title: NF L HY24


title: NF S HY20

status: Public on Mar 06 2023

type: SRA

city: Orange

first: Patricia

middle: C

last: Lopes

state: CA

address: 450 N Center St

department: Biological Sciences

country: USA

institute: Chapman University

library_source: transcriptomic

data_processing:
Data filtering: reads containing adapters, reads containing N > 10% and low quality reads were filtered out
Mapping was done using HISAT2
HTSeq (v0.6.1) was used to count numbers of mapped reads.
Assembly: taeGut3.2.4, release 96, downloaded from Ensembl
Supplementary files format and content: tab-delimited text file includes raw (not normalized) readcount values for each sample

molecule: polyA RNA

organism: Taeniopygia guttata

source_name: HY

extract_protocol:
Total RNA was isolated from the aqueous layer produced after chloroform precipitation, using the RNA Clean & Concentrator Kit-5 (Zymo Research, item # R1013) following manufacturer’s instructions and including the DNase I in-column treatment step.
RNA libraries were prepared for sequencing using NEBNext® UltraTM RNA Library Prep Kit, following standard protocols

tag: tissue

value: HY

tag: social treatment

value: NF

tag: injection treatment

value: S


title: Atg16L1fl/fl LysMcre+/+ macrophages, infected with M. tuberculosis, biol rep 2

city: Berkeley

first: Guillaume

last: Golovkine

address: 1951 Oxford Street

institute: UC Berkeley

data_processing:
remove adapter, polyA and low quality sequences using htstream/1.3.3, minimum read length after quality control is 50bp
map to GRCm39 using STAR (v2.7.9a)
deduplication using umi_tools (v1.1.2)
generate counts table using featureCounts function in subread package v1.6.3
Assembly: GRCm39
Supplementary files format and content: Excel file with mouse genes listed in the first column. Each sample in a separate column.

molecule: total RNA

organism: Mus musculus

source_name: Bone-marrow derived macrophages

growth_protocol: Macrophages were seeded at a density of 2 x 106 cells per well in 6-well non-TC treated plate and incubated in DMEM, high glucose (Gibco) supplemented with 10% FBS, 2 mM glutamine, 0.11 mg/ml sodium pyruvate and 10% MCSF derived from 3T3-MCSF cell culture supernatants. Cells were maintained in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Cells were resuspended in 1 ml of Trizol after 48 h of infection. 200 microliters of chloroform were added before centrifugation at 15,000 g for 10 min at 4°C. An equal volume of 70% ethanol was added to the aqueous layer, and RNA was extracted using silica spin columns (Invitrogen PureLink RNA Mini Kit). Purified RNA samples were treated with DNase (Purelink) and EDTA.
Gene expression profiling was carried out using a 3’ Tag-RNA-Seq protocol. Barcoded sequencing libraries were each prepared from 200 ng total RNA sample using the QuantSeq 3' mRNA-Seq Library Prep FWD kit for multiplexed sequencing, according to the recommendations of the manufacturer (Lexogen, Vienna, Austria). The fragment size distribution of the libraries was verified via micro-capillary gel electrophoresis on a LabChip GX system (PerkinElmer, Waltham, MA). The libraries were quantified by fluorometry on a Qubit fluorometer (LifeTechnologies, Carlsbad, CA), and pooled in equimolar ratios. The library pool was Exonuclease VII treated (NEB, Ipswich, MA), SPRI-bead purified with KapaPure beads (Kapa Biosystems/Roche, Basel, Switzerland), quantified via qPCR with a Kapa Library Quantification kit (Kapa Biosystems) on a QuantStudio5 RT-PCR system (Applied Biosystems, Foster City, CA). Libraries were sequenced on a NextSeq500 sequencer (Illumina, San Diego, CA) with single-end 85 bp reads.
3’ Tag-RNA-Seq (see: https://dnatech.genomecenter.ucdavis.edu/tag-seq-gene-expression-profiling/)

treatment_protocol: Macrophage monolayers were overlaid with M. tuberculosis suspensions and infected at a multiplicity of infection of 2 using a ‘spinfection protocol’ during which cells and bacteria were centrifuged for 10 min at 400 g. Cells were returned to regular macrophage media. Media was replaced daily until RNA harvest.

tag: cell type

value: Bone-marrow derived macrophages

tag: genotype

value: Atg16L1fl/fl LysMcre+/+

tag: treatment

value: Infection with M. tuberculosis for 48h


title: Atg16L1fl/fl LysMcre+/- macrophages, infected with M. tuberculosis, biol rep 2

value: Atg16L1fl/fl LysMcre+/-


title: Normal kidney allograft rep 1

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

description:
isolated single nuclei - RNA
KUT023

data_processing:
Count matrices were generated using cellranger
Seurat objects were created using count matrices and the counts were normalized for library size
Seurat objects of normalized counts for all samples were integrated into one combined object
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files of raw counts for each sample generated using cellranger

organism: Homo sapiens

source_name: Kidney allograft

extract_protocol:
Single nuclei were isolated using Nuclei EZ lysis buffer with protease inhibitor. The homgenate was filtered with a 40um cell strainer and, then, centrifuged at low speed. The nuclei pellet was resuspended in Nuclei resuspspension buffer and passed through the 40um filter.
Libraries were prepared according to standard 10x Genomics and Illumina instructions. Libraries were generated using the 10x 5' Gene Expression kit.
Single nuclei RNA-seq (10x genomics platform)

tag: group

value: Normal kidney allograft

tag: est. conc. of cells

tag: mean reads per cells

tag: fraction of reads mapped to genome (%)


title: NF L HY19

value: L


title: S40

city: Beijing

first: Yiming

last: Lu

address: Taiping Road

country: China

institute: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine

data_processing:
The Cell Ranger software (version 2.2.0) provided by 10x Genomics was used to align the reads from droplet-based scRNA-seq to an indexed mouse genome (mm10, NCBI Build 38), generating a digital gene expression matrix (UMI counts per gene per cell) for each sample. Expression matrices for all samples were filtered, normalized, integrated and clustered using the standard Seurat (version 2.3.4) package procedures.
Genome_build: mm10
Supplementary_files_format_and_content: normalized and raw counts

source_name: Single cells in mouse intestine tissue

extract_protocol:
To isolate single cells, duodenum were amputated (about 5 cm beyond the pylorus) and 10 cm jejunum segments following the incision of the mice on day 0, 1, 3, 7, 14 after irradiation were washed in cold PBS, cut longitudinally into roughly 2-mm-long pieces and were isolated using the Liver Dissociation Kit (mouse) and GentleMACS Dissociator (Miltenyi Biotec, Germany) according to the manufacturer’s instructions. Tissues were filtered through a 40-μm-mesh cell strainer on ice, pelleted by centrifugation at 4 °C and washed twice with the ice-cold regular medium to remove the debris.
An estimated 5,000 single cells per sample were then subjected to 10x Genomics single-cell isolation and RNA sequencing following the manufacturer’s recommendations. Illumina HiSeq 3000 was used for deep sequencing.

value: Intestine

value: Radiation

tag: time point


title: ISO L HY16

value: ISO


title: ISO L HY14


title: Atg5fl/fl LysMcre+/- macrophages, infected with M. tuberculosis, biol rep 2

value: Atg5fl/fl LysMcre+/-


title: ISO S HY13


title: Atg7fl/fl macrophages, infected with M. tuberculosis, biol rep 2


title: Atg5fl/fl macrophages, infected with M. tuberculosis, biol rep 2


title: PIN 161 Tumour

type: RNA

city: Dublin

first: Fiona

last: O'Neill

state: Dublin

address: National Institute for Cellular Biotechnology, Dublin City University

country: Ireland

institute: DCU

hyb_protocol: Following Biotin Labeling, samples hybridized for 16-18 hrs at 48C on GeneChipmi RNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data was analysed using the Transcription Analysis console 4.0.2 using Affymetrix default analysis settings. RMA.

label: biotin

source_name: Human pancretic tumour material

label_protocol: FlashTag Biotin HSR ligation samples were prepared according to the standard Affymetrix protocol from 1000ng total RNA (FlashTag Biotin HSR RNA labeling Kit, 2013, Affymetrix).

growth_protocol: Samples were snap frozen in liquid nitrogen once received from pathology department

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

treatment_protocol: Not applicable

value: Human Pancreas Tumour


title: PIN 65 F1 Generation

source_name: 1st generation of PDX tumour material from SCID mice

value: Tumour generated in SCID mice


title: S17


title: S15


title: PIN 160 F1 Generation


title: PIN 161 F1 Generation


title: PIN 160 Tumour


title: PIN 89 Tumour


title: ISO S HY12


title: PIN 65 Normal

source_name: Normal human tumour afjacent material

value: Normal Adjacent


title: PIN 89 F1 Generation


title: Atg7fl/fl LysMcre+/- macrophages, mock infected, biol rep 1

value: Atg7fl/fl LysMcre+/-

value: Mock infected


title: S14


title: S38


title: Atg16L1fl/fl macrophages, infected with M. tuberculosis, biol rep 2


title: ISO L HY9

value: HY


title: Atg5fl/fl LysMcre+/+ macrophages, infected with M. tuberculosis, biol rep 2

value: Atg5fl/fl LysMcre+/+


title: Atg7fl/fl macrophages, mock infected, biol rep 1

value: Bone-marrow derived macrophages


title: ISO L HY8


title: S10


title: S37


title: PIN 140 F1 Generation


title: Atg16L1fl/fl LysMcre+/+ macrophages, mock infected, biol rep 1

value: Atg16L1fl/fl LysMcre+/+


title: S9


title: ISO L HY6


title: PIN 140 Tumour


title: PIN 120 F1 Generation


title: ISO S HY5

value: S


title: Atg16L1fl/fl LysMcre+/- macrophages, mock infected, biol rep 1

value: Atg16L1fl/fl LysMcre+/-


title: S8


title: Atg16L1fl/fl macrophages, mock infected, biol rep 1


title: S35


title: S3


title: PIN 160 Normal


title: NF L HY3

value: NF


title: Atg5fl/fl LysMcre+/- macrophages, mock infected, biol rep 1


title: NF S HY4


title: Atg5fl/fl macrophages, mock infected, biol rep 1


title: PIN 140 Normal


title: S2


title: Atg7fl/fl LysMcre+/+ macrophages, infected with M. tuberculosis, biol rep 1

value: Atg7fl/fl LysMcre+/+

value: Infection with M. tuberculosis for 48h


title: S26

value: Intestine

value: Control


title: S1

value: Radiation


title: Atg7fl/fl LysMcre+/- macrophages, infected with M. tuberculosis, biol rep 1


title: S23


title: PIN 112 Tumour

value: Human Pancreas Tumour


title: Atg7fl/fl macrophages, infected with M. tuberculosis, biol rep 1


title: PIN 120 Tumour


title: S22


title: Atg5fl/fl LysMcre+/+ macrophages, mock infected, biol rep 1


title: PIN 120 Normal


title: pBIC2_6068

city: Pamplona

first: SERGIO

last: ROA

address: Irunlarrea, 1

department: Biochemistry and Genetics

country: Spain

institute: University of Navarra

description: SE50 sequencing of oligo dT-based mRNA enrichment (polyA RNA)

data_processing:
QC control of sample sequencing was verified using FastQC software.
Fastq files were mapped to mm10 mouse assembly using STAR 2.5.2b with default parameters.
Gene expression quantification was carried out with featureCounts v1.6.0 using read counts of exonic gene regions.
The gene annotation reference was Gencode vM25.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are tab-delimited text files including raw counts values for each annotated gene.

source_name: FACS-sorted B220+GFP+ cells from spleen

extract_protocol:
Murine spleens were submitted to cellular disggregation, followed by lysis of erythrocytes using ACK buffer. Then, single-cell preparations were stained with B220 and submitted to fresh cellular sorting in a FACSAria Ilu sorter (BD) after exclusion of dead cells with 7AAD. Total RNA was extracted from sorted cells using TRIzol (Invitrogen) as described in manufacturer´s protocol and quality control of extracted RNA was measured using Agilent 2100 Bioanalyzer.
DNBseq SE50 20M reads

treatment_protocol: Fresh murine spleens were collected from moribund or control mice.

