (EDTA). DNA was purified from these elutions using a PCR purification kit (Qiagen) and stored at −20 °C.
Samples were stored at -80° C until being shipped to Admera Biosciences (NJ), who performed the sequencing experiments. Briefly, the library was prepared using a KAPA HyperPrep Kit (Kapa Biosystems) following the manufacturer’s recommendation. Input DNA was end-repaired and 3’-dA tailed. Adapter was then ligated to the DNA, and the ligated product was PCR amplified and cleaned up using the SPRIselect Reagent (Beckman Coulter). Quality control was then performed for the final library, followed by sequencing.

value: Foreskin

value: HFKs

value: Keratinocytes

tag: chip antibody

value: Anti-Histone H3 (tri methyl K36) antibody - ChIP Grade (ab9050)


title: MCF10Ca1a, rep2


title: MCF10Ca1a, rep1


title: 2098311007533

value: BALF


title: FCPN, Layer3, CTR, h297_Layer3

value: CTR


title: Heart, male, Control, ZT05, rep1

description:
33_M_4_5L_HEART_S203
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Heart, female, Control, ZT05, rep3

description:
47_F_4_5L_HEART_S214
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: MCF10A, rep2


title: Heart, female, Control, ZT17, rep1

description:
32_F_16_5L_HEART_S202
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: MCF10AT1, rep1


title: FCPN, Layer3, CTR, h296R_Layer3


title: MCF10A, rep1


title: Heart, female, Control, ZT05, rep2

description:
39_F_4_5L_HEART_S209
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer3, CTR, h295B_Layer3


title: FCPN, Layer3, CTR, h295AR_Layer3


title: H37Rv Usp8KD 72h-3

city: St Louis

first: Pallavi

last: Chandra

state: MO

address: 660 S Euclid Ave

department: Department of Medicine, Div of Infectious Diseases

institute: Washington University School of Medicine

description: H37Rv Usp8KD 72h-3

data_processing:
convert fastq files to unaligned .bam files (Samtools:FastqToSam)
adapter trimming (Trimmomatic)
genome indexing and read mapping (HiSat2)
genewise read counts (featureCounts)
Assembly: GRCm38.97
Supplementary files format and content: genomic features read count matrix (tab delimited)

source_name: Bone marrow derived macrophage

growth_protocol: BMDMs were seeded at E6 cells per well in a 6-well plate and transfected with 50nM scrambled or Usp8 siRNA

extract_protocol:
At 24 and 72 hpi, RNA was extracted using the Direct-Zol RNA Mini-Prep Kit (Zymo Research)
RNA-Seq by poly-A selection

treatment_protocol: Cells were uninfected or H37Rv-infected at MOI 5

value: Bone marrow derived macrophage

tag: mtb strain

tag: time point


title: H37Rv Usp8KD 72h-4

description: H37Rv Usp8KD 72h-4


title: H37Rv Usp8KD 72h-2

description: H37Rv Usp8KD 72h-2


title: Pituitary, male, Deficient, ZT17, rep3

description:
62_M_16H_PIT_S176
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Pituitary

value: Pituitary


title: FCPN, Layer3, CTR, h294B_Layer3


title: Heart, female, Control, ZT05, rep1

description:
31_F_4_5L_HEART_S201
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Control


title: Heart, female, Control, ZT17, rep2

description:
48_F_16_5L_HEART_S215
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: H37Rv Usp8KD 72h-5

description: H37Rv Usp8KD 72h-5


title: MCF10AT1, rep3


title: H37Rv Usp8KD 72h-1

description: H37Rv Usp8KD 72h-1


title: H37Rv Scrambled 72h-5

description: H37Rv Scrambled 72h-5


title: FCPN, Layer3, CTR, h294AR_Layer3


title: H37Rv Scrambled 72h-3

description: H37Rv Scrambled 72h-3


title: Pituitary, male, Deficient, ZT17, rep1

description:
38_M_16H_PIT_S160
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: male


title: H37Rv Scrambled 72h-2

description: H37Rv Scrambled 72h-2


title: FCPN, Layer3, CTR, h292R_Layer3


title: MCF10A, rep3


title: H37Rv Scrambled 72h-1

description: H37Rv Scrambled 72h-1


title: Uninfected Usp8KD 72h-6

description: Uninfected Usp8KD 72h-6


title: Pituitary, male, Deficient, ZT05, rep2

description:
45_M_4H_PIT_S165
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: CBA/CaJ


title: Uninfected Usp8KD 72h-3

description: Uninfected Usp8KD 72h-3


title: FCPN, Layer3, DS, h287B_Layer3

value: DS


title: Pituitary, male, Deficient, ZT05, rep1

description:
37_M_4H_PIT_S159
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Uninfected Usp8KD 72h-2

description: Uninfected Usp8KD 72h-2


title: FCPN, Layer3, DS, h286B_Layer3

value: frontal cortex pyramidal neurons from Layer 3


title: IVF_1_pESC_FIW_rep1

city: Cheongju

first: Sang-Hwan

last: Hyun

state: Please select your state

address: 1 Chungdae-ro, Seowon-gu

department: Veterinary Medical Center and College of Veterinary Medicine

country: South Korea

institute: Chungbuk national university

data_processing:
The adapter sequences and the ends of the reads less than Phred quality score 20 were trimmed and simultaneously the reads shorter than 50 bp were removed by using cutadapt v.2.8
Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.7.1a [2] following ENCODE standard options (refer to “Alignment” of “Help” section in the html report) with “-quantMode TranscriptomeSAM” option for estimation of transcriptome expression level.
Assembly: Sscrofa11.1 (GCA_000003025.6)
Supplementary files format and content: To normalize sequencing depth among samples, FPKM and TPM values were calculated.

organism: Sus scrofa

source_name: Stem cells

extract_protocol:
mRNA molecules were purified and fragmented from 1μg of total RNA using oligo (dT) magnetic beads.
The libraries were prepared for 151bp paired-end sequencing using TruSeq stranded mRNA Sample Preparation Kit (Illumina, CA, USA).

