title: GC, 0-20 hr, scATAC-seq, RNA part

description:
10x Genomics
scATAC_snRNA_0-20 hr

molecule: nuclear RNA

source_name: embryonic gonad

value: embryonic gonad

value: 0-20 hr after egg laying


title: GC, 8-20 hr, scRNA-seq

status: Public on Aug 10 2023

type: SRA

city: Kweishan, Taoyuan

first: Shu Yuan

last: Yang

address: Wenhua 1st Rd, No. 259

department: Biomedical science

country: Taiwan

institute: Chang Gung University

description:
10x Genomics
scRNA_8-20 hr
scRNA_0-20hr_aggr_matrix.mtx.gz
scRNA_0-20hr_aggr_barcodes.tsv.gz
scRNA_0-20hr_aggr_features.tsv.gz
The reason why scRNA_0-20hr_aggr_barcodes.tsv.gz has barcodes that end in -1 or -2 is we combined our previous 0-8 hr scRNA-seq data using Cell Ranger v6.1.2.  Barcodes ending in -1 correspond to 0-8 hr embryos and -2 to 8-20 hr embryos.

library_source: transcriptomic single cell

data_processing:
The scRNA-seq fastq files were demultiplexed, barcode processing, gene counting and aggregated along with our previous  0-8 hr. scRNA-seq data (SRX8341666) using Cell Ranger v6.1.2. Its downstream analysis was made using Monocle3 R package.
1. The scATAC-seq fastq files were demultiplexed, barcode processing using Cell Ranger ARC v1.0.0. 2. Low-quality nuclei were filtered out using DropletUtils, scDblFinder and Signac R packages. 3. The scATAC-seq downstream analysis was made using Signac R package.
Assembly: BDGP6.28.102
Supplementary files format and content: scRNA-seq data: Tab-separated values files and an matrix file
Supplementary files format and content: scATAC-seq data: comma-separated values files

molecule: polyA RNA

organism: Drosophila melanogaster

extract_protocol:
scRNA-seq: 1. Homogenization of 8-12 and 12-20 hr. embryos 2. Collect vas-GFP cells using Fluorescence-activated cell sorting
scATAC-seq: 1. Homogenization of 0-4, 4-8, 8-12, 12-16 and 16-20 hr. embryos 2. Collect vas-GFP cells using Fluorescence-activated cell sorting 3. Nuclei isolation using 10 mM Tris-HCl (pH7.4) conatining 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 1 mM DTT, 0.01% NP-40, 0.001% Digitonin and 1 U/μl RNase inhibitor
The protocols were based on the manufacturer's instructions using Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 for scRNA-seq and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle for scATAC-seq

tag: tissue

tag: developmental stage

value: 8-20 hr after egg laying

tag: genotype

value: vas-GFP


title: iPCR_EEP_Ap1m1

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute (NKI)

library_source: genomic

data_processing:
Basecalling, filtering and demultiplexing were performed using standard software of the Illumina MiSeq, NextSeq or NovaSeq platforms
For cDNA and pDNA samples, the barcode sequence was extracted from the read (using a custom python scripts) and counted.
For iPCR samples the insert sequence was aligned to a custom genome (using bowtie2) containing only the target sequences extracted from the mm10 genome, and the barcode was extracted from the ead using a custom python script.
Barcodes were clustered using Starcode (version 1.1) {Zorita, 2015, 25638815} to remove errors from barcode sequencing.
barcodes  matched with multiple element combinations were removed from the data
Per  combination an activity value was calculated as the ratio of the mean readcount in the RNA samples and the mean readcount in the pDNA library samples across all barcodes assigned to the singlet or combination.
Baselines were calculated across control-control combinations and then used to calculate boost indices as the log2 ratio between the activity of a combination and the baseline
Assembly: mm10
Supplementary files format and content: tsv format, each row contains a unique EEP combination, with fragment identifiers, calculated activities, baselines and Boost indices

molecule: genomic DNA

organism: Mus musculus

growth_protocol: E14TG2a mouse embryonic stem cells (mESC) (ATCC CRL-1821) were cultured in 2i+LI. 2i+LIF was made according to the 4DN nucleome protocol for culturing mESCs (https://data.4dnucleome.org/protocols/cb03c0c6-4ba6-4bbe-9210-c430ee4fdb2c/).

extract_protocol:
For iPCR samples, each library was digested overnight with I-CeuI (#R0699S, NEB), barcode-insert fragments were then circularized, remaining linear fragments digested, and barcode-insert fragments were linearized again with I-SceI (#R0694S; NEB). Barcode-insert fragments were then amplified by PCR with Illumina adapters and sequenced on an Illumina NextSeq 550 platform using 150 bp paired-end sequencing. For cDNA samples, cells were collected 24 hours after transfection in 5 ml of TRIsure. From each sample, the aqueous phase containing the total RNA of the TRIsure solution was extracted and purified on an RNA extraction column (#K0732, Thermo Scientific). Total RNA was digested with 10 units of DNase I (#04716728001; Roche) for 30 minutes in 10-8 10 µl reactions containing 5 µg of RNA. DNase I was inactivated by addition of 1 µl of 25 mM EDTA and incubation at 70°C for 10 min. cDNA was produced in 20 µl reactions (1 per 10 µDNAse reaction) using Maxima Reverse transcriptase (#EP0743; ThermoFisher Scientific) and a gene specific (targeting the GFP reporter) primer (JvA304, see Supplementary table 3 for sequence). dNTPs and the primer were mixed with the DNAse digested RNA and incubated at 65°C for 5 minutes. The RT buffer, enzyme and RNAse inhibitor were added and the reaction was incubated at 50 °C for 1 hour. cDNA was then amplified by two nested PCRs to make it strand specific. The first PCR reaction uses (index variants of 285JvA containing the S2, index and p7 adaptor)  and 305JvA (targeting the adapter introduced by 304JvA). Each 20 µl RT reaction was amplified in a 100-µl PCR reaction with MyTaq Red mix (#BIO-25043; Bioline). The second PCR reaction was performed using 10 µl of the product of the previous reaction in a 100 µl reaction using the same index variant primer and index variants of 437JvA (containing the S1, index and p5 adaptor) (see Supplementary table 3 for primer sequences). The first PCR was run for 10 cycles and the second one for 8 cycles using the recommended Mytaq Red mix conditions ( for both PCRs: 1 min 96 °C, then each cycle 15 s 96 °C, 15 s 60 °C, 15 s 72 °C). PCR products were purified with magnetic beads and mixed for sequencing in an Illumina NovaSeq 6000 platform using 100bp single end reads. For pDNA samples, 1 µg of each plasmid library was digested with I-SceI in order to linearise the plasmid. Barcodes were amplified by PCR for 9 cycles from 50 ng of material. Primers and reaction conditions were the same as in the amplification of cDNA. PCR products were purified using magnetic beads and mixed for sequencing.
PCR