tag: strain

tag: murine model

value: Eµ-hBCL2-expressing ABC-DLBCL lymphoma (pBIC2)

tag: cell type/tissue

value: splenic lymphoma B cells (B220+GFP+)


title: S0


title: Atg16L1fl/fl LysMcre+/+ macrophages, infected with M. tuberculosis, biol rep 1


title: WTS_wortm_2

city: Kyoto

first: Masao

last: Doi

department: Department of Systems Biology

country: Japan

institute: Kyoto University, Graduate School of Pharmaceutical Sciences

description: RNase I footprinting, ribosome pelleting, RNA extraction

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
rRNA and other non-coding RNA alignment with STAR v2.7.0
Alignment with STAR v2.7.0
Read quantitation using custom scripts
Assembly: mm10
Supplementary files format and content: Text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Library strategy: Ribo-Seq

source_name: mouse embryonic fibroblasts

growth_protocol: Cells were grown in dish to full confluence before experiments.

extract_protocol:
Cells were lysed with a lysis buffer containing cycloheximide. Following digestion of genomic DNA with DNase I, the lysate was centrifuged at 20,000 × g and the resultant supernatant was processed for library generation.
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification

treatment_protocol: WTS (35°C -> 38.5°C) was applied 24-h after Dex synchronization with or without wortm treatment.

value: wild-type

value: mouse embryonic fibroblasts

value: wortm


title: PIN 80 F1 Generation

value: Tumour generated in SCID mice


title: PIN 80 Tumour


title: PIN 112 F1 Generation


title: pBIC2_6074


title: WTS_wortm_1


title: Atg16L1fl/fl LysMcre+/- macrophages, infected with M. tuberculosis, biol rep 1

value: Bone-marrow derived macrophages


title: WTS_cont_2

value: control


title: pBIC2_4794


title: Atg16L1fl/fl macrophages, infected with M. tuberculosis, biol rep 1


title: WTS_cont_1


title: Atg5fl/fl LysMcre+/+ macrophages, infected with M. tuberculosis, biol rep 1

value: Atg5fl/fl LysMcre+/+


title: PIN 80 Normal

value: Normal Adjacent


title: ribo_WTS(+)_1

data_processing:
Library strategy: Ribo-seq
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
rRNA and other non-coding RNA alignment with STAR v2.7.0
Alignment with STAR v2.7.0
Read quantitation using custom scripts
Genome_build: mm10
Supplementary_files_format_and_content: Text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

extract_protocol:
RNase I footprinting, ribosome pelleting, RNA extraction
Cells were lysed with a lysis buffer containing cycloheximide. Following digestion of genomic DNA with DNase I, the lysate was centrifuged at 20,000 × g and the resultant supernatant was processed for library generation.
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for Ribo-seq) or TruSeq (illumina) (for mRNA-seq)

treatment_protocol: WTS (35°C -> 38.5°C) was applied 24-h after Dex synchronization. Otherwise the cells were kept at 35°C.

value: WTS+


title: PIN 112 Normal


title: Atg5fl/fl LysMcre+/- macrophages, infected with M. tuberculosis, biol rep 1

value: Atg5fl/fl LysMcre+/-


title: ribo_WTS(-)_1

value: WTS-


title: 7S,  prefix: RIT735A3, replicate 1, scRNAseq

city: London

first: Tiago

last: Rito

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

description:
3' RNA
10x Genomics Chromium Single-Cell 3′ mRNA V3.1

library_source: transcriptomic single cell

data_processing:
Reads were aligned to the Gallus gallus GRCg6a.101 reference genome using CellRanger (v4.0.0, 10X Genomics) and a custom-made reference 10X package including a gtf file with the protein_coding, pseudogene and lncRNA gene biotypes. Read counts were computed using DropEst61 (v0.8.6) with the parameters “-f -V -w -L eiEIBA”. The remaining analyses were performed using Scanpy62 (v1.7.0) unless otherwise indicated. Data for the different chick stages were independently filtered for high percentages of mitochondrial UMIs (6-7.5%) and low total counts (2500). Potential doublet cells were filtered out using Scrublet63 with thresholds between 0.2-0.3. Counts were normalized to a target sum of 10000 excluding 1% of highly expressed genes. “Highly variable genes” were called using Scanpy’s function with the same name with default parameters. Data of different stages were integrated using harmonypy, a port of the harmony64 R package by Ilya Korsunsky. Clustering of cells was performed unbiasedly using the Leiden algorithm with a resolution parameter of 3.5. PCA and UMAP were run with default parameters, with neighbourhood graph being computed for 10 neighbours and 40 principal components.
Assembly: Gallus gallus GRCg6a.101

organism: Gallus gallus

source_name: trunk tissue caudal to third somite

extract_protocol:
Fertilized chicken eggs obtained from Henry Stewart & Co. Ltd were incubated at 37°C with ~40% humidity for 29 to 45 hours to yield a minimum of 4 embryos with specific somite numbers: 4, 7, 10 and 13somites. All embryos were dissected to keep solely the tissue caudal to the third somite (inclusive). A single-cell suspension was obtained by incubating the dissected embryos at 37°C in a dissociation solution consisting of accutase (Stemcell Technologies) with 3U/mg Papain (Sigma-Aldrich, 10108014001) and 1mg/mL of Collagenase 4 (Gibco, 17104019) for 20 min. Half-way through incubation and at the end, the embryos were mechanical dissociated with a P1000 pipet. After dissociation 200uL of resuspension buffer (DMEM/F12 with 1% BSA) was added. The cell suspension was then spined for 4min at 0.6xg, resuspended in 250µL of resuspension buffer and filtered through a 40µm Flowmi cell strainer (cat. no. 136800040) and twice through a pre-wet 20µm pluriSelect strainer (43-10020-60). The yield and cell viability for the 4S, 7S, 10S and 13S samples were 640, 500, 1300 and 1600 cells/µL with a viability of 88%, 93%, 92% and 95% respectively.
A single-cell suspension was loaded independently for each sample onto the channels of Chromium Chip G for use in the 10x Chromium Controller (PN-1000120) with the goal of obtaining 10000 cells. The cells were partitioned into nanolitre scale gel beads in emulsions (GEMs) and lysed using the 10x Genomics Single Cell 3′ Chip V3.1 GEM, Library and Gel Bead Kit (PN-1000121). cDNA synthesis and library construction were performed as per the manufacturer's protocol for the Chromium Single-Cell 3′ mRNA V3.1 protocol. cDNA amplification involved 12 PCR cycles. Libraries for the samples were multiplexed so that the number of reads matched one lane per sample and sequenced on an Illumina HiSeq4000 using 100 bp paired-end runs.

value: trunk

value: trunk tissue caudal to third somite

tag: age

value: chicken embryo with 7 Somites


title: 13S, prefix: RIT735A1, replicate 1, scRNAseq

value: chicken embryo with 13 Somites


title: 4S, prefix: RIT735A2, replicate 1, scRNAseq

value: chicken embryo with 4 Somites


title: PDSN09, snATAC-seq

status: Public on Mar 05 2023

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

library_source: genomic single cell

data_processing:
To demultiplex the data for pooled libraries, the nuclei were clustered based on individual genetic variants using souporcell, using the same parameters (--min_alt 8 --min_ref 8 --no_umi True --skip_remap True --ignore True) used in Fiskin et al. study. The genetic variants from bulk ChIP-seq data was obtained by using freebayes (-iXu -C 2 -q 20 -n 3 -E 1 -m 30 --min-coverage 20 --pooled-continuous --skip-coverage 100000). The feature-barcode matrix was generated using the cellranger-atac count (10x Genomics, v1.1.0), aligning the sequenced reads were aligned to the human reference genome (hg19). Then the count matrices were aggregated by cellranger-atac aggr function with default parameters. The following analysis was performed using Signac R package v1.4.0. Nucleosome signal was computed with Signac’s NucleosomeSignal function. Low-quality nuclei were removed from snATAC-seq dataset based on the following criteria: fewer than 2,000 or greater than 30,000 fragments mapped to peak regions, less than 15% of reads in peak regions, nucleosome signal greater than 10, and transcription start site (TSS) enrichment less than 2. Doublets were identified using Scrublet, and excluded from analysis. We selected top 50% most common features as the variable features, and performed LSI dimensionality reduction by implementing term frequency-inverse document frequency (TF-IDF) transformation followed by singular value decomposition (SVD). Then, reciprocal LSI projection was conducted to identify integration anchors for each sample, and the snATAC-seq data was integrated across the samples by using low-dimensional cell embeddings with Signac’s IntegrateEmbeddings function. The identical method used in snRNA-seq for graph-based clustering and non-linear dimension reduction by UMAP was applied to the snATAC-seq dataset. Gene activity scores were computed for protein coding genes by summing snATAC-seq reads mapped in the gene body and the promoter (5 kb upstream to TSS) by using GeneActivity function in Signac R package.
Genome_build: hg19
Supplementary_files_format_and_content: h5, tsv

molecule: genomic DNA

source_name: Substantia nigra

extract_protocol:
About 15 mg of tissue was placed in an extra-thick tissue processing tube (Covaris, 520140) while kept in liquid nitrogen, and repeatedly hammered to produce frozen tissue powder. The frozen tissue was transferred to lysis buffer of 0.2% Triton X-100, protease inhibitor (Roche, 04-693-159-001), 1 mM DTT (Sigma-Aldrich, D9779), 0.2 U/µL RNAsin (Promega, N211B), and 2% BSA (Sigma-Aldrich, SRE0036) in PBS. Sample was pipetted 10 times, rotated for 5 min at 4°C, and centrifuged at 500g for 5 min. The pellet was resuspended in sorting buffer of 1 mM EDTA, 0.2 U/µL RNAsin, and 2% BSA in PBS, and passed through a 30 µm strainer (Sysmex, 04-0042-2316) to remove excessive debris. The nuclei were stained with DRAQ7 (1:100, Cell Signaling, 7406) for snRNA-seq, and with DAPI (10 ug/mL, Sigma, 32670) for snATAC-seq. Between 100,000 and 150,000 nuclei were sorted using a MoFlo Astrios EQ sorter (Beckman coulter, laser/filter) into a collection tube with 1 U/ µL RNAsin and 5% BSA in PBS. Sorted nuclei were centrifuged at 1000 g for 15 min at 4°C, and supernatant was removed. Nuclei were resuspended in resuspension buffer (0.2 U/µL RNAsin and 1% BSA in PBS) and counted using a cell counter (Cellometer Auto 2000, Nexcelom Biosicence) with AO/PI staining. The isolated nuclei were subject to permeabilization in a lysis buffer with Tris-HCl (pH8.0), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40 Substitute (Sigma-Aldrich, 74385), 0.01% digitonin (Thermo Fisher Scientific, BN2006), and 1% BSA.
snATAC-seq libraries were generated using the Chromium Single Cell ATAC Library & Gel Bead Kit v1 (10x Genomics).