value: Stem cells

value: Embryonic stem cells

value: WT


title: PA_3_pESC_FIW_rep2


title: IVF_1_pESC_FIW_rep2


title: Uninfected Usp8KD 72h-1

description: Uninfected Usp8KD 72h-1


title: FCPN, Layer3, DS, h286AR_Layer3


title: Uninfected Scrambled 72h-5

description: Uninfected Scrambled 72h-5


title: Pituitary, male, Deficient, ZT17, rep2

description:
54_M_16H_PIT_S171
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Deficient


title: FCPN, Layer3, CTR, h293_Layer3


title: FCPN, Layer3, DS, h285B_Layer3


title: Pituitary, male, Control, ZT17, rep3

description:
58_M_16L_PIT_S173
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: PA_3_pESC_FIW_rep1


title: H37Rv Scrambled 72h-4

description: H37Rv Scrambled 72h-4


title: Pituitary, male, Control, ZT17, rep2

description:
50_M_16L_PIT_S169
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Pituitary, male, Control, ZT17, rep1

description:
34_M_16L_PIT_S156
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer3,DS, h285AR_Layer3


title: PA_1_pESC_FIW_rep2


title: Pituitary, male, Control, ZT05, rep3

description:
49_M_4L_PIT_S168
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Pituitary, male, Deficient, ZT05, rep3

description:
53_M_4H_PIT_S170
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Uninfected Usp8KD 72h-4

description: Uninfected Usp8KD 72h-4


title: Uninfected Scrambled 72h-3

description: Uninfected Scrambled 72h-3


title: FCPN, Layer3,DS, h284_Layer3


title: FCPN, Layer3, DS, h287AR_Layer3


title: Pituitary, male, Control, ZT05, rep1

description:
33_M_4L_PIT_S155
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Uninfected Scrambled 72h-1

description: Uninfected Scrambled 72h-1


title: Uninfected Scrambled 72h-2

description: Uninfected Scrambled 72h-2


title: FCPN, Layer3,DS, h283R_Layer3


title: FCPN, Layer3,DS, h283B_Layer3


title: M2-like BMDMs, recombinant IFNbeta, 72h, rep3

city: Heidelberg

first: Julia

last: Gellert

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

data_processing:
Sequencing reads were mapped to the GRCm39 mm10 reference genome using RSEM (v1.3.3).
Assembly: mm10
Supplementary files format and content: comma-separated value file includes unnormalized counts (RSEM .genes.results output) of each Sample which can be used as an input for differential gene expression analysis using DESeq2.

source_name: Bone marrow-derived macrophages

growth_protocol:
(isolation protocol)  Bone marrow cells were extracted from hip bones, femur and tibia from C575Bl/6J donor mice sacrificed by cervical dislocation by grinding the bones in IMDM medium (ThermoFisher). Cells were mashed through a 40 µm strainer and erythrocytes lysed using ACK lysis buffer (Gibco).
(differentiation protocol)  Bone marrow cells were seeded at a concentration of 1x10^6 cells/ml IMDM medium supplemented with 10% FBS, 100 U/mL penicillin, 0.1 mg/ml streptomycin and 20 ng/mL M-CSF (Peprotech). After 72 hours half of the medium including M-CSF was changed and cells were cultured for another 48 hours.
(polarization protocol)  In vitro-differentiated macrophages were polarized into M2-like macrophages by supplementing BMDM medium with 10 ng/mL IL-4 (Peprotech) for 48 hours.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) and on-column DNase digestion using the RNAse-Free DNase Set (Qiagen) was performed. 600 ng of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using the TruSeq Stranded Total RNA Kit (Illumina).

treatment_protocol: Following M2-like polarization, BMDM medium supplemented with recombinant IFN-β (Peprotech), YUMM5.2 Ifnb1eGFP cell culture supernatant with tumoral IFNβ, YUMM5.2 GFP cell culture supernatant or unsupplemented medium was added to the BMDMs. Cell culture supernatant was obtained from YUMM5.2 Ifnb1eGFP or YUMM5.2 eGFP cells after 72 hours of treatment with 1 µg/mL Dox. IFNβ concentration in YUMM5.2 Ifnb1eGFP cell culture supernatant was measured with ELISA and supernatant was diluted with BMDM medium to a concentration of 1,500 pg/ml IFNβ. Recombinant IFNβ was diluted with BMDM medium to an equivalent concentration. Supernatant obtained from YUMM5.2 GFP cells was diluted at the same ratio as YUMM5.2 Ifnb1eGFP supernatant. BMDM were cultured for 72 hours before cells were harvested for RNA isolation.

value: Bone marrow-derived macrophages

tag: polarization

value: Recombinant IFN beta

tag: time


title: M2-like BMDMs, recombinant IFNbeta, 72h, rep2


title: H37Rv Usp8KD 24h-4

description: H37Rv Usp8KD 24h-4


title: Pituitary, female, Deficient, ZT17, rep2

description:
44_F_16H_PIT_S164
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: female


title: Pituitary, female, Deficient, ZT17, rep3

description:
60_F_16H_PIT_S175
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Pituitary, female, Deficient, ZT17, rep1

description:
36_F_16H_PIT_S158
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: H37Rv Usp8KD 24h-3

description: H37Rv Usp8KD 24h-3


title: FCPN, Layer3,DS, h282B_Layer3


title: M2-like BMDMs, recombinant IFNbeta, 72h, rep1


title: Uninfected Scrambled 72h-4

description: Uninfected Scrambled 72h-4


title: FCPN, Layer3,DS, h281B_Layer3


title: M2-like BMDMs, YUMM5.2 Ifnb1eGFP cm, 72h, rep2

value: YUMM5.2 Ifnb1eGFP cell culture supernatant after Dox-treatment


title: H37Rv Usp8KD 24h-2

description: H37Rv Usp8KD 24h-2


title: M2-like BMDMs, YUMM5.2 Ifnb1eGFP cm, 72h, rep1


title: FCPN, Layer3,DS, h281AR_Layer3


title: PA_1_pESC_FIW_rep1


title: Pituitary, female, Deficient, ZT05, rep2

description:
43_F_4H_PIT_S163
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: H37Rv Usp8KD 24h-1

description: H37Rv Usp8KD 24h-1


title: M2-like BMDMs, YUMM5.2 eGFP cm, 72h, rep3

value: YUMM5.2 eGFP cell culture supernatant after Dox-treatment


title: FCPN, Layer3,DS, h280B_Layer3


title: Pituitary, male, Control, ZT05, rep2

description:
41_M_4L_PIT_S162
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: H37Rv Usp8KD 24h-5

description: H37Rv Usp8KD 24h-5


title: H37Rv Scrambled 24h-6

description: H37Rv Scrambled 24h-6


title: FCPN, Layer3,DS, h280AR_Layer3


title: M2-like BMDMs, YUMM5.2 eGFP cm, 72h, rep2


title: M2-like BMDMs, YUMM5.2 Ifnb1eGFP cm, 72h, rep3


title: H37Rv Scrambled 24h-5

description: H37Rv Scrambled 24h-5


title: Pituitary, female, Control, ZT17, rep3

description:
56_F_16L_PIT_S172
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer3,DS, h279_Layer3


title: Pituitary, female, Control, ZT17, rep2

description:
48_F_16L_PIT_S167
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: M2-like BMDMs, YUMM5.2 eGFP cm, 72h, rep1


title: H37Rv Scrambled 24h-4

description: H37Rv Scrambled 24h-4


title: H37Rv Scrambled 24h-3

description: H37Rv Scrambled 24h-3


title: M2-like BMDMs, control, 72h, rep3

value: control


title: Pituitary, female, Deficient, ZT05, rep3

description:
59_F_4H_PIT_S174
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Pituitary, female, Control, ZT17, rep1

description:
32_F_16L_PIT_S154
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer3,DS, h282AR_Layer3


title: FCPN, Layer3,DS, h277_Layer3


title: M2-like BMDMs, control, 72h, rep2


title: Pituitary, female, Control, ZT05, rep3

description:
47_F_4L_PIT_S166
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer3,CTR, h270B_Layer3

value: CTR


title: H37Rv Scrambled 24h-2

description: H37Rv Scrambled 24h-2

value: Bone marrow derived macrophage


title: M2-like BMDMs, control, 72h, rep1


title: Pituitary, female, Control, ZT05, rep1

description:
31_F_4L_PIT_S153
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Pituitary

value: Control


title: Pituitary, female, Control, ZT05, rep2

description:
39_F_4L_PIT_S161
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: CBA/CaJ


title: Pituitary, female, Deficient, ZT05, rep1

description:
35_F_4H_PIT_S157
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: FCPN, Layer3,CTR, h270AR_Layer3


title: BT972.T54C [GBM_29]

description: sgRNA amplified from gDNA

data_processing:
*library strategy: CRISPRseq
FASTQ files were pre-processed to extract Cas9 guide sequence using a bespoke Perl script.
The Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'.
Trimmed FASTQ files were then aligned to the TKOv3 FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.
Assembly: hg19
Supplementary files format and content: tab-delimited read count matrix

value: recurrent GBM

value: Untreated


title: Uninfected Usp8KD 24h-4

description: Uninfected Usp8KD 24h-4


title: GC122775, HuNoV-infected, replicate 2,scRNAseq

city: Leuven

first: Joana

last: Rocha-Pereira

address: Herestraat 49 box 1043

department: Department of Microbiology, Immunology, and Transplantation

country: Belgium

institute: KU Leuven, Rega Institute

description: 10x Genomics

data_processing:
Cell Ranger v3.0 (10X Genomics, Pleasanton, California, USA) was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome (Ensembl GRCz11.106) and the HuNoV reference genome (Genbank JX459908.1). Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio.
Assembly: zebrafish reference genome (Ensembl GRCz11.106) and the HuNoV reference genome (Genbank JX459908.1)
Supplementary files format and content: Count Matrix Cell Ranger

organism: Danio rerio

source_name: Intestines

extract_protocol:
Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase, 40 µg/mL proteinase K, 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol.
The single-cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.

value: Intestines

value: wildtype AB

value: 120 hpf

tag: infection

value: HuNoV-infected


title: Uninfected Usp8KD 24h-5

description: Uninfected Usp8KD 24h-5


title: FCPN, Layer3,DS, h278_Layer3

value: frontal cortex pyramidal neurons from Layer 3

value: DS


title: GC145382,HuNoV-infected, replicate 1, scRNAseq

description:
10x Genomics
FACS-sorted macrophages of human norovirus infected zebrafish of the transgenic line Tg-mpeg:mCherry

data_processing:
Cell Ranger v3.0 (10X Genomics, Pleasanton, California, USA) was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome (Ensembl GRCz11.106) and the HuNoV reference genome (Genbank JX459908.1). Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio.
Assembly: hg38
Supplementary files format and content: Count Matrix Cell Ranger


title: Uninfected Usp8KD 24h-2

description: Uninfected Usp8KD 24h-2


title: BT972.T54B [GBM_28]

description: sgRNA amplified from gDNA


title: BT972.T54A [GBM_27]

description: sgRNA amplified from gDNA


title: GC122773, uninfected, replicate 2, scRNAseq

description: 10x Genomics

tag: tissue

value: uninfected


title: Uninfected Usp8KD 24h-3

description: Uninfected Usp8KD 24h-3


title: Uninfected Usp8KD 24h-1

description: Uninfected Usp8KD 24h-1


title: BT972.T0 [GBM_14]

description: sgRNA amplified from gDNA

tag: cell line


title: WT-D0-R2

first: Jiajian

last: Zhou

state: Guangdong

address: No. 2 Lujing Road, Yuexiu District,

department: Dermatology Hospital

institute: Southern Medical University

data_processing:
The adapter and low-quality sequences were trimmed from 3′ to 5′ ends. Reads shorter than 36 bp were discarded.
The remaining reads were mapped to the mouse reference genome (GRCm38) using STAR2 (v2.5.3).
Cufflinks (v2.1.1) were then applied to estimate transcript abundance. Abundance was reported in Fragments Per Kilobase Million (FPKM).
Differentially expressed genes were identified if the expression level change exceeded a fold change threshold (log2(fold change) > 1).
Assembly: mm10
Supplementary files format and content: The FPKM values for all samples in plain text format. The first 3 columns contain the gene name and genomics loci of each gene, and the remaining columns contain FPKM values for 12 samples separated with a tab delimiter.

source_name: Embryonic Stem Cells

growth_protocol: Mouse embryonic stem cells were cultured on 0.1% gelatin-coated plates in serum + LIF medium, which consisted of KnockOut DMEM (Gibco, Cat. # 10829081) with 15%FBS (Hyclone, Cat. # SH3007103 or PANSera), 1,000 U/ml mouse leukemia inhibitory factor (1,000 U/ml), 0.1 mM nonessential amino acids (Gibco, Cat. # 11140050), 0.1 mM β-mercaptoethanol, 1mM L-glutamine (Gibco, Cat. # 25030081), and penicillin (100 U/ml) and streptomycin (100 μg/ml). The medium was changed daily for the culture of ESC lines, and cells were routinely passaged every other day.

extract_protocol:
Total RNA was extracted following standard Trizol protocol (Invitrogen, Cat. # 15596026).
Total RNA was extracted from mESCs cells and subjected to poly(A) selection followed by library preparation using NEBNext® Ultra™ II RNA Library Preparation Kit (NEB). Libraries with barcodes were pooled at equal concentrations and sequenced on the Illumina Nova platform.