value: Substantia nigra

tag: chip antibody


title: PDSN07, snATAC-seq


title: PDSN06, snATAC-seq


title: PDSN04, snATAC-seq


title: NOSN06, snATAC-seq


title: PDSN02, snATAC-seq


title: PDSN03, snATAC-seq


title: PDSN05, snATAC-seq


title: PDSN01, snATAC-seq


title: NOSN05, snATAC-seq


title: NOSN03, snATAC-seq


title: NOSN04, snATAC-seq


title: PDSN09, snRNA-seq

data_processing:
To demultiplex the data for pooled libraries, the nuclei were clustered based on individual genetic variants using souporcell, and assigned to the corresponding donor by matching the genetic variants obtained from bulk RNA-seq data. The genetic variants from bulk RNA-seq data was obtained by using freebayes (-iXu -C 2 -q 20 -n 3 -E 1 -m 30 --min-coverage 20 --pooled-continuous --skip-coverage 100000). The feature-barcode matrix was generated using cellranger count (10x Genomics, v3.0.2), aligning the sequenced reads to the human reference genome (hg19; 10x Cell Ranger reference GRCh37 v3.0.0). Then the count matrices were aggregated by cellranger aggr function across the samples with default parameters. The following analysis was performed using Seurat R package v4.0.5. Nuclei with fewer than 200 or greater than 10,000 genes detected were filtered from the snRNA-seq dataset. Low-quality nuclei with mapped reads in the mitochondrial genes greater than 10% were removed. Doublets were identified using Scrublet, and nuclei with doublet score greater than 0.4 were excluded from analysis. The snRNA-seq data was integrated to correct for technical differences across individual samples. For this, the feature-barcode matrix was individually normalized by the total read count and log transformed, and top 5,000 variable genes were selected for each sample using Seurat’s FindVariableFeatures function. Data integration was conducted based on anchors identified by using FindIntegrationAnchors function. The aligned nuclei were scaled, and principal component analysis (PCA) was conducted on the scaled expression matrix. The top 45 principal components (PCs) were used to compute Shared Nearest Neighbors (SNNs), which were then used to cluster nuclei based on the Louvain algorithm (resolution = 1.5) in FindClusters function in Seurat R package. The top 45 PCs were used for the Uniform Manifold Approximation and Projection (UMAP) embedding.
Genome_build: hg19
Supplementary_files_format_and_content: h5

molecule: nuclear RNA

extract_protocol:
About 15 mg of tissue was placed in an extra-thick tissue processing tube (Covaris, 520140) while kept in liquid nitrogen, and repeatedly hammered to produce frozen tissue powder. The frozen tissue was transferred to lysis buffer of 0.2% Triton X-100, protease inhibitor (Roche, 04-693-159-001), 1 mM DTT (Sigma-Aldrich, D9779), 0.2 U/µL RNAsin (Promega, N211B), and 2% BSA (Sigma-Aldrich, SRE0036) in PBS. Sample was pipetted 10 times, rotated for 5 min at 4°C, and centrifuged at 500g for 5 min. The pellet was resuspended in sorting buffer of 1 mM EDTA, 0.2 U/µL RNAsin, and 2% BSA in PBS, and passed through a 30 µm strainer (Sysmex, 04-0042-2316) to remove excessive debris. The nuclei were stained with DRAQ7 (1:100, Cell Signaling, 7406) for snRNA-seq, and with DAPI (10 ug/mL, Sigma, 32670) for snATAC-seq. Between 100,000 and 150,000 nuclei were sorted using a MoFlo Astrios EQ sorter (Beckman coulter, laser/filter) into a collection tube with 1 U/ µL RNAsin and 5% BSA in PBS. Sorted nuclei were centrifuged at 1000 g for 15 min at 4°C, and supernatant was removed. Nuclei were resuspended in resuspension buffer (0.2 U/µL RNAsin and 1% BSA in PBS) and counted using a cell counter (Cellometer Auto 2000, Nexcelom Biosicence) with AO/PI staining.
We generated snRNA-seq libraries using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics).


title: NOSN01, snATAC-seq


title: PDSN07, snRNA-seq


title: 10S, prefix: RIT735A4, replicate 1, scRNAseq

value: chicken embryo with 10 Somites


title: PDSN06, snRNA-seq


title: PDSN04, snRNA-seq


title: PDSN02, snRNA-seq


title: NOSN06, snRNA-seq


title: PDSN01, snRNA-seq


title: Atg5fl/fl macrophages, infected with M. tuberculosis, biol rep 1

value: Infection with M. tuberculosis for 48h


title: NOSN05, snRNA-seq


title: NOSN03, snRNA-seq


title: NOSN01, snRNA-seq


title: NOSN02, snRNA-seq


title: NOSN04, snRNA-seq


title: U3 Control acIP Rep2

city: Guangzhou

first: Ruihui

last: Xie

state: Guangdong

address: 107 Yan Jiang West Road

institute: Sun Yat-sen Memorial Hospital, SYSU

description: UM-UC-3_Control_Rep RIP PEAK

data_processing:
Base-calling: bcl2fastq2 v2.19.1
Data filtering : in house
Read alignment: hisat2 v2.1.0
transcript assemble: htseq-count v0.6.1
Assembly: hg19
Supplementary files format and content: excel files include normalize values for each Sample

growth_protocol: UM-UC-3 was cultured in DMEM (Gibco), T24 was cultured in 1640 (Gibco), supplemented with 10% FBS (Shanghai ExCell Biology, China) and 1% penicillin/streptomycin (Gibco). Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. Acetylated RNA immunoprecipitation (acRIP) was performed using EpiTM ac4C immunoprecipitation kit according to the manufactures’ instructions.The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA transfections were done with 75 nM siRNA and Lipofectamine RNAimax (Life technologies) following manufacturer's instructions.

tag: cell line

value: bladder cancer cell line

tag: sirna

value: Negetive control

tag: sirna sequence

value: UUCUCCGAACGUGUCACGUTT


title: U3 Control acinput Rep2

description: UM-UC-3_Control_Rep RIP PEAK


title: U3 NAT10-si acinput Rep2

description: UM-UC-3_NAT10-si_Rep RIP PEAK

value: siRNA targeting NAT10 was transfected in the cell

value: CCAUCUCUCGCAUCUAUUUTT


title: U3 Control Rep3

description: UM-UC-3 -Rep Control&NAT10-si


title: U3 NAT10-si Rep2

description: UM-UC-3 -Rep Control&NAT10-si


title: U3 Control Rep2

description: UM-UC-3 -Rep Control&NAT10-si


title: HCT116 shCNT REP C

city: Boston

first: Abigail

middle: L

last: Miller

state: MA

address: 77 Avenue Louis Pasteur NRB 466

institute: Mass General Brigham

data_processing:
FASTQ files were aligned using Hisat2 v.2.0.5
Assembly: hg38
Supplementary files format and content: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.

source_name: cell line

growth_protocol: Cells were transduced with  shCNT or shDAB2IP lentivirus.  After selection and recovery, cells were seed at 5x10^5 and collected 2 days later (70% confluency).

extract_protocol:
RNA was extracted using Qiagen RNAeasy Plus kit.
NEBNEXT Ultra II RNA library prep

tag: tissue

value: cell line

value: colon cancer

value: shCNT


title: HCT116 shCNT REP B

tag: cell type


title: HCT116 shDAB2IP REP A

tag: genotype


title: HCT116 shDAB2IP REP B

tag: treatment


title: HCT116 shCNT REP A


title: CD4+ T cells, SATB1-Rep2

city: shanghai

first: bao

last: wang

address: jin zun road

institute: shanghai jiao tong university school of medicine

library_source: genomic

data_processing:
Raw data was trimmed by trim_galore. Trimmed sequence reads were aligned to the human referenece genome (GRCH38/hg38) , and sorted using bowtie2 and samtools. Duplicates reads were removed by sambamba.
Bigwig files were created using bamCoverage and normalized to RPKM.
Assembly: hg38
Library strategy: CUT&Tag

source_name: peripheral blood

growth_protocol: RPMI 1640, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin, CD3/CD28 beads and 100 ng/ml IL-2. Cells were cultured at 37C at 5% CO2.

extract_protocol: CUT&Tag experiments was performed using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme, TD901-01).

value: peripheral blood

value: expanded CD4+ T cells

value: SATB1 (Abcam, #ab109122)


title: CD4+ T cells, SATB1-Rep1


title: CD4+ T cells, CTCF-Rep2

value: CTCF (Abcam, #ab128873)


title: HiChIP_VCaP_CTCF_Rep2

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

country: Canada

institute: UNIV HEALTH NETWORK

description: CTCF HiChIP in VCaP cells

data_processing:
Pair-end HiChIP reads were mapped to hg19 human reference genome by Bowtie2 within HiCUP pipeline (v0.7.2). The digested reference genome was created by hiccup using the MboI cutting site. The resulting bam files from HiCUP pipeline were converted into valid fragment pairs by samtools and bedtools. The HiChIP valid pairs and matched ChIP-Seq peaks were then subjected to hichipper pipeline (v0.7.7) to generate bedpe files containing HiChIP loops. In this study, only the filtered intra-chromosome loops were used for downstream analyses.
To identify high confidence HiChIP loops, we considered that the mated PE reads could be located at any possible loop anchor pair by a binomial distribution and calculated the significance for each loop based on this model.
Assembly: hg19
Supplementary files format and content: The hichipper output .bedpe files contains intrachromosomal looping between anchor loci where loops meet min/max distance requirements.

source_name: VCaP cells

extract_protocol:
HiChIP was performed as previously described with a few modifications. Ten million cells were collected and pelleted and resuspended in 1% formaldehyde for 10 min with rotation at room temperature. The crosslinking was then quenched in 125 mM glycine for 5 min. The cells were washed twice by PBS and then resuspended in 500 μL ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP-40, 1× protease inhibitor) followed by 30 min rotation at 4 °C. Nuclei were pelleted by 2500 rcf centrifugation for 5 min at 4 °C followed by washing once in Hi-C lysis buffer. The pelleted nuclei were resuspended in 100 μL 5% SDS and incubated at 62 °C for 10 minutes. To quench the SDS, 335 μL 1.5% Triton X-100 was then added and the mixture was incubated at 37 °C for 15 minutes. The chromatin was digested by adding 50 μL NEB buffer 2 and 375 U MboI restriction enzyme (NEB, R0147) and incubating at 37 °C for 20 minutes. MboI restriction enzyme was then inactivated by 62 °C incubation for 10 minutes. The fill-in master mix (1.5 μL of 10 mM dTTP, 1.5 μL of 10 mM dCTP, 1.5 μL of 10 mM dGTP, 37.5 μL of 0.4 mM biotin-dATP, 10 μL of 5U/μL DNA Polymerase I (NEB, M0210) was added and the tube was incubated at 37 °C for 1 hours with rotation. The ligation mix, containing 10 μL 400 U/μL T4 DNA Ligase (NEB, M0202), 150 μL 10X NEB T4 DNA ligase buffer with 10 mM ATP (NEB, B0202), 125 μL 10% Triton X-100, 3 μL 50 mg/mL BSA, 660 μL H2O, was added and the tube was incubated at room temperature for 4 hours with rotation. The nuclei was pelleted and then resuspended in 880 μL nuclear lysis buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS, 1× protease inhibitor). Nuclei was sonicated in a water bath sonicator (Diagenode bioruptor) to generate chromatin fragments at 300~800 bp. Immunoprecipitation was performed by adding protein A beads and appropriate antibodies  to sheared chromatin before incubation at 4 °C overnight with rotation. The ChIPed DNA was eluted from beads by 200 μL ChIP elution buffer (50 mM NaHCO3, 1% SDS) and purified by Zymo DNA Clean & Concentrator kit.
The biotin-labelled DNA was captured by streptavidin C1 beads (Invitrogen, 65001) and subjected to tagmentation using 2.5 μL Tn5 (Illumina) for 50 ng DNA. The HiChIP DNA was amplified by ~8 cycles using primers containing Illumina sequencing linkers. Each HiChIP library was sequenced by an Illumina NovaSeq system to generate ~150 million 2 ×150 bp paired-end reads.
HiChIP (PE 150)

treatment_protocol: No treatment

value: VCaP cells

tag: antibody for_ip

value: anti-CTCF, 3418S, CST


title: HiChIP_22RV1_CTCF_Rep2

description: CTCF HiChIP in 22Rv1 cells

source_name: 22Rv1 cells

value: 22Rv1 cells


title: HiChIP_22RV1_CTCF_Rep1

description: CTCF HiChIP in 22Rv1 cells


title: HiChIP_VCaP_CTCF_Rep1

description: CTCF HiChIP in VCaP cells


title: U3 NAT10-si acIP Rep2

description: UM-UC-3_NAT10-si_Rep RIP PEAK


title: CD70_NC_PBMC

city: Hong Kong

first: Xin-Yuan

last: Guan

address: L10-56, Laboratory Block, LKS Faculty of Medicine

department: Clinical Oncology

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Cell Ranger (version 6.0)
The single-cell suspension was converted to uniquely barcoded RNA libraries by using the Chromium Single Cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics), per manufacturer’s instructions. The libraries were sequenced on a Novaseq 6000, and mapped to the human genome (hg38) using CellRanger (version 6.0, 10x Genomics). Gene positions were annotated as per Ensembl build 85 and filtered for biotype (only protein-coding, long intergenic non-coding RNA, antisense and immunoglobulin).
The raw gene expression matrix generated from each sample were aggregated using CellRanger (version 6.0).
Assembly: hg38
Supplementary files format and content: feature_bc_matrix.h5; The file contains information about cell-unique barcodes and features

source_name: Peripheral blood mononuclear cells

extract_protocol:
Chromium Single Cell 3' Reagent Kits
The libraries were constructed using the following kits: Chromium Single Cell 3’ Library & Gel Bead Kit, as per manufacturer’s instructions

value: Peripheral blood mononuclear cells

tag: sample type

value: Primary

value: co-culture with CD70-NC-C666 cells


title: Matrin_3_CUT&Tag_Rep_1

data_processing:
Raw data was trimmed by trim_galore. Trimmed sequence reads were aligned to the human referenece genome (GRCH38/hg38) , and sorted using bowtie2 and samtools. Duplicates reads were removed by sambamba.
Bigwig files were created using bamCoverage and normalized to RPKM.
SEACR were used to call peaks. Thresholds of calling peaks using SEACR were set as 0.01
Assembly: hg38
Supplementary files format and content: bw files contain CUT&Tag signal for each replicate.
Supplementary files format and content: peaks files contain CUT&Tag peaks for each replicate.
Library strategy: CUT&Tag

source_name: Jurkat

growth_protocol: Jurkat cells were cultured in RPMI 1640 medium (Gibco) with addition of 10% FBS (Sigma), 1% GlutaMAX (Gibco), 1% Sodium Pyruvate (Gibco) and anti-bacteria-mycoplasmas-fungi solution (InvivoGen, Primocin).