treatment_protocol: For embryoid bodies (EB) differentiation, ESCs were dissociated and washed once with 1xPBS and changed to medium, which consisted of KnockOut DMEM (Gibco, Cat. # 10829081) with 10%FBS (Hyclone, Cat. # SH3007103 or PANSera), 0.1 mM nonessential amino acids (Gibco, Cat. # 11140050), 0.1 mM β-mercaptoethanol, 1mM L-glutamine (Gibco, Cat. # 25030081), and penicillin (100 U/ml) and streptomycin (100 μg/ml), then cultured in low-adherent plates to form embryoid bodies (EB). EBs kept in suspension culture for 16 days.

value: Embryonic Stem Cells

tag: cell type

value: WT

value: Day 0


title: GC122774, HuNoV-infected, replicate 1, scRNAseq

description: 10x Genomics


title: WT-D8-R2

value: Day 8


title: 16GT_pooled

description: 10x Genomics

data_processing:
Raw fastq dataset was processed by the Cell Ranger single-cell software suite (v3.0.2, ) (10x Genomics) with the default parameters.
The raw reads were aligned to the synthetic mouse genome combined with the GFP sequence (GRCm38) using a STAR aligner, resulting in the digital gene expression matrix.
The quality of the FASTQ file was evaluated by the count matrix produced by Cell Ranger.
The genotype deconvolution analysis was performed: 1) a cell is marked as unknown if no reads mapped to the GFP gene; 2) the 8 nt barcode sequence for each genotype is aligned to the short reads derived from the GFP gene using smiths-waterman algorithm; a cell is marked as a corresponding genotype if a genotype barcode sequence is found; otherwise, a cell is marked as unknown. As a result, we retrieved 18833 cells with GFP expression and 9875 (52%) cells with a genotype barcode assignment. Then, the expression level for each transcript was determined using the number of unique molecular identifiers (UMI) assigned to the transcript.
The filtered gene expression matrices with genotype information were then used for downstream analyses using the Seurat R package (v4.0.1) (Hao et al. 2021). Briefly, cells with fewer than 500 genes or more than 6,000 genes detected and more than 5% of mitochondrial genes were further excluded from the downstream analyses. Then, the short reads for each gene were normalized to total UMIs in each cell to obtain normalized expression values using the “NormalizeData” function. Furthermore, the “ScaleData” function was used to scale and center expression levels in the data set for dimensional reduction. Subsequently, the cell clustering was performed by the “FindClusters” function, and the cell clusters were visualized by Uniform Manifold Approximation and Projection (UMAP) using the “RunUMAP” function. Marker genes for each cluster were determined with the Wilcoxon rank-sum test by the “FindAllMarkers” function. Only those with |‘avg_logFC’| > 0.25 and ‘p_val_adj’ < 0.05 were considered marker genes.
Assembly: mm10
Supplementary files format and content: RDS file export by R seurat package, which is used to save a single R object.

extract_protocol: The harvested cells were subjected to droplet-based single-cell separation using 10X genomics technologies, and the barcoded cells were lysis to establish an RNA-seq library. Libraries with barcodes were sequenced on the Illumina Novaseq platform.

treatment_protocol: Each single KO mESCs of 8 lncRNA and their combinations were tagged with a GFP and a barcode with 8 nts in length so that we could perform genotype deconvolution in the cell mixture of the co-culture. 16 genotypes mES cell lines were pooled and maintained at 37 °C under 5% CO2 and cultured on 0.1% gelatin-coated plates in  LIF medium supplemented with serum for 16 days.

value: 15 lincRNA KO types and WT


title: Uninfected Scrambled 24h-6

description: Uninfected Scrambled 24h-6

value: Bone marrow derived macrophage


title: BT594.T85C [GBM_58]

description: sgRNA amplified from gDNA

value: primary GBM

tag: treatment

value: DMSO


title: GC122772, uninfected, replicate 1, scRNAseq

description: 10x Genomics


title: Uninfected Scrambled 24h-4

description: Uninfected Scrambled 24h-4


title: BT594.T85B [GBM_57]

description: sgRNA amplified from gDNA


title: WT+1343KO-a14-D16-R1

value: Day 16


title: CIN 612 H3K36me3 2

source_name: Cervix

value: Cervix

value: CIN 612

value: Keratinocytes

value: Anti-Histone H3 (tri methyl K36) antibody - ChIP Grade (ab9050)

value: HPV positive


title: CIN 612 H3K36me3 1


title: WT-D16-R2


title: Uninfected Scrambled 24h-3

description: Uninfected Scrambled 24h-3


title: BT594.T85A [GBM_56]

description: sgRNA amplified from gDNA


title: WT+1343KO-a14-D0-R1


title: Uninfected Scrambled 24h-2

description: Uninfected Scrambled 24h-2


title: CIN 612 Input 1 (control for H3K36me3 ChIP)


title: WT-D16-R1


title: Uninfected Scrambled 24h-1

description: Uninfected Scrambled 24h-1


title: CIN 612 Input 2 (control for H3K36me3 ChIP)


title: BT241.T35C [GBM_7]

description: sgRNA amplified from gDNA

value: recurrent GBM

value: Untreated


title: WT-D8-R1


title: WT-D0-R1


title: HFK Input 1 (control for H3K36me3 ChIP)

value: Foreskin

value: HFKs


title: HFK H3K36me3 1


title: BT594.T0 [GBM_55]

description: sgRNA amplified from gDNA


title: BT241.T35B [GBM_6]

description: sgRNA amplified from gDNA


title: RNA-seq - day 7 X-GFP high iPSCs IFNγ Rep 2

data_processing:
FastQ files passing the quality control were aligned to the mm10 reference genome, which contained CAST/EiJ and 129S1/SvImJ SNPs positions masked. The SNPs positions of the mouse strains were obtained fromftp://ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi. A VCF file containing only the SNPs positions from CAST/EiJ and 129S1/SvImJ strains was generated. Alignment of reads to the reference genome was done using STAR (Dobin et al. 2013) with implementation of the WASP method (van de Geijn et al. 2015) to filter allele specific alignments. The output BAM files were used to obtain the read counts using the HTseq tool (v0.6.1) (Anders, Pyl, and Huber 2015). These steps were performed using a published Nextflow pipeline (Di Tommaso et al. 2017) and following the workflow described in https://github.com/biocorecrg/allele_specific_RNAseq. Read counts were normalized to library size using DESeq2 R package.
Assembly: mm10
Supplementary files format and content: txt file of non-allelic normalized expression counts of RNA-seq data obtained with DESeq2
Supplementary files format and content: txt file of allelix ratio (X mus proportion) of X-linked genes expressed on X cas (over 25% of total expression)

source_name: hybrid 129S1/SvImJ, CAST/EiJ

growth_protocol: Mouse embryonic stem cells were incubated at 37 °C with 5% CO2 and cultured on 0.2% gelatin-coated plates in serum/LIF medium: DMEM medium (Thermo Fisher Scientific, 31966021) supplemented with 10% FBS (ES pre-tested, Capricorn, FBS-ES-12A), 1,000 U/ml LIF (ORF Genetics, 01-A1140-0100), 25mM HEPES (Thermo Fisher Scientific, 15630056), 1mM Sodium Pyruvate (Thermo Fisher Scientific, 11360070), 1x MEM NEAA (Thermo Fisher Scientific, 11140050), 50U/ml penicillin/streptomycin (Ibian Tech, P06-07100) and 0.1mM 2-mercaptoethanol (Thermo Fisher Scientific, 31350010). Neural Precursor cells were differentiated from ESCs and cultured in RHBA medium (Takara Bio, Y40001) supplemented with 10 ng/ml EGF (R&D Systems, 236-EG-200), 10 ng/ml bFGF (Thermo Fisher Scientific, 13256029) and ROCK inhibitor 10 µM (Selleck Chemicals, S1049). Cells undergoing reprogramming were grown on top of male irradiated Mouse Embryonic Fibroblasts (iMEFs) on 0.2% gelatin coated plates in iPSC medium: DMEM medium (Thermo Fisher Scientific, 31966021) supplemented with 15% FBS (ES pre-tested, Capricorn, FBS-ES-12A), 25mM HEPES (Thermo Fisher Scientific, 15630056), 1mM Sodium Pyruvate (Thermo Fisher Scientific, 11360070), 1x MEM NEAA (Thermo Fisher Scientific, 11140050), 50U/ml penicillin/streptomycin (Ibian Tech, P06-07100) and 0.1mM 2-mercaptoethanol (Thermo Fisher Scientific, 31350010), supplemented with 1,000 U/ml LIF, 25 mg/ml L-ascorbic acid and 1 mg/ml doxycycline.

extract_protocol:
Cells were dissociated and sorted based on SSEA1-APC and X-GFP expression. Cell pellets were frozen at -80ºC until processed. RNA was extracted from cell pellets by using a RNeasy Plus Mini Kit (Qiagen, 74136) or RNeasy Micro Kit (Qiagen, 74004).
RNA libraries preparation was performed by ribosomal RNA depletion using the TruSeq Stranded Total RNA Library Preparation Kit (Illumina, 20020596)
Paired-end sequencing (2 x 50 bp) on an Illumina HiSeq 2500.

treatment_protocol: Mouse recombinant IFNγ (10 ng/ml) (R&D Systems, 485-MI-100) was added to the reprogramming medium from day 0 to day 5.

value: hybrid 129S1/SvImJ, CAST/EiJ

value: reprogramming cell

value: day 7 X-GFP high iPSCs IFNγ


title: BT241.T35A [GBM_5]

description: sgRNA amplified from gDNA


title: WT+1343KO-a14-D16-R2

value: Embryonic Stem Cells


title: RNA-seq - day 7 X-GFP high iPSCs IFNγ Rep 1


title: RNA-seq - day 7 X-GFP high iPSCs control Rep 2

value: day 7 X-GFP high iPSCs control


title: Lenvatinib resistant 2

city: Shanghai

first: Mengyuan

last: Wu

address: 180 Fenglin Road

institute: Zhongshan hospital, Fudan university

data_processing:
Sequence reads were trimmed using Cutadapt and bases with average quality scores below 20 were filtered
Sequencing reads were mapped by using HISAT2 with BWT algorithm
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: All cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) with 10% FBS (Thermo Fisher Scientific, MA, USA) containing 10% fetal bovine serum (FBS) (Gibco, USA) and 1% penicillin/streptomycin (Gibco) at 5% CO2 at 37°C.

extract_protocol:
RNA was extracted by RNAiso Plus (9109, Takara) following the manufacturer’s instructions, 1.5 ug of total RNA was used to construct sequencing libraries
RNA libraries for RNA-seq were prepared by using Agilent 2100 Bioanalyzer

treatment_protocol: For lenvatinib resistant  PLC/PRF/5 cells, they were cultured with increasing doses of Lenvatinib (Selleck) at 20 μmol/L initially.The cell culture media was replaced every 48 h until the cells have occupied 90% of the culture dish, at which point they were passaged and replated. After passage, the concentration of Lenvatinib was increased by 0.5 mmol/L until PLC/PRF/5 cells proliferated rapidly at 40 mmol/L.

value: human heptocellular carcinoma

value: Lenvatinib resistant

value: Lenvatinib


title: WT+1343KO-a14-D8-R2

value: Day 8


title: RNA-seq - day 7 X-GFP high iPSCs control Rep 1


title: DNA methylation array - Day  7 GFP- iPSC IFNg Rep2_BS

type: genomic

hyb_protocol: 1µg of each sample was evenly splitted for the oxidation reaction and the mock-oxidation reaction where the oxidant solution was replaced by water following the TrueMethyl oxBS Module manufacturer’s instructions (NuGEN-Tecan, 0414). Both aliquots were then processed in parallel for all stages of the protocol. After the oxidation reaction where 5-hydroxymethylcytosine is oxidized to 5-formylcytosine (5fC) and 5-methylcytosine (5mC) stays unchanged, the bisulfite treatment converts 5fC and all non-methylated cytosines to uracil, while 5mC is not altered.  For samples to be run on the Illumina Infinium® Mouse Methylation BeadChip Array (Illumina, 20041558), 7 μL of recovered TrueMethyl template were mixed with 1 μL of 0.4 N NaOH following manufacturer’s instructions. All subsequent steps were completed following the Infinium HD Assay Methylation protocol  (https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/infinium_assays/infinium_hd_methylation/infinium-hd-methylation-guide-15019519-01.pdf).