extract_protocol:
CUT&Tag experiments was performed using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme, TD901-01).
Cells were incubated with pG-Tn5 and DNA were digested 1 h at 37 ℃. Sample DNA was extracted by phenol-chloroform-isoamyl alcohol and amplified by PCR followed by sequencing.

value: Jurkat


title: NPC_patient_2

description: Visium Spatial Transcriptome Sequencing on Fresh Frozen Tissues

data_processing:
Spatial Ranger (v 1.3.1)
The processed gene-voxel matrices contained spatial information of 1,089 (patient 1) and 1,331 (patient 2) spots and were further analyzed in Seurat (v 4.0). The spatial sequencing data were normalized, dimensionally reduced and clustered by Seurat (v 4.0).
Assembly: hg38
Supplementary files format and content: filtered_feature_bc_matrix.h5; The file contains information about cell-unique barcodes and features

source_name: Nasopharyngeal carcinoma tissue

extract_protocol:
Visium Spatial Gene Expression Slide & Reagents Kit
The frozen tissues were placed onto Visium spatial gene expression slide (10× Genomics), fixed and permeabilized to release RNA which bond to adjacent capture probes. Next, RNA reverse transcription, cDNA synthesis, denaturation and amplification, quality control as well as spatial gene library construction were performed using Visium spatial gene expression reagents kit (10× Genomics). The spatial transcriptome library was sequenced on a NovaSeq 6000 (llumina), and mapped to the human genome (hg38) using Spatial Ranger (v 1.3.1, 10× Genomics).

value: Nasopharyngeal carcinoma tissue


title: CD70_KO_PBMC

value: co-culture with CD70-KO-C666 cells


title: U3 NAT10-si Rep3

description: UM-UC-3 -Rep Control&NAT10-si

value: bladder cancer cell line

value: siRNA targeting NAT10 was transfected in the cell

value: CCAUCUCUCGCAUCUAUUUTT


title: HCT116 shDAB2IP REP C

value: cell line

value: colon cancer


title: Matrin_3_CUT&Tag_Rep_2


title: NPC_patient_1


title: RNASeq_22RV1_Control_2

description: Control 22Rv1 cells

data_processing:
Sequencing reads were aligned to hg19 human genome using STAR (version 2.4.2a) and the raw read count matrix was used for differential gene expression analysis by DESeq2.
Assembly: hg19
Supplementary files format and content: The .txt file contains raw read counts of all RNASeq samples.

growth_protocol: 22Rv1 cells were grown in RPMI-1640 containing 10% FBS (Vivacell, C04001-500); 22Rv1 cells were infected with lenti-viral MYC expression vector or control lenti-viral vector, and selected on puromycin (0.6 ug/ml)

extract_protocol:
Total RNA was extracted using RNeasy MiniKit (74106, Qiagen) following manufacturer’s procedure.
Whole transcriptome sequencing libraries were prepared using TruSeq® Stranded mRNA Library Prep Kit (RS-122-2101, Illumina, San Diego, CA, USA) by following the manufacturer’s instructions.

tag: genotype/variation

value: control


title: RNASeq_22RV1_Control_1

description: Control 22Rv1 cells


title: RNASeq_22RV1_MYC_2

description: 22Rv1 cells with MYC overexpression

value: MYC


title: HICHIP-22RV1-C2-H3K27ac

description: H3K27ac HiChIP in control 22Rv1 cells

data_processing:
Library strategy: HiChIP
Pair-end HiChIP reads were mapped to hg19 human reference genome by Bowtie2 within HiCUP pipeline (v0.7.2). The digested reference genome was created by hiccup using the MboI cutting site. The resulting bam files from HiCUP pipeline were converted into valid fragment pairs by samtools and bedtools. The HiChIP valid pairs and matched ChIP-Seq peaks were then subjected to hichipper pipeline (v0.7.7) to generate bedpe files containing HiChIP loops. In this study, only the filtered intra-chromosome loops were used for downstream analyses.
To identify high confidence HiChIP loops, we considered that the mated PE reads could be located at any possible loop anchor pair by a binomial distribution and calculated the significance for each loop based on this model.
Assembly: hg19
Supplementary files format and content: The hichipper output .bedpe files contains intrachromosomal looping between anchor loci where loops meet min/max distance requirements.

extract_protocol:
HiChIP was performed as previously described with a few modifications. Ten million cells were collected and pelleted and resuspended in 1% formaldehyde for 10 min with rotation at room temperature. The crosslinking was then quenched in 125 mM glycine for 5 min. The cells were washed twice by PBS and then resuspended in 500 μL ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP-40, 1× protease inhibitor) followed by 30 min rotation at 4 °C. Nuclei were pelleted by 2500 rcf centrifugation for 5 min at 4 °C followed by washing once in Hi-C lysis buffer. The pelleted nuclei were resuspended in 100 μL 5% SDS and incubated at 62 °C for 10 minutes. To quench the SDS, 335 μL 1.5% Triton X-100 was then added and the mixture was incubated at 37 °C for 15 minutes. The chromatin was digested by adding 50 μL NEB buffer 2 and 375 U MboI restriction enzyme (NEB, R0147) and incubating at 37 °C for 20 minutes. MboI restriction enzyme was then inactivated by 62 °C incubation for 10 minutes. The fill-in master mix (1.5 μL of 10 mM dTTP, 1.5 μL of 10 mM dCTP, 1.5 μL of 10 mM dGTP, 37.5 μL of 0.4 mM biotin-dATP, 10 μL of 5U/μL DNA Polymerase I (NEB, M0210) was added and the tube was incubated at 37 °C for 1 hours with rotation. The ligation mix, containing 10 μL 400 U/μL T4 DNA Ligase (NEB, M0202), 150 μL 10X NEB T4 DNA ligase buffer with 10 mM ATP (NEB, B0202), 125 μL 10% Triton X-100, 3 μL 50 mg/mL BSA, 660 μL H2O, was added and the tube was incubated at room temperature for 4 hours with rotation. The nuclei was pelleted and then resuspended in 880 μL nuclear lysis buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS, 1× protease inhibitor). Nuclei was sonicated in a water bath sonicator (Diagenode bioruptor) to generate chromatin fragments at 300~800 bp. Immunoprecipitation was performed by adding protein A beads and appropriate antibodies  to sheared chromatin before incubation at 4 °C overnight with rotation. The ChIPed DNA was eluted from beads by 200 μL ChIP elution buffer (50 mM NaHCO3, 1% SDS) and purified by Zymo DNA Clean & Concentrator kit.
The biotin-labelled DNA was captured by streptavidin C1 beads (Invitrogen, 65001) and subjected to tagmentation using 2.5 μL Tn5 (Illumina) for 50 ng DNA. The HiChIP DNA was amplified by ~8 cycles using primers containing Illumina sequencing linkers. Each HiChIP library was sequenced by an Illumina NovaSeq system to generate ~150 million 2 ×150 bp paired-end reads.

tag: antibody for ip

value: anti-H3K27ac, ab4729, Abcam


title: HICHIP-22RV1-M2-H3K27ac

description: H3K27ac HiChIP in 22Rv1 cells with MYC overexpression

value: MYC overexpression


title: HICHIP-22RV1-M1-H3K27ac


title: RNASeq_22RV1_MYC_1

description: 22Rv1 cells with MYC overexpression


title: HICHIP-22RV1-C1-H3K27ac

description: H3K27ac HiChIP in control 22Rv1 cells


title: HICHIP-22RV1-M2-CTCF

description: CTCF HiChIP in 22Rv1 cells with MYC overexpression

value: anti-CTCF, 3418S, CST


title: CD4+ T cells, CTCF-Rep1

value: peripheral blood

value: expanded CD4+ T cells

value: CTCF (Abcam, #ab128873)


title: HICHIP-22RV1-C2-CTCF

description: CTCF HiChIP in control 22Rv1 cells


title: HICHIP-22RV1-M1-CTCF


title: HICHIP-22RV1-C1-CTCF

description: CTCF HiChIP in control 22Rv1 cells


title: ChIP-MYC-MYC2

description: MYC ChIPSeq in 22Rv1 cells with MYC overexpression

data_processing:
ChIP-Seq reads were aligned to hg19 human genome by Bowtie2 (version 2.2.1). The bam files were then subjected to MACS2 for peak calling with the parameter “--SPMR” on and --keep-dup=1. Significant peaks were identified by q-value < 0.05. UCSC bedGraphToBigWig tool was used to convert Resultant bedgraph files to bigWig files, which were then used for peak shape visualization in IGV (version 2.8.2) and heatmap analysis by deeptools (version 3.3.1).
Assembly: hg19
Supplementary files format and content: The bw files contain normalized ChIP-Seq signal in the whole genome. The IP signal was normalized to corresponding input.

extract_protocol:
ChIP experiment was performed as previously described. Briefly, cell crosslinking was conducted in 1% formaldehyde for 10 minutes and quenched by glycine. Cell nuclear fraction was extracted by LB1 buffer (50 mM Hepes–KOH, pH 7.5; 1 mM EDTA; 140 mM NaCl; 10% Glycerol; Igepal CA-630; 0.25% Triton X-100) followed by washing in LB2 (10 mM Tris–HCL,pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA) and LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine). Chromatin was sheared to 300-500 bp by Diagenode’s bioruptor sonicator and then incubated with antibody-conjugated protein A and G beads for overnight at 4°C with rotation. After washing in RIPA buffer (50 mM Tris, pH 7.6, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% Igepal CA630, 0.5% sodium deoxycholate, Protease inhibitor and RNase inhibitor), the beads were eluted in elution buffer (0.1M NaHCO3, 1% SDS and Proteinase K) for 8~16 hours at 65°C. ChIPed DNA was purified by phenol–chloroform extraction and then used for ChIP-qPCR or ChIP-Seq library preparation.
ThruPLEX DNA-Seq kit

value: anti-MYC, ab32072, Abcam


title: ChIP-MYC-Con2

description: MYC ChIPSeq in control 22Rv1 cells


title: ChIP-MYC-MYC1


title: ChIP-MYC-Con1

description: MYC ChIPSeq in control 22Rv1 cells


title: ChIP-Input-MYC1

description: ChIPSeq input in 22Rv1 cells with MYC overexpression


title: ChIP-Input-MYC2


title: ChIP-Input-Con1

description: ChIPSeq input in control 22Rv1 cells


title: ChIP-Input-Con2

description: ChIPSeq input in control 22Rv1 cells


title: ChIP-H3K27ac-MYC1

description: H3K27ac ChIPSeq in 22Rv1 cells with MYC overexpression


title: ChIP-H3K27ac-Con2

description: H3K27ac ChIPSeq in control 22Rv1 cells


title: ChIP-CTCF-MYC2

description: CTCF ChIPSeq in 22Rv1 cells with MYC overexpression


title: ChIP-H3K27ac-MYC2


title: ChIP-H3K27ac-Con1

description: H3K27ac ChIPSeq in control 22Rv1 cells


title: ChIP-CTCF-Con2

description: CTCF ChIPSeq in control 22Rv1 cells


title: ChIP-CTCF-MYC1


title: ChIP-CTCF-Con1

description: CTCF ChIPSeq in control 22Rv1 cells


title: shSATB1, RNA-seq, rep 3

data_processing:
Sequenced reads were trimmed for adaptor sequence using trim_galore with the default parameters,then mapped to hg38 whole genome using STAR.
After align to the hg38 genome, counts file was created by htseq-count with parameters -m union -s no.
Assembly: hg38
Supplementary files format and content: counts