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
IDAT files were preprocessed and analyzed using the minfi R package (v1.42.0). Probes were filtered for a detection p-value threshold of 0.01, and cross-reactive probes were removed. The remaining data was normalized using the preprocessQuantile method. Limma R package was used to do an experimental batch-correction.
Normalized beta values (normalization was done for array intensity using the preprocessQuantile method and then an experimental batch-correction was done using the Limma R package)

label: Cy5 and Cy3

label_protocol: Cy5 and Cy3

growth_protocol: Reprogramming was induced in the presence or absence of IFNγ (from day 0 to 5). SSEA1+ day 5 iPSCs (4 replicates from different reprogramming rounds) and SSEA1+ X-GFP+/X-GFP- day 7 iPSCs (2 replicates from different reprogramming rounds) were sorted by FACS.

extract_protocol: Genomic DNA was extracted and purified from reprogramming sorted cells using Qiagen DNeasy Kit according to standard instructions

tag: agent

value: IFNg


title: WT+1343KO-a14-D8-R1

tag: genotype


title: BT241.T0 [GBM_1]

description: sgRNA amplified from gDNA


title: Lenvatinib sensitive 3

value: WT

value: control


title: DNA methylation array - Day  7 GFP- iPSC IFNg Rep2_BS_OX


title: RNA-seq - day 7 X-GFP medium iPSCs IFNγ Rep 2

value: day 7 X-GFP medium iPSCs IFNγ


title: mutant-2 replicate 3

city: Berlin

first: Zhimin

address: Robert-Rössle-Straße 10

institute: MDC

data_processing:
A 30 million 100 bp paired-end reads were obtained per sample.
Discarding low-quality reads, trimming adaptor sequences, and eliminating poor-quality bases were done using FASTX-Toolkit and Trimmomatic.
Building index and alignment, the reads were performed using Salmon after discarding outliers with over 30 % disagreement.
GC content and gene length biases were checked using R package NOISeq to quality control of count data.
Mean-variance and PCA were calculated between biological replicates using the tximport package in R.
The parameters of lengthscaledTPM were CPM cutoff >2 and sample cutoff 2 between the replicates for the analyzed groups.
The RUv package from Bioconductor was used to eliminate batch effects.
All of the samples were normalized to TMM (weighted trimmed mean of M-values).
Genome_build: hg19
Supplementary_files_format_and_content: Gene TPM

source_name: hESCs

extract_protocol:
Total RNA of samples was extracted from cells using the Direct-zol RNA MiniPrep Plus kit.
BGI Hongkong prepared the DNA libraries and sequenced the libraries on a DNBseq Eukaryotic-T resequencing.

value: hESCs_H1-derived pancreatic Beta-like cells

tag: age

value: day 32 of differentiation


title: DNA methylation array - Day  7 GFP- iPSC IFNg Rep1_BS


title: RNA-seq - day 7 X-GFP medium iPSCs IFNγ Rep 1


title: mutant-2 replicate 2


title: Lenvatinib sensitive 2


title: RNA-seq - day 7 X-GFP medium iPSCs control Rep 2

value: day 7 X-GFP medium iPSCs control


title: DNA methylation array - Day  7 GFP- iPSC IFNg Rep1_BS_OX


title: Lenvatinib resistant 3


title: mutant-1 replicate 3


title: LM3_JQ1_rep2

first: Li

last: Peng

address: No. 107 Yanjiang West Road

institute: Sun Yat-Sen Memorial Hospital

data_processing:
library strategy: lncRNA-seq
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: HCC cell lines

extract_protocol:
Total RNA from HCC cells were extracted using Trizol method.
Concentration and integrity of total RNA were assessed with a Nano Drop and Agilent 2100 Bioanalyzer system. Afterwards, 1 μg total RNA per sample was prepared to deplete rRNA and build library. The cDNA libraries were subjected to paired-end sequencing on Hiseq 4000 platform. The library preparation and sequencing were conducted by BGI Genomics.

treatment_protocol: HCC cells with the treatment of JQ1.

value: Hepatocellular carcinoma (HCC) cell line


title: DNA methylation array - Day  7 GFP- iPSC control Rep2_BS_OX

first: Mercedes

address: Dr. Aiguader, 88

institute: Centre for Genomic Regulation


title: RNA-seq - day 7 X-GFP medium iPSCs control Rep 1

value: hybrid 129S1/SvImJ, CAST/EiJ


title: RNA-seq - day 7 X-GFP negative iPSCs IFNγ Rep 1

value: reprogramming cell

value: day 7 X-GFP negative iPSCs IFNγ


title: mutant-1 replicate 2


title: mutant-2 replicate 1


title: DNA methylation array - Day  7 GFP- iPSC control Rep2_BS


title: Lenvatinib sensitive 1


title: LM3_Vehicle_rep2

value: Vehicle (DMSO)


title: DNA methylation array - Day  7 GFP- iPSC control Rep1_BS


title: RNA-seq - day 7 X-GFP negative iPSCs IFNγ Rep 2


title: LM3_Vehicle_rep1


title: Lenvatinib resistant 1


title: LM3_JQ1_rep1


title: DNA methylation array - Day  7 GFP- iPSC control Rep1_BS_OX


title: WT+1343KO-a14-D0-R2

value: Embryonic Stem Cells

value: Day 0


title: RNA-seq - day 7 X-GFP negative iPSCs control Rep 2

value: day 7 X-GFP negative iPSCs control


title: mutant-1 replicate 1


title: DNA methylation array - Day  7 GFP+ iPSC IFNg Rep2_BS

hyb_protocol: 1µg of each sample was evenly splitted for the oxidation reaction and the mock-oxidation reaction where the oxidant solution was replaced by water following the TrueMethyl oxBS Module manufacturer’s instructions (NuGEN-Tecan, 0414). Both aliquots were then processed in parallel for all stages of the protocol. After the oxidation reaction where 5-hydroxymethylcytosine is oxidized to 5-formylcytosine (5fC) and 5-methylcytosine (5mC) stays unchanged, the bisulfite treatment converts 5fC and all non-methylated cytosines to uracil, while 5mC is not altered. For samples to be run on the Illumina Infinium® Mouse Methylation BeadChip Array (Illumina, 20041558), 7 μL of recovered TrueMethyl template were mixed with 1 μL of 0.4 N NaOH following manufacturer’s instructions. All subsequent steps were completed following the Infinium HD Assay Methylation protocol  (https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/infinium_assays/infinium_hd_methylation/infinium-hd-methylation-guide-15019519-01.pdf).

data_processing:
IDAT files were preprocessed and analyzed using the minfi R package (v1.42.0). Probes were filtered for a detection p-value threshold of 0.01, and cross-reactive probes were removed. The remaining data was normalized using the preprocessQuantile method. Limma R package was used to do an experimental batch-correction.
Normalized beta values; normalization was done for array intensity using the preprocessQuantile method and then an experimental batch-correction was done using the Limma R package

source_name: Day  7 GFP+ iPSC

growth_protocol: Reprogramming was induced in the presence or absence of IFNγ (from day 0 to 5). SSEA1+ day 5 iPSCs (4 replicates from different reprogramming rounds) and SSEA1+ X-GFP+ day 7 iPSCs (2 replicates from different reprogramming rounds) were sorted by FACS.