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Jurkat

value: SATB1 knockdown


title: shCtrl, RNA-seq, rep 2

value: shCtrl


title: shSATB1, Jurkat, CTCF, CUT_Tag, Rep 3

data_processing:
Library strategy: CUT&Tag
Raw data was trimmed by trim_galore. Trimmed sequence reads were aligned to the human referenece genome (GRCH38/hg38) , and sorted using bowtie2 and samtools. Duplicates reads were removed by sambamba.
Bigwig files were created using bamCoverage and normalized to RPKM.
MACS2 and SEACR were used to call peaks. Thresholds of calling peaks using SEACR were set as 0.01 and 0.007 for CTCF and SATB1 respectively.
Assembly: hg38
Supplementary files format and content: bw files contain CUT_Tag signal for each replicate.
Supplementary files format and content: peaks files contain CUT_Tag peaks for each replicate.

extract_protocol:
CUT_Tag experiments was performed using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme, TD901-01).
Cells were incubated with pG-Tn5 and DNA were digested 1 h at 37 ℃. Sample DNA was extracted by phenol-chloroform-isoamyl alcohol and amplified by PCR followed by sequencing.

treatment_protocol: Jurkat cells were seeded into a 6-well plate, and Hitrans G A Lentivirus Transduction Reagent (Shanghai GeneChem, REVG004) was used to enhanced the shRNA lentivirus infection.


title: shCtrl, RNA-seq, rep 1


title: shSATB1, RNA-seq, rep 2


title: shCtrl, Jurkat, CTCF, CUT_Tag, Rep 3


title: shSATB1, RNA-seq, rep 1


title: shCtrl, RNA-seq, rep 3


title: shSATB1, Jurkat, H3K27Ac, CUT_Tag, Rep 2


title: shCtrl, Jurkat, CTCF, CUT_Tag, Rep 1


title: shCtrl, Jurkat, H3K27Ac, CUT_Tag, Rep 1


title: shSATB1, Jurkat, CTCF, CUT_Tag, Rep 1


title: shCtrl, Jurkat, H3K27Ac, CUT_Tag, Rep 2


title: shCtrl, Jurkat, CTCF, CUT_Tag, Rep 2


title: shSATB1, Jurkat, Hi-C, All Replicates, Merged

data_processing:
Sequenced reads were trimmed for adaptor sequence, then created cool file using Hicexplorer
Assembly: hg38
Supplementary files format and content: cool

extract_protocol: Hi-C experiments was perfomed according to Hi-C 2.0


title: shCtrl, Jurkat, SATB1, CUT_Tag, Rep 2


title: shCtrl, Jurkat, SATB1, CUT_Tag, Rep 1


title: shCtrl, Jurkat, Hi-C, All Replicates, Merged


title: TADA2B_1_unstimulated_rep2_24hr

city: Cambridge

first: Paul

last: Blainey

address: 415 Main Street

institute: Broad Institute

data_processing:
Samples were demultiplexed with bcl2fastq v2.20 to generate fastq files.
Transcript counts were quantified using the command "kallisto quant" with default parameters and human reference hg19.annot.cdna and Sendai genome AB856846.1 (kallisto v0.45.0).
Genome_build: hg19
Supplementary_files_format_and_content: Transcript counts determined by kallisto are stored in a tab-delimited table with one row per transcript feature.

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum and 100U/mL penicillin/streptomycin

extract_protocol: Cells were washed once with PBS and lysed in 1X TCL buffer (Qiagen, supplemented with 1% beta-mercaptoethanol). Smart-seq2 was performed as described (Trombetta et al., 2014).

treatment_protocol: Virus or hpRNA/Lyovec were added to culture medium

value: HeLa

value: TADA2B sgRNA1

tag: stimulation

value: Unstimulated

tag: stimulation time


title: shCtrl, Jurkat, Hi-C, Rep 1


title: TADA2B_1_unstimulated_rep3_24hr


title: TADA2B_1_unstimulated_rep1_24hr


title: shCtrl, Jurkat, Hi-C, Rep 2


title: shSATB1, Jurkat, Hi-C, Rep 1


title: TADA2B_1_SeV_rep3_6hr

value: SeV


title: TADA2B_1_SeV_rep3_15hr


title: shSATB1, Jurkat, CTCF, CUT_Tag, Rep 2


title: shSATB1, Jurkat, H3K27Ac, CUT_Tag, Rep 1


title: TADA2B_1_SeV_rep2_15hr


title: TADA2B_1_SeV_rep2_6hr


title: TADA2B_1_SeV_rep1_6hr


title: TADA2B_1_SeV_rep1_15hr


title: TADA2B_1_hpRNA_rep3_24hr

value: hpRNA


title: TADA2B_0_SeV_rep3_6hr

value: TADA2B sgRNA0


title: TADA2B_0_SeV_rep2_6hr


title: TADA2B_1_hpRNA_rep2_24hr


title: TADA2B_0_SeV_rep2_15hr


title: TADA2B_0_unstimulated_rep3_24hr


title: TADA2B_1_hpRNA_rep1_24hr


title: TADA2B_0_unstimulated_rep2_24hr


title: TADA2B_0_hpRNA_rep2_24hr


title: TADA2B_0_SeV_rep3_15hr


title: TADA2B_0_unstimulated_rep1_24hr


title: TADA2B_0_hpRNA_rep3_24hr


title: shSATB1, Jurkat, Hi-C, Rep 2


title: nontargeting_1_unstimulated_rep2_24hr

value: NT sgRNA1


title: TADA2B_0_hpRNA_rep1_24hr


title: nontargeting_1_SeV_rep3_6hr


title: nontargeting_1_unstimulated_rep4_24hr


title: nontargeting_1_unstimulated_rep3_24hr


title: nontargeting_1_SeV_rep4_6hr


title: nontargeting_1_SeV_rep4_15hr


title: nontargeting_1_unstimulated_rep1_24hr


title: nontargeting_1_SeV_rep1_15hr


title: nontargeting_1_SeV_rep3_15hr


title: nontargeting_1_SeV_rep1_6hr


title: nontargeting_1_SeV_rep2_6hr


title: TADA2B_0_SeV_rep1_15hr


title: nontargeting_1_hpRNA_rep4_24hr


title: TADA2B_0_SeV_rep1_6hr


title: R5, resistant lung tumor cell line

city: Madrid

first: Ruth

last: Álvarez-Díaz

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

institute: Spanish National Cancer Research Center (CNIO)

description: MSH204T3 CLON 2

data_processing:
Nextpresso v1.9.2.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using bbduk
Trimmed sequence reads were mapped to GRCm38 using tophat-2.0.10
Read count extraction and normalization were performed using HTSeq-count and DESeq2
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample

source_name: lung tumor cell line

extract_protocol:
Total RNA extraction was performed using the RNeasy Mini Kit (Qiagen). 1 ug of total RNA was used for library construction.
Library construction was performed with the TruSeq Stranded mRNA Sample Prep Kit (Illumina) and subsequently sequenced on an Illumina instrument according to manufacturer's protocols

value: lung tumor cell line


title: R2, resistant lung tumor cell line

description: MSH204T1 CLON 2


title: nontargeting_1_SeV_rep2_15hr


title: nontargeting_1_hpRNA_rep2_24hr


title: R1, resistant lung tumor cell line

description: MSH204T1 CLON 1


title: nontargeting_1_hpRNA_rep1_24hr


title: MED24_1_unstimulated_rep3_24hr

value: MED24 sgRNA1


title: MED24_1_SeV_rep3_6hr


title: MED24_1_unstimulated_rep2_24hr


title: P3, parental lung tumor cell line, control

value: Kras (+/loxG12Vlox);Trp53(-/-)


title: MED24_1_SeV_rep3_15hr


title: MED24_1_SeV_rep2_6hr


title: MED24_1_SeV_rep2_15hr


title: MED24_1_SeV_rep1_6hr


title: R-T8, lung tumor, sotorasib-resistant

description: MKI301T1, batch 2

data_processing:
Nextpresso v1.9.2.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using bbduk
Trimmed sequence reads were mapped to GRCm38 using tophat-2.0.10
Read count extraction was performed using HTSeq-count
Batch correction was performed using ComBat-seq
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: lung

extract_protocol:
Total RNA extraction was performed using the RNeasy Mini Kit (Qiagen). 1 ug of total RNA was used for library construction.
Library construction was performed with the QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen, Cat.No. 015) and subsequently sequenced on an Illumina instrument according to manufacturer's protocols

value: lung

value: Kras-G12C, Trp53-KO

value: sotorasib


title: R-T6, lung tumor, sotorasib-resistant

description: MBE677T1, batch 1


title: R-T5, lung tumor, sotorasib-resistant

description: MBE674T1, batch 2


title: MED24_1_SeV_rep1_15hr


title: nontargeting_1_hpRNA_rep3_24hr


title: R-T7, lung tumor, sotorasib-resistant

description: MBE677T2, batch 2


title: MED24_1_hpRNA_rep3_24hr


title: R-T2, lung tumor, sotorasib-resistant

description: MBE362T2, batch 1


title: R-T3, lung tumor, sotorasib-resistant

description: MBE366T1, batch 2


title: C-T8, lung tumor, control

description: MBE155T6, batch 1

value: control


title: P5, parental lung tumor cell line, control


title: MED24_0_unstimulated_rep3_24hr

value: MED24 sgRNA0


title: R-T4, lung tumor, sotorasib-resistant

description: MBE397T2, batch 1


title: MED24_0_unstimulated_rep2_24hr


title: P4, parental lung tumor cell line, control


title: R-T1, lung tumor, sotorasib-resistant

description: MBE357T1, batch 1


title: C-T5, lung tumor, control

description: MBE218T1, batch 2


title: C-T6, lung tumor, control

description: MBE266T2, batch 2


title: C-T4, lung tumor, control

description: MBE189T1, batch 1


title: MED24_0_SeV_rep3_6hr


title: C-T3, lung tumor, control

description: MBE168T1, batch 2


title: MED24_1_hpRNA_rep1_24hr


title: C-T7, lung tumor, control

description: MBE167T6, batch 1


title: Root, no Pi, 3

city: Sutton Bonington

first: Alexander

middle: George

last: Ware

state: Leicestershire

address: Sutton Bonington Campus

institute: University of Nottingham

data_processing:
Raw reads (.fastq) were processed using Perl. Clean reads were obtained by removing reads containing adapters and poly-N.
An index was built (Spirodela polyrhiza (oxford_v3)) using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5 (Kim et al., 2019).
FeatureCounts v1.5.0-p3 was used to count reads mapping to each gene. FPKM was calculated.
Assembly: Spirodela polyrhiza 9509 (oxford_V3; CoGe ID: id51364)
Supplementary files format and content: Excel table of FPKM counts.

organism: Spirodela polyrhiza

source_name: Root

growth_protocol: Spirodela polyrhiza 9509 was seeded into 250ml flasks containing 100 ml N-Media. Media was removed and replaced at day 10. Plants from each flask were harvested on day 11, separated into fronds and roots, pooled and snap frozen, representing a biological replicate (4 total per tissue type).