value: Day  7 GFP+ iPSC

value: D7 IFNg


title: RNA-seq - day 7 X-GFP negative iPSCs control Rep 1


title: HepG2_JQ1_rep2


title: UC replicate 3

value: CRISPR/Cas9 transfected but unmofied KCNQ1


title: UC replicate 2


title: RNA-seq - day 5 iPSCs IFNγ Rep 2

value: day 5 iPSCs IFNγ


title: DNA methylation array - Day  7 GFP+ iPSC IFNg Rep2_BS_OX


title: HepG2_JQ1_rep1


title: UC replicate 1


title: RNA-seq - day 5 iPSCs IFNγ Rep 1


title: DNA methylation array - Day  7 GFP+ iPSC control Rep2_BS

value: D7 control


title: DNA methylation array - Day  7 GFP+ iPSC IFNg Rep1_BS


title: WT replicate 1

source_name: human embryonic stem cells (hESCs)

value: wild type


title: WT replicate 2

value: hESCs_H1-derived pancreatic Beta-like cells


title: RNA-seq - day 5 iPSCs control Rep 2

value: day 5 iPSCs control


title: RNA-seq - day 2 iPSCs IFNγ Rep 2

value: day 2 iPSCs IFNγ


title: DNA methylation array - Day  7 GFP+ iPSC control Rep1_BS


title: HepG2_Vehicle_rep1

value: Hepatocellular carcinoma (HCC) cell line


title: RNA-seq - day 5 iPSCs control Rep 1

value: hybrid 129S1/SvImJ, CAST/EiJ


title: RNA-seq - day 2 iPSCs IFNγ Rep 1

value: reprogramming cell


title: DNA methylation array - Day  7 GFP+ iPSC control Rep2_BS_OX


title: DNA methylation array - Day  7 GFP+ iPSC IFNg Rep1_BS_OX


title: LM3 cells - input DNA

data_processing:
For the analysis of ChIP-seq data, Bowtie2 was used to align sequencing reads onto the human reference genome hg19.
MACS2 was used to call peaks, deeptools was used to rorate bigwig files, and ROSE was used to identify SEs.
Genome_build: hg19
Supplementary_files_format_and_content: peak text files

growth_protocol: Hepatocellular carcinoma (HCC) cell lines HepG2 and HCC-LM3 (LM3) were cultured in DMEM (Thermo, USA) supplemental with 10% FBS (Gibco, USA) and penicillin & streptomycin (Hyclone, USA) in an incubator with 5% CO2 at 37°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody histone-3-lysine-27 acetylation (H3K27ac).
The purified ChIP DNA samples and their input DNA were diluted and send to BGI Genomics for library construction and sequencing.

treatment_protocol: No special treatment

tag: strain

value: untreated


title: BUN3 Cut&Tag

city: Hangzhou

first: Yanxiao

last: Zhang

state: Zhejiang

address: N0.600, Dunyu Road

department: School of Life Sciences

institute: Westlake University

data_processing:
CUT&Tagdata analysis Data quality was checked byFastQCv0.11.9(https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).Reads were trimmedusingtrim_galore(0.6.6)(https://github.com/FelixKrueger/TrimGalore)and alignedto thedrosophila genomedm6using bowtie2(https://bowtie-bio.sourceforge.net/bowtie2/index.shtml).Samtoolswas applied to remove duplicates andfilter the fragments that more than 120bp. Considering the properties of transcription factors,only reads with a fragment size <120 bp were kept for downstream analysis.Peaks were called by MACS2 (https://pypi.org/project/MACS2/).Peaks were loaded into R version 4.2.1, andtheChIPseekerRpackage(https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html)was applied forpeak distribution acrossthegenome, nearest gene annotation, and visualization. The enrichmentmotifwasanalyzed byHomer(http://homer.ucsd.edu/homer/).Bigwig files wereconvertedusingdeeptoolsbamCoveragecommand(https://test-argparse-readoc.readthedocs.io/en/latest/content/tools/bamCoverage.html)with RPKM normalization flagand used for visualizationinIntegrative Genomics Viewer (IGV,https://igv.org/).
Assembly: dm6
Supplementary files format and content: bigWig, bed
Library strategy: CUT&Tag

organism: Drosophila melanogaster

source_name: wing disc

growth_protocol: The flies were cultured at 25℃

extract_protocol:
The wing imaginal discs of third instar larvae were dissected on ice and dissociated at 37℃ for fifteen minutes
DNA libraries are  generated following the procedures of  the Vazyme CUT&Tag Kit (TD903)

value: wing disc

value: nub>GFP;UAS-BunA-HA

value: the third instar larvae


title: LM3 cells - H3K27ac

value: H3K27ac (ABCam, ab4729)


title: JOL2941 (yihO knockout) rep1

city: Iksan

first: Khristine Kaith

middle: Sison

last: Lloren

address: 79 Gobong-ro

institute: Jeonbuk National University

data_processing:
Sequencing runs were performed on NovaSeq 6000 system
Raw sequences were quality-checked using FastQC v0.11.7 for data integrity (reads over score of 20 are accepted as good quality); Adapter sequences and bases with base quality lower than three from the ends were trimmed using Trimmomatic 0.38
Reads were mapped to the reference genome with Bowtie 1.1.2 and read number of each gene was counted using HTSeq v0.6.1
Low quality transcripts are filtered and TMM normalization are performed
Statistical analysis of DEG is performed using Fold Change, exactTest using edgeR per comparison pair. The significant results are selected on conditions of |fc|>=2 & exactTest raw p-value<0.05
Assembly: ASM694v2
Supplementary files format and content: excel file includes original raw data of the read count and FPKM of known genes obtained through the HTSeq for each sample
Supplementary files format and content: excel file includes fold change and raw.pval after TMM normalization

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: bacteria

growth_protocol: JOL401 WT and JOL2941 ∆yihO Salmonella Typhimurium mutant were grown overnight in LB medium. The overnight cultures were diluted at 1:100 in fresh LB medium and grown to mid-log phase.