extract_protocol:
Tissues were ground in liquid nitrogen and RNA was extracted using TRIZOL followed by binding and washing with Qiagen RNeasy columns
RNA integrity was assessed using the RNA Nano 6000 Assay Kit on a Bioanalyzer 2100 (Agilent Technologies, CA, USA). Total RNA was used as input. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, adaptors with hairpin loop structure were ligated to prepare for hybridization. In order to preferentially select cDNA fragments of 370~420 bp in length, library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to manufacturer’s instructions. After cluster generation, library preparations were sequenced on an Illumina Novaseq platform generating 150 bp paired-end reads

treatment_protocol: For the -Pi experiment, replaced media did not contain KH2PO4

value: Root

value: No phosphate


title: C-T2, lung tumor, control

description: MBE167T5, batch 2


title: Root, no Pi, 2


title: MED24_0_SeV_rep2_15hr

value: HeLa


title: MED24_0_SeV_rep3_15hr


title: MED24_0_SeV_rep1_6hr


title: C-T1, lung tumor, control

description: MBE167T1, batch 2


title: MED24_0_SeV_rep2_6hr


title: Root, no Pi, 1


title: MED24_0_unstimulated_rep1_24hr


title: Root, control, 4

value: Control


title: Root, no Pi, 4


title: Root, control, 3


title: MED24_0_SeV_rep1_15hr


title: CDNRM DNA-seq

city: Saint Louis

first: Michael

middle: Aaron

last: White

state: MO

address: 660 South Euclid Ave

department: Genetics

institute: Washington University in St. Louis School of Medicine

description: DNA-seq on reporter gene barcode amplicons from plasmid DNA library

library_source: other

data_processing:
All raw reads were processed regardless of quality score. Reads with the expected in-line multiplexing barcode for each sample followed by the spacer sequence were identified using custom python scripts.
Demultiplexed reads were used to determine the read counts for each barcode. Read counts for each barcode were normalized by total reads in the sample (counts per million, cmp) and then dividing by the normlized DNA read counts to generate the activity scores, which are reported as log2 scores in the supplemental file. Data processing was performed using custom python scripts.
Assembly: mm10
Supplementary files format and content: Processed data are in the tab-delimited file cdnrm_mpra_library.txt. Column 1: synthetic cis-regulatory element name. Column 2: log2 activity scores (RNA/DNA)
Library strategy: Amplicon-seq

molecule: other

organism: synthetic construct

source_name: plasmid pool from E. coli DH5alpha

growth_protocol: P0 mouse retinal explants were electroporated with plasmid library and cultured ex vivo for 8 days.

extract_protocol:
RNA was extracted from retinas with TRIzol and treated with Turbo Dnase. cDNA was prepared using SuperScript III.
Sequence barcodes from reporter genes were amplified by PCR and purified with Monarch PCR cleanup kit. Custom Illumina adapters were added by PCR.


title: MED24_0_hpRNA_rep3_24hr


title: MED24_0_hpRNA_rep2_24hr


title: Root, control, 1


title: Root, control, 2


title: Liver, H3

first: Hancheng

last: Qin

address: No.600 Tianhe Road

department: Department of Endocrinology and Metabolism

institute: the Third Affiliated Hospital of Sun Yat-sen University

description: Seven-week-old male C57BL/6 mice with a high fat diet for 16 weeks.

data_processing:
Quality trimmed reads were mapped onto the mouse genome (mm10) by HISAT2, and gene expression in terms of fragments per kilobase of transcript per million (FPKM) mapped reads of genes overlapping with gene annotations in Ensembl release 96 was calculated using RSEM (v1.1.17).
RNAs differential expression analysis was performed using edgeR (v 3.14.0) software between two different groups (n= 4). Genes with a false discovery rate < 0.05 and absolute fold change≥ 2 were considered differentially expressed genes.
Assembly: mm10
Supplementary files format and content: Processed data files include gene expression for each sample.

source_name: Liver, H

extract_protocol:
RNeasy Plus Mini kit (QIAGEN, Hilden, Germany)
the NEBNext ultra RNA Library Prep Kit (New England Biolabs, Beijing, China)

treatment_protocol: Seven-week-old male C57BL/6 mice were purchased from GemPharmatech (Nanjing, China). After an acclimation period of one week, the mice were randomly divided into chow diet (N), high fat diet (H), HC (a high fat diet or chow diet sequentially at 2-week intervals for 16 weeks.), and HK (a high fat diet or ketogenic diet sequentially at 2-week intervals for 16 weeks.) groups (n = 6/group).

tag: strain

tag: Sex

value: male

value: Seven-weeks-old

tag: diet

value: high fat diet for 16 weeks

value: Liver


title: Liver, H4

tag: age


title: Liver, N1

description: Seven-week-old male C57BL/6 mice with a chow diet for 16 weeks.

source_name: Liver, N

value: chow diet for 16 weeks


title: Liver, HC4

description: Seven-week-old male C57BL/6 mice with a high fat diet or chow diet sequentially at 2-week intervals for 16 weeks.

source_name: Liver, HC


title: Liver, N4


title: Liver, H1


title: Liver, N2


title: Liver, HC3

value: high fat diet or chow diet sequentially at 2-week intervals for 16 weeks


title: Liver, H2


title: Liver, N3


title: Liver, HC2


title: MED16_1_unstimulated_rep3_24hr

tag: cell line

value: MED16 sgRNA1

value: Unstimulated


title: Liver, HC1


title: Liver, HK4

description: Seven-week-old male C57BL/6 mice with a high fat diet or ketogenic diet sequentially at 2-week intervals for 16 weeks.

source_name: Liver, HK


title: MED16_1_unstimulated_rep2_24hr


title: Liver, HK3

value: high fat diet or ketogenic diet sequentially at 2-week intervals for 16 weeks


title: Frond, no Pi, 3

source_name: Frond

value: Frond


title: Liver, HK2


title: MED16_1_unstimulated_rep1_24hr


title: Liver, HK1


title: Frond, no Pi, 1


title: MED24_0_hpRNA_rep1_24hr

value: hpRNA


title: Renal tubule, cKO genotype, ZT20, rep 5

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

country: Switzerland

institute: Swiss Institute of Bioinformatics

description:
12
12_ZT20_KO6_rep5

data_processing:
Sequencing data were demultiplexed, filtered for failed reads, and written to FASTQ files using the bcl2fastq2 conversion software (version 2.20, Illumina).
Adapter sequences were removed from reads and low-quality sequences trimmed off with Cutadapt (v. 1.8).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065).
Reads were aligned against Mus musculus.GRCm38.98 genome using STAR (v. 2.5.3a).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1) using Mus musculus.GRCm38.98 gene annotation.
Assembly: Mus musculus GRCm38.98
Supplementary files format and content: *.txt: Read counts for all annotated genes.

source_name: Renal tubule

growth_protocol: All experiments were performed on male mice housed under 12-hours light/12-hours dark cycles with ad libitum access to drinking water and a standard laboratory chow diet (KLIBA NAFAG diet 3800). A Bmal1lox/lox/Pax8-rtTA/LC-1 Cre mouse strain was bred on the genetic background of the C57BL/6J mouse from The Jackson Laboratory. Eight weeks old Bmal1lox/lox/Pax8-rtTA/LC1 mice (referred as cKOt mice) and their Bmal1lox/lox littermates (referred as CTRL or control mice) were treated for 2 weeks with Doxycycline (DOX; 2 mg/ml in drinking water along with 20mg/ml sucrose) to induce the Cre recombinase inactivation of the Bmal1 (Arntl) gene.

extract_protocol:
RNA from renal tubules of 60 mice was directly extracted using RNeasy MiniElute Spin Column (Qiagen).
RNA-seq libraries were prepared from 200 ng of total RNA with the Illumina TruSeq Stranded mRNA reagents (Illumina) using a unique dual indexing strategy. Cluster generation was performed with 2 nM of an equimolar pool from the resulting libraries using the Illumina HiSeq 3000/4000 SR Cluster Kit reagents.

value: Renal tubule

value: Conditional knockout of Arntl (Bmal1)

value: Male

tag: zeitgeber time


title: Renal tubule, cKO genotype, ZT20, rep 4

description:
44
44_ZT20_KO5_rep4


title: Frond, no Pi, 4

value: No phosphate


title: Frond, control, 4


title: Renal tubule, cKO genotype, ZT20, rep 3

description:
24
24_ZT20_KO4_rep3


title: Renal tubule, cKO genotype, ZT20, rep 2

description:
71
71_ZT20_KO3_rep2


title: Renal tubule, cKO genotype, ZT16, rep 4

description:
47
47_ZT16_KO5_rep4


title: Renal tubule, cKO genotype, ZT20, rep 1

description:
36
36_ZT20_KO2_rep1


title: Frond, no Pi, 2


title: Frond, control, 2


title: Renal tubule, cKO genotype, ZT16, rep 5

description:
11
11_ZT16_KO6_rep5


title: Frond, control, 3


title: MED16_1_SeV_rep2_6hr

value: HeLa

value: SeV


title: Frond, control, 1

value: Control


title: Renal tubule, cKO genotype, ZT16, rep 2

description:
22
22_ZT16_KO3_rep2


title: MED16_1_SeV_rep2_15hr


title: Renal tubule, cKO genotype, ZT16, rep 1

description:
10
10_ZT16_KO1_rep1


title: MED16_1_SeV_rep1_6hr


title: Renal tubule, cKO genotype, ZT12, rep 5

description:
56
56_ZT12_KO6_rep5


title: MED16_1_SeV_rep1_15hr


title: MED16_1_SeV_rep3_6hr


title: Renal tubule, cKO genotype, ZT12, rep 3

description:
38
38_ZT12_KO3_rep3


title: sciPlexATAC2_A549_NIH3T3

city: Seattle

first: Gregory

middle: Thomas

last: Booth

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

data_processing:
The sequence processing strategy used here for sciATAC reads was based on procedures established for sciATAC-seq2 and sciATAC-seq3, and is described in previous publications (Cusanovich et al. Cell, 2018; Domcke et al. science 2020) as well as in our manuscript. each of the four barcodes associated with each read pair, together comprising a cell ID, was required to be within an edit distance of 2 from expected barcode sequences. Valid barcodes were corrected for any errors and read pairs were trimmed with Trimmomatic-0.36 to remove adapter sequences. Trimmed reads were then aligned to either a hybrid human/mouse (GRCh38/mm9) genome (for species mixed samples) or the human (GRCh38) genome alone using bowtie2 (Langmead and Salzberg, 2012) with options “-X 2000 -3 1”.  Properly aligned read pairs with a quality score of at least 10 were retained for downstream analysis using samtools with options “-f3 -F12 -q10”.
Bam files containing aligned barcoded chromatin fragments were processed into Arrow files using the ArchR (version 0.9.5) package (Granja et al., 2020) with the following arguments; filterFrags = 500 and filterTSS = 3 (Note that tNhe "fragments" files included with the processed data can also be used to create Arrow files for downstream analysis using ArchR). Likely-doublets were then identified based on chromatin profiles using a modified version of the scrublet algorithm, which has been described in detail previously (Domcke et al., 2020). Cells were also filtered to remove those with low hashing quality as described in the manuscript.
Sequenced nuclear barcode (hash) reads were processed either from separately sequenced hash libraries (sciPlex-ATAC-seq2), or the trimmed fastq files containing both ATAC and hash sequencing reads (sciPlex-ATAC-seq3), bonafide hash labels were retrieved for sample assignment if the first 10nt of read 2 were an exact match to one of the hash indices employed for a given experiment.  Hash reads were then grouped by their cell barcodes and collapsed based on UMIs within read 1.  Ultimately we obtain a vector of hash oligo UMI counts hi for each nucleus i in the experiment.
Genome_build: GRCh38 and mm9
Supplementary_files_format_and_content: Feature-by-cell (5KB windows, Peak, GeneScore) and peak-by-motif files are in matrix market exchange format and the cell (columns) and feature annotation (row) files that accompany these files are in tsv file format. Peak-by-cell,  gene score-by-cell, and peak-by-motif matrices were generated using ArchR (0.9.5), while the 5kb window matrices are output by our pipeline.  HashTable.out files are in tsv file format, where the columns represent: "experiment", "cell barcode", "hash Well", "axis", "UMIs".  The "hashCellAssignments" files are generated from the hashTable.out files and are in tsv file format with column headers describing the processed hash properties and assignments for each cell. "Fragments" files are included for the chemical screen and MLR experiments and contain tsv formated list of aligned fragments where columns represent: "chromosome", "frag_start", "frag_end", "cell_barcode", "count".  "Peak_cds" and "GeneScore_cds" files contain cds objects created using Monocle3 and formated as R data sets (RDS).  "Peakset" files are tsv formatted and included for the chemical screen and MLR experiments and describe non-overlaping 500bp sites of chromatin accessiblity identified using ArchR (0.9.5). "cellMetaData" files are tsv formated and included from the chemical screen and MLR experiments.  "cellMetaData" files describe all relevant information about the final cell sets used in each experiment, including quality metrics, hash assignments, celltype annotations, etc.

organism:
Homo sapiens
Mus musculus

source_name: A549 and NIH3T3 cells

growth_protocol: cell lines were cultured in RPMI supplemented with 10% FBS and 1% penn-strep.

extract_protocol:
For all experiments, cells were harvested following the sciPlex-ATAC-seq protocol as described in the methods section of our manuscript. Nuclei were isolated in-well and barcoded by fixation of well-specific barcode containing oligonucleotides. After fixation wells were pooled and nuclei pellets flash frozen until sciPlex-ATAC-seq library preparation.
Nucle were subjected to two- or three-level sciPlex-ATAC-seq following the protocols described in detail in the methods section of our manuscript. Briefly: Two-level library construction: To capture poly-adenylated hash molecules within the context of sciATAC-seq, we modified the original sciATAC-seq protocol (Cusanovich et al., Science, 2015), to include an indexed primer extension step. The indexed extension of the hash molecules is followed by indexed transposition within the reaction same well, creating a known pairing between well barcodes of hash and tagmented genomic DNA (gDNA). By design, extended hash molecules and tagmented gDNA possess nextera P5 and P7 PCR handles. After tagmentaiton, nuclei are pooled, stained with DAPI, and flow-sorted into 96 well plates for crosslink reversal and PCR. Amplification with indexed PCR primers adds an additional level of barcoding to both hash labels and accessible chromatin fragments. This protocol leverages unique combinations of well barcodes on hash and chromatin fragments to pair single cell chromatin profiles with their corresponding hash identifiers. Three-level library construction:  Accessible chromatin within all nuclei is tagmented using a single commercially-available transposome complex containing universal Nextera adaptors. Two separate splinted ligation reactions are then used to sequentially add well-specific barcodes separately to each side of the transposed DNA fragments, followed by a final PCR-based barcode addition (Domcke et. al. Science, 2020). In these three-level experiments, hash oligos bearing the universal Nextera P7 sequence are annealed to a capture oligo possessing the Nextera P5 sequence prior to ligation steps, and thus resemble transposed genomic DNA. Therefore, annealed nuclear labels and chromatin fragments can undergo the exact same indexing reactions as chromatin within each nucleus.

treatment_protocol: Untreated

value: Human lung adenocarcinoma derived epithelial cells (A549) and mouse embryonic fibroblast (NIH3T3) cells.

value: Untreated


title: MED16_1_hpRNA_rep3_24hr


title: Renal tubule, cKO genotype, ZT12, rep 2

description:
20
20_ZT12_KO2_rep2


title: MED16_1_SeV_rep3_15hr


title: Renal tubule, cKO genotype, ZT12, rep 1

description:
32
32_ZT12_KO1_rep1


title: MED16_1_hpRNA_rep2_24hr


title: Renal tubule, cKO genotype, ZT08, rep 5

description:
54
54_ZT08_KO6_rep5


title: Renal tubule, cKO genotype, ZT08, rep 4

description:
18
18_ZT08_KO5_rep4


title: MicF

city: SHERBROOKE

first: Eric

last: Massé

state: Québec

address: 3201, Jean Mignault

department: Biochemistry

institute: University of Sherbrooke

data_processing:
Basecalls performed using MCS Version 2.4.1.3
Reads were aligned to the Escherichia coli K12 genome assembly using Bowtie for Illumina (Galaxy Project)
Read counts were normalized by coverage according to Oshlack et al., 2010
Supplementary_files_format_and_content: tab-delimited text file including normalized reads for each sample and MS2-MicF/MicF ratio

organism: Escherichia coli K-12

source_name: Bacterium

growth_protocol: Cells were harvested in exponential (OD600nm=0.5; 100 mL LB medium) and in stationary phase (OD600nm=1.2; 100 mL LB medium).

extract_protocol:
Cells were resuspended in 3 mL of buffer A and lysed using a French Press (430 psi, four times). Lysate was then cleared by centrifugation. The soluble fraction was subjected to affinity chromatography. The column was prepared by adding 100 µL of amylose resin (New England Biolabs) to Bio-Spin disposable chromatography columns (Bio-Rad). The column was washed with 3 mL of buffer A. Next, 200 pmol of MS2-MPB protein was immobilized on the amylose resin, and the column was washed with 2 mL of buffer A. The cleared lysate was then loaded onto the column, which was washed with 8 mL of buffer A. RNA was eluted from the column with 1 mL of buffer A containing 15 mM maltose. Eluted RNA was extracted with phenol-chloroform, followed by ethanol (3 vol) precipitation of the aqueous phase in the presence of 20 mg of glycogen. RNA samples were treated with TURBO DNA-free (DNase treatment) and precipitated again.
cDNA libraries were prepared with ScriptSeq™ RNA-Seq Library Preparation Kit (Illumina)

treatment_protocol: 0.1% arabinose was added to induce the expression of MS2-MicF/MicF during 10 min. Cells were chilled for 10 min on ice. Cells were then centrifuged, resuspended in 1 mL of buffer A (20 mMTris-HCl at pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT), and centrifuged again.

value: MG1655 rne131 delta-micF

tag: growth phase

value: exponential and stationary phases


title: MS2-MicF


title: Renal tubule, cKO genotype, ZT16, rep 3

description:
34
34_ZT16_KO4_rep3

tag: tissue


title: NDNF_biol rep3

first: cheng

last: wei

address: haike road 230

institute: shanghaitech

data_processing:
High-throughput sequencing of total RNA isolated from lumbar spinal cord was performed on Illumina NovaSeq PE150 system with average length of 150 nucleotides for every read of paired end
Raw data were filtered by Cutadapt to generate clean reads and then mapped to mouse reference genome (mm10) using HISAT2
Counts tables were generated with HTSeq
Transcript levels were normalized using DESeq2 package
Differentially expressed genes were identified using DESeq2 package
Assembly: mm10
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

source_name: Lumbar spinal cord

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen Life Technologies). 0.5 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina).

value: Lumbar spinal cord

value: Intrathecal injection of AAV-NDNF

tag: time

value: Day 104


title: MED16_1_hpRNA_rep1_24hr

tag: genotype

value: MED16 sgRNA1


title: Renal tubule, cKO genotype, ZT08, rep 3

description:
30
30_ZT08_KO4_rep3


title: Renal tubule, cKO genotype, ZT08, rep 2

description:
06
06_ZT08_KO3_rep2


title: NDNF_biol rep2

tag: treatment


title: NDNF_biol rep1


title: Renal tubule, cKO genotype, ZT12, rep 4

description:
68
68_ZT12_KO4_rep4


title: Ctrl_biol rep3

value: Intrathecal injection of AAV-GFP


title: Renal tubule, cKO genotype, ZT08, rep 1

description:
43
43_ZT08_KO2_rep1


title: Renal tubule, cKO genotype, ZT04, rep 2

description:
66
66_ZT04_KO2_rep2


title: Renal tubule, cKO genotype, ZT04, rep 3

description:
04
04_ZT04_KO3_rep3


title: Ctrl_biol rep2


title: Renal tubule, cKO genotype, ZT04, rep 4

description:
52
52_ZT04_KO4_rep4


title: MED16_0_SeV_rep3_6hr

value: MED16 sgRNA0


title: Renal tubule, cKO genotype, ZT04, rep 1

description:
39
39_ZT04_KO1_rep1

value: Renal tubule


title: MED16_0_SeV_rep3_15hr


title: Ctrl_biol rep1


title: Renal tubule, cKO genotype, ZT0, rep 5

description:
14
14_ZT0_KO6_rep5

value: Conditional knockout of Arntl (Bmal1)


title: Renal tubule, cKO genotype, ZT0, rep 4

description:
50
50_ZT0_KO5_rep4

value: Male


title: Renal tubule, cKO genotype, ZT0, rep 2

description:
02
02_ZT0_KO3_rep2


title: Renal tubule, cKO genotype, ZT0, rep 1

description:
37
37_ZT0_KO1_rep1


title: MED16_0_unstimulated_rep3_24hr

value: Unstimulated


title: Renal tubule, cKO genotype, ZT04, rep 5

description:
16
16_ZT04_KO5_rep5


title: Renal tubule, control genotype, ZT20, rep 5

description:
59
59_ZT20_C5_rep5

value: Control Genotype


title: Renal tubule, control genotype, ZT20, rep 4

description:
58
58_ZT20_C4_rep4


title: Renal tubule, control genotype, ZT20, rep 3

description:
35
35_ZT20_C3_rep3


title: GM-Mac_1

city: Seoul

first: Hyunju

last: In

state: Select One...

address: ABMRC #326, 50-1 Yonsei-ro, Seodaemun-gu

department: college of medicine

institute: Yonsei University

description:
73
Expression_Profile_GM-DC_Mac

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using STAR version 2.6.0c with parameter --runThreadN 20 --genomeDir --sjdbGTFfile --twopassMode Basic --outFileNamePrefix --outSAMtype --readFilesIn
Read Count were calculated by using Htseq(htseq-count) version 0.10.0, with parameter -f bam -r name -t exon -i gene_id -m intersection-nonempty -s reverse -o --nonunique none
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 1.3.4d, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: mm10(RefSeq_2017_06_12)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: BM culture with GM-CSF

growth_protocol: After lysing red blood cells, freshly isolated BM cells from murine femurs and tibias were seeded on 24-well tissue culture plate (typically 1-2 x 10^6 cells per wells) in DMEM containing L-glutamine, high glucose, and pyruvate (HyClone, Logan, UT, USA) and 7% fetal calf serum (HyClone) and primocin (InvivoGen, San Diego, CA, USA) supplemented with 1× solutions of non-essential amino acids (HyClone) and antibiotic-antimycotic (HyClone) with GM-CSF or FLT3L.

extract_protocol:
BM culture was harvested by gentle pipetting, purified by FACSorting, and RNA was isolated using MiniBEST Universal RNA Extraction kit (TaKaRa Bio, Shiga, Japan).
RNA libraries were prepared for sequencing using standard SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara) and Illumina protocols