extract_protocol:
RNA was extracted using Trizol reagent and Hybrid R Kit (GeneAll) following the manufacturer's protocol;
RNA libraries for RNA-seq were prepared using NEBNext rRNA Depletion (Bacteria) and TruSeq Stranded Total RNA Library Prep Gold Kit

value: bacteria

value: yihO knockout


title: DNA methylation array - Day 7 GFP+ iPSC control Rep1_BS_OX

city: Barcelona

last: Barrero

source_name: Day 7 GFP+ iPSC

value: Day 7 GFP+ iPSC


title: BUN4 Cut&Tag


title: JOL2941 (yihO knockout) rep2


title: BUN2 Cut&Tag


title: DNA methylation array - Day 5 iPSC IFNg Rep4_BS

source_name: Day 5 iPSC

value: Day 5 iPSC

value: D5 IFNg


title: RNA-seq - day 2 iPSCs control Rep 2

value: day 2 iPSCs control


title: JOL401 WT rep2

value: WT


title: RNA-seq - NPC Rep 2

value: neural precursor cell

value: NPC


title: RNA-seq - day 2 iPSCs control Rep 1


title: HepG2_Vehicle_rep2

value: Hepatocellular carcinoma (HCC) cell line

value: Vehicle (DMSO)


title: DNA methylation array - Day 5 iPSC IFNg Rep4_BS_OX


title: JOL401 WT rep1


title: WT replicate 3

value: hESCs_H1-derived pancreatic Beta-like cells

value: day 32 of differentiation

value: wild type


title: RNA-seq - NPC Rep 1

value: hybrid 129S1/SvImJ, CAST/EiJ


title: NIL-R leaves.RBSDV, 16 days, rep1

city: Beijing

first: Suining

last: Deng

address: 2 West Yuanmingyuan r.d.

institute: China Agricultural Univesity

data_processing:
The raw data (raw reads) in FASTQ format were subjected to quality control, with the removal of adaptor sequences and low-quality reads to get clean reads.
These clean reads were then aligned to the Maize genome (B73 RefGen_v4, AGPv4) using HISAT (2.0.4) with default parameters.
FPKM (fragments per kilobase of transcript per million mapped reads) values of each gene were calculated using HTSeq (version 0.6.1) software.
Differentially expressed genes (DEGs) were analyzed using DESeq (1.12.0) software, with significant DEGs defined based on a p-value threshold (log2 fold change > 1, p < 0.05). The z-score scale represents the mean-subtracted, regularized log-transformed FPKM values.
The abundance of reads was visualized using the Integrative Genomics Viewer (2.16.1). Gene ontology (GO) enrichment analysis was performed using the accession numbers of significant DEGs via GOseq (version 2.12). Pathway enrichment analysis of DEGs was conducted using KOBAS (version 2.0).
Assembly: Maize genome (B73 RefGen_v4, AGPv4)
Supplementary files format and content: Tab-delimited file includes raw counts for each samples.
Supplementary files format and content: Tab-delimited files include FPKM values for each samples.

organism: Zea mays

source_name: Leaves

growth_protocol: Seedings of  NILs were germinated in vermiculite soil in pots in a greenhouse at 25℃ (16h/light, 8h/dark).

extract_protocol:
Total RNA was extracted from maize leaves or internodes with a PLANTpure plant RNA Kit (Aidlab, China), following the manufacturer's protocol.
RNA libraries were constructed by were constructed and sequenced on an Illumina Hiseq platform, generating 125 bp/150 bp paired-end reads.

treatment_protocol: The seedlings were artificially inoculated by viruliferous planthoppers carrying RBSDV during the bud stage for a duration of 3 days. After inoculation, the seedlings were transplanted into the field. We collected

value: Leaves

value: uppper leaves cells

value: Uppper leaves cells

value: NIL-R

value: Infected with RBSDV


title: NIL-R leaves.RBSDV, 16 days, rep2


title: DNA methylation array - Day 5 iPSC control Rep4_BS_OX

value: Day 5 iPSC

value: D5 control


title: GSC11 cells, shDHRS13 #2, Day 2

city: Seoul

first: Min Ji

last: Park

institute: Korea University

description: Fold change_GSC11-shNT vs shDHRS13 #2.xls

data_processing:
Raw fragments per kilobase million (FPKM) and probability values (PA) were calculated using the performer’s algorithm and used for further analysis. Genes with PA > 0.8, whose expression levels increased or decreased by more than 2-fold after the knockdown of DHRS13, were grouped and designated as DEGs.
Assembly: mm10
Supplementary files format and content: Excel files include Log2(Fold Change) values and q-values for each Sample

source_name: Brain

growth_protocol: 528NS and GSC11 cells were cultured in Dulbecco’s modified Eagle’s medium/F12 (DMEM/F12) supplemented with 0.2% B27, 20 ng/mL epidermal growth factor (EGF), 20 ng/mL basic fibroblast growth factor (b-FGF), 1% penicillin/streptomycin, 2 mM L-glutamine, and 50 μg/mL gentamicin.

extract_protocol:
Total RNA was extracted from cells using QIAzol lysis reagent (Qiagen) according to the manufacturer’s instructions. RNase-free, DNase-treated RNA (1 μg) was used as the template.
RNA libraries for RNA-seq were prepared using Ditrct-zol™ RNA MiniPrep Kit following manufacturer's protocols.

value: Brain

value: Cancer stem-like cells

value: DHRS13 knockdown


title: GSC11 cells, shDHRS13 #1, Day 2

description: Fold change_GSC11-shNT vs shDHRS13 #1.xls


title: NIL-S leaves.RBSDV, 16 days, rep2

value: NIL-S


title: DNA methylation array - Day 5 iPSC control Rep4_BS


title: NIL-S leaves.RBSDV, 16 days, rep1


title: DNA methylation array - Day 5 iPSC IFNg Rep3_BS

value: D5 IFNg


title: RNA-seq - ESC Rep 1

value: embryonic stem cell

value: ESC


title: DNA methylation array - Day 5 iPSC IFNg Rep3_BS_OX


title: gRNA sequencing -  Late Pluripotent Biol Rep2

data_processing:
The gRNA sequencing from the CRISPR KO screening was analyzed with MAGeCK software (Li et al. 2014). The gRNA abundance of each population was determined by taking into account the two biological replicates (with two technical replicates each). The gRNA abundance comparisons were performed pairwise.
Assembly: mm10
Supplementary files format and content: xlsx file containing raw counts for each gRNA in each sample

extract_protocol:
Cells were dissociated and sorted based on BFP, SSEA1-APC and X-GFP expression using a BD FACSAria II SORP.
Genomic DNA was extracted from cell pellets using the DNeasy Blood and Tissue Kit (Qiagen, 69504). For amplification of the gRNAs and introduction of the Illumina-sequencing adapters, two consecutive PCRs were performed by using the Q5 High-Fidelity DNA Polymerase (NEB, M0491), adding the Illumina adapsters for NGS.
Single-end sequencing (1 x 50 bp) on an Illumina HiSeq 2500. Each sample contains two technical replicates

value: reprogramming cell

value: Late Pluripotent


title: GSC11 cells, shNT, Day 2

description:
Fold change_GSC11-shNT vs shDHRS13 #1.xls
Fold change_GSC11-shNT vs shDHRS13 #2.xls

value: WT