value: bone marrow cells

tag: cell type

value: BM culture with GM-CSF

tag: subset


title: GM-Mac_2

description:
110
Expression_Profile_GM-Mac_110


title: GM-DC_2

description:
98
Expression_Profile_GM-DC_98


title: GM-DC_1

description:
74
Expression_Profile_GM-DC_Mac


title: MED16_0_unstimulated_rep2_24hr

value: HeLa


title: Renal tubule, control genotype, ZT20, rep 1

description:
48
48_ZT20_C1_rep1


title: MED16_0_unstimulated_rep1_24hr


title: MED16_0_SeV_rep1_6hr

value: SeV


title: MED16_0_SeV_rep1_15hr


title: CD115- CX3CR1- CD83+ cDC1

description:
89
Expression_Profile_83+_cDC1

source_name: BM culture with FLT3L

value: BM culture with FLT3L

value: CD115- CX3CR1- CD83+ cDC1


title: MED16_0_hpRNA_rep3_24hr

value: hpRNA


title: Renal tubule, control genotype, ZT16, rep 5

description:
65
65_ZT16_C6_rep5


title: Renal tubule, cKO genotype, ZT0, rep 3

description:
26
26_ZT0_KO4_rep3


title: Renal tubule, control genotype, ZT16, rep 4

description:
33
33_ZT16_C5_rep4


title: Renal tubule, control genotype, ZT16, rep 3

description:
21
21_ZT16_C4_rep3


title: CD115- CX3CR1- CD83- cDC1_2

description:
60
Expression_Profile_83-_cDC1

value: CD115- CX3CR1- CD83- cDC1


title: MED16_0_SeV_rep2_6hr


title: Renal tubule, control genotype, ZT16, rep 1

description:
09
09_ZT16_C1_rep1


title: CD115- CX3CR1- CD83- cDC1_1

description:
53
Expression_Profile_83-_cDC1


title: MED16_0_SeV_rep2_15hr


title: Renal tubule, control genotype, ZT12, rep 5

description:
31
31_ZT12_C6_rep5


title: CD115- CX3CR1- CD83+ cDC2_2

description:
27
Expression_profile_cDC2s

value: CD115- CX3CR1- CD83+ cDC2


title: Renal tubule, control genotype, ZT16, rep 2

description:
61
61_ZT16_C3_rep2


title: Renal tubule, control genotype, ZT12, rep 3

description:
55
55_ZT12_C3_rep3


title: Renal tubule, control genotype, ZT20, rep 2

description:
23
23_ZT20_C2_rep2


title: Renal tubule, control genotype, ZT12, rep 4

description:
64
64_ZT12_C5_rep4


title: MAVS_1_unstimulated_rep3_24hr

value: MAVS sgRNA1


title: MED16_0_hpRNA_rep2_24hr


title: CD115- CX3CR1- CD83- cDC2_1

description:
19
Expression_profile_cDC2s

value: CD115- CX3CR1- CD83- cDC2


title: MAVS_1_unstimulated_rep4_24hr


title: Renal tubule, control genotype, ZT08, rep 4

description:
63
63_ZT08_C5_rep4


title: Renal tubule, control genotype, ZT08, rep 5

description:
17
17_ZT08_C6_rep5


title: Renal tubule, control genotype, ZT12, rep 1

description:
19
19_ZT12_C1_rep1


title: CD115- CX3CR1- CD83+ cDC2_1

description:
20
Expression_profile_cDC2s


title: Renal tubule, control genotype, ZT12, rep 2

description:
41
41_ZT12_C2_rep2


title: CD115- CX3CR1- CD83- cDC2_2

description:
26
Expression_profile_cDC2s


title: MAVS_1_unstimulated_rep2_24hr


title: Renal tubule, control genotype, ZT08, rep 2

description:
05
05_ZT08_C2_rep2


title: Renal tubule, control genotype, ZT08, rep 3

description:
67
67_ZT08_C4_rep3


title: CD115+ CX3CR1+ cDC2_2

description:
30
Expression_profile_cDC2s

value: CD115+ CX3CR1+ cDC2


title: MAVS_1_SeV_rep4_6hr


title: MAVS_1_unstimulated_rep1_24hr


title: Renal tubule, control genotype, ZT08, rep 1

description:
29
29_ZT08_C1_rep1

value: Renal tubule


title: Renal tubule, control genotype, ZT04, rep 4

description:
62
62_ZT04_C5_rep4


title: CD115+ CX3CR1+ cDC2_1

description:
18
Expression_profile_cDC2s


title: MED16_0_hpRNA_rep1_24hr

value: MED16 sgRNA0


title: MAVS_1_SeV_rep4_15hr


title: Renal tubule, control genotype, ZT04, rep 1

description:
51
51_ZT04_C2_rep1

value: Male


title: Naive CD4+ T cells, Satb1_cko_Rep3

data_processing:
The sequencing data were aligned to the mouse reference genome (mm10) using the STAR aligner (version 2.7.3a). All mapped reads were subsequently counted using HTSeq (version 0.12.4).
Assembly: mm10
Supplementary files format and content: counts

source_name: spleens

extract_protocol: RNA-seq libraries were constructed by Anoroad (Beijing, China) using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (NR604-01/02) according to the manufacturer’s instructions.

treatment_protocol: Mice spleen were harvested and CD4+ naive T cells were enriched by magnetic beads followed by RNA-sequencing.

value: spleens

value: Naive CD4+ T cells

value: Satb1 conditional knockout


title: MAVS_1_SeV_rep3_6hr

source_name: HeLa


title: Renal tubule, control genotype, ZT04, rep 2

description:
15
15_ZT04_C3_rep2

value: Control Genotype


title: Renal tubule, control genotype, ZT0, rep 5

description:
01
01_ZT0_C5_rep5


title: Naive CD4+ T cells, Satb1_cko_Rep2


title: MAVS_1_SeV_rep3_15hr

value: HeLa


title: Naive CD4+ T cells, Satb1_cko_Rep1


title: Renal tubule, control genotype, ZT0, rep 1

description:
46
46_ZT0_C1_rep1


title: Arabidopsis root 4

data_processing:
Raw reads (.fastq) were processed using Perl. Clean reads were obtained by removing reads containing adapters and poly-N.
An index for A. thaliana (TAIR10) was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5 (Kim et al., 2019).
FeatureCounts v1.5.0-p3 was used to count reads mapping to each gene. FPKM was calculated.
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: Excel table of FPKM counts.

organism: Arabidopsis thaliana

growth_protocol: Pistia stratiotes was seeded  (1 mature individual per flask) into 500ml flasks and grown for 10 days on 200ml SH-media. Emerging plants with 3-4 leaves were selected for sampling. For the leaf  sample, the largest emerged leaf was harvested from all the plants in a flask, pooled and snap frozen.  For the root sample, roots with the apex and laterals removed were harvested in the same manner.  Pooled tissue from a flask represented a biological replicate (4 total per tissue type).

extract_protocol:
TRIZOL/Qiagen RNEasy
RNA integrity was assessed using the RNA Nano 6000 Assay Kit on a Bioanalyzer 2100 (Agilent Technologies, CA, USA). Total RNA was used as input. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, adaptors with hairpin loop structure were ligated to prepare for hybridization. In order to preferentially select cDNA fragments of 370~420 bp in length, library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to manufacturer’s instructions. After cluster generation, library preparations were sequenced on an Illumina Novaseq platform generating 150 bp paired-end reads

value: Root

value: Tissue type


title: Renal tubule, control genotype, ZT0, rep 4

description:
49
49_ZT0_C4_rep4


title: Renal tubule, control genotype, ZT0, rep 3

description:
13
13_ZT0_C3_rep3


title: MAVS_1_SeV_rep2_6hr

value: SeV


title: Arabidopsis root 2


title: Renal tubule, control genotype, ZT04, rep 5

description:
03
03_ZT04_C6_rep5


title: MAVS_1_SeV_rep2_15hr


title: Arabidopsis shoot 3

source_name: Shoot

value: Shoot


title: Renal tubule, control genotype, ZT04, rep 3

description:
27
27_ZT04_C4_rep3


title: MAVS_1_SeV_rep1_15hr


title: Arabidopsis root 3


title: Renal tubule, control genotype, ZT0, rep 2

description:
25
25_ZT0_C2_rep2


title: Arabidopsis shoot 1


title: Arabidopsis shoot 2


title: Arabidopsis shoot 4


title: MAVS_1_SeV_rep1_6hr


title: MAVS_1_hpRNA_rep4_24hr

value: hpRNA


title: Brain, Phe31KO, repB

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

data_processing:
Sequenced reads were trimmed with Trim Galore 42 (0.6.4_dev) using cutadapt 43 (1.18) (with parameters: --paired --fastqc --illumina, corresponding to cutadapt parameters: -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA).
Trimmed reads were aligned to the mouse genome downloaded from GENCODE (GRCm38.p6, primary assembly) masked for nuclear mitochondrial sequences with the vM24 GENCODE mouse gene annotation with STAR 44 (v2.7.8a) (--quantMode TranscriptomeSAM).
The transcriptome alignments produced by STAR were quantified with Salmon 45 (-l ISR --seqBias --gcBias) against a transcriptome fasta produced from the GENCODE gene annotation and genome sequence with gffread.
The output files were imported into R (https://www.R-project.org) with tximport and tRNA knockouts were analysed for differential expression against wild types with DESeq2 per tissue, utilising apeglm and a log fold change threshold of log2(1.5).
Assembly: GRCm38.p6
Supplementary files format and content: .txt files with DESeq2 output for each comparison
Supplementary files format and content: .txt files with normalised counts for each sample

source_name: Brain

growth_protocol: Heterozygous tRNA-Phe gene deleted transgenic mice on a C57BL/6N background were generated by the Monash Genome Modification Platform (MGMP) and the Australian Phenomics Network (APN). Male age- and littermate-matched wild-type (WT) and homozygous mutant mice were housed in standard cages (45 cm x 29 cm x 12 cm) under a 12-h light/dark schedule (lights on 7 a.m. to 7 p.m.) in controlled environmental conditions of 22 + 2 C and 50 + 10% relative humidity. Normal chow diet (NCD) and water were provided ad libitum.

extract_protocol:
3 mm x 3 mm tissue pieces (liver or brain) were homogenized in 200 l of cell extraction buffer (CEB; 100 mM Tris, 2 mM Na3VO4, 100 mM NaCl, 1% Triton X-100, 1 mM EDTA, 10% glycerol, 1 mM EGTA, 0.1% SDS, 1 mM NaF, 0.5% deoxycholate, 20 mM Na4P2O7), pH 7.4, containing PhosSTOP Phosphatase Inhibitor Cocktail (Roche) and EDTA-free Complete protease inhibitor cocktail (Roche). The homogenates were prepared using a bead beater and the homogenates were centrifuged at 9,000 g for 5 min at 4C. The previous steps were repeated until a clear tissue homogenate was produced. The tissue homogenate protein concentration was quantified using the bicinchoninic acid (BCA) assay using BSA as a standard. The tissues were snap frozen and stored at -80oC prior to RNA isolation and RNA was isolated using the miRNeasy Mini kit (Qiagen) incorporating an on-column RNase-free DNase digestion to remove all DNA. RNA (2-5 g) was resolved on 1.2% agarose formaldehyde gels, then transferred to 0.45 m Hybond-N+ nitrocellulose membrane (GE Lifesciences) and hybridized with biotinylated oligonucleotide probes speci?c to nuclear tRNAs and 18S rRNA (probe sequences are listed in Table S4). Hybridizations were carried out overnight at 50C in 5x SSC, 20 mM Na2HPO4, 7% SDS and 100 g.ml-1 heparin, followed by washing. The signal was detected using streptavidin-linked infrared-labelled antibody (diluted 1: 10,000 in 3x SSC, 5% SDS, 25 mM Na2HPO4, pH 7.5) by the Odyssey Infrared Imaging System (LI-COR Biosciences).
RNA sequencing librarys were constructed using the Illumina TruSeq Sample Prep Kit according to the manufacturers instructions and sequenced on an Illumina NovaSeq 6000.

value: Brain


title: PDSN09.HiC, in situ Hi-C

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

institute: KAIST

description: in situ Hi-C

data_processing:
The sequencing output from Hi-C libraries were mapped to the reference genome (hg19) using BWA-mem (‘–M’ option).
In-house scripts were used to remove low quality reads (MAPQ < 10), the reads that span ligation sites, chimeric reads, and self-interacting reads (two fragments located within 5kb).
The chimeric reads were removed since they are by-products of proximity ligation during Hi-C experiments, and cannot be properly processed by paired-end BWA-mem command.
The read-pairs were merged together as paired-end aligned BAM files, and PCR duplicates were removed with Picard (v2.6.0).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw Hi-C interaction frequencies between two 5kb bins within 1mb window

source_name: Substantia nigra

extract_protocol: Hi-C libraries were prepared manually by performing DNA end repair, removal of un-ligated ends, adenosine addition at 3’ end (NEB, M0212), ligation of Illumina indexed adapters (NEB, M2200), and PCR amplification (Thermo Fisher Scientific, F549). The number of cycles for PCR amplification was determined based on KAPA library quantification kit (KAPA, KK4854).

value: Substantia nigra

tag: chip antibody


title: MAVS_1_hpRNA_rep3_24hr

value: MAVS sgRNA1


title: PDSN08.HiC, in situ Hi-C

description: in situ Hi-C


title: PDSN04.HiC, in situ Hi-C

description: in situ Hi-C


title: Brain, Phe31KO, repA


title: Arabidopsis root 1

source_name: Root


title: PDSN02.HiC, in situ Hi-C

description: in situ Hi-C


title: PDSN01.HiC, in situ Hi-C

description: in situ Hi-C


title: Brain, Phe31KO, repC


title: MAVS_1_hpRNA_rep1_24hr


title: DDX58_1_unstimulated_rep4_24hr

value: DDX58 sgRNA1

value: Unstimulated


title: NOSN05.HiC, in situ Hi-C

description: in situ Hi-C


title: NOSN06.HiC, in situ Hi-C

description: in situ Hi-C


title: NOSN04.HiC, in situ Hi-C

description: in situ Hi-C