treatment_protocol: Each EEP library was transfected separatedly. Cells were transiently transfected using Amaxa nucleofector II, program A-30, and Mouse Embryonic Stem Cell NucleofectorTM Kit (#VPH-1001, Lonza). Three independent biological replicates were done for each library mix. For each biological replicate 20 million cells were transfected (5 million cells with 4 µg plasmid per cuvette).

tag: cell line

tag: cell type

value: mESCs


title: BlCa: NPCs_Control_RNAseq_rep1

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
NPCs_Control_RNAseq.bw
NPCs_Control_RNAseq.genome1.bw
NPCs_Control_RNAseq.genome2.bw
NPCs_DEseq_basic_DEresults.tsv
NPCs_DEseq_allelic_DEresults.tsv
NPCs_DEgenes_classification.txt

library_source: transcriptomic

data_processing:
RNAseq and TTseq: The data are processed via snakePipes mRNA-seq pipeline (developing branch) (Bhardwaj et al., 2019). SnakePipes removed adapters and low quality bases (< Q20) using TrimGalore (v0.6.5) with parameters '-q 20 --trim-n'. The trimmed reads are aligned with STAR (v2.7.4) (Dobin et al., 2013) to an ‘N-masked’ genome, which is a version of the mouse reference genome mm10 where all the polymorphicsites (SNPs) for Mus musculus CAST/EiJ and Mus musculus C57BL/6 (or 129S1/SvImJ) are masked by ambiguity nucleobase ‘N’ (Keane et al., 2011). The mapped reads are then passed to SNPSplit (0.3.4) (Krueger and Andrews, 2016) to generate allele-specific BAM files by separating the alignment into two distinct alleles (CAST/EiJ and C57BL/6 or 129S1/SvImJ) based on SNPs information downloaded from Mouse Genome Database (Keane et al., 2011). The aligned reads of standard and allele specific level are counted separately on Gencode GTF (m9) via featureCounts (v2.0.0) (Yang et al., 2014).
ChIPseq: The data are processed via snakePipes DNA-mapping and ChIP-seq pipeline (developing branch) (Bhardwaj et al., 2019). Adapters and low quality bases (< Q20) are removed using TrimGalore (v0.6.5) with parameters '-q 20 --trim-n'. For all samples, reads are then mapped to the ‘N-masked’’ genome with Bowtie2 (2.3.5) (Langmead and Salzberg, 2012). Reads mapped on blacklisted regions from Encode Consortium are discarded. Duplicated reads are also filtered with Picard MarkDuplicates (1.65) (https://broadinstitute.github.io/picard/). In the end, only properly paired mapped reads and reads with mapping quality over 3 are kept for further analysis. SNPSplit (0.3.4) (Krueger and Andrews, 2016) is then used to generate allele-specific BAM files and deepTools (v3.3.2) (Ramirez et al., 2014) is used to check data quality. In the ChIP-seq part, peak calling is performed with MACS2 (v2.2.6) (Zhang et al., 2008) with options [--qvalue 0.001]. It is done with input as control on total and allele specific ChIP-seq signals respectively. CSAW (v1.20.0) (Lun and Smyth, 2015) is additionally used to calculate log2FC on peak regions between MSL2 KO and WT or between allele2 and allele1. Bigwig files are created with deepTools bamCompare (v3.3.2) (Ramirez et al., 2014), using input normalization method and log2ratio and subtract option.
ATACseq: The data are processed via snakePipes DNA-mapping and ATAC-seq pipeline (developing branch) (Bhardwaj et al., 2019). In the DNA-mapping part, adapters and low quality bases (< Q20) are removed using TrimGalore (v0.6.5) with parameters '-q 20 --trim-n'. For all samples, reads are then mapped to the ‘N-masked’’ genome with Bowtie2 (v2.3.5) (Langmead and Salzberg, 2012). Reads mapped on blacklisted regions from Encode Consortium are discarded. Duplicated reads are also filtered with Picard MarkDuplicates (v1.65) (https://broadinstitute.github.io/picard/). In the end, only properly paired mapped reads and reads with mapping quality over 3 are kept for further analysis. SNPSplit (0.3.4) (Krueger and Andrews, 2016) is then used to generate allele-specific BAM files and deepTools (v3.3.2) (Ramirez et al., 2014) is used to check data quality. In the ATAC-seq part, the BAM files are filtered to include only properly paired reads with appropriate fragment sizes (<150 bases). To identify open/accessible regions, peak calling is done with MACS2 (v2.2.6) (Zhang et al., 2008) with options [--qvalue 0.001], on total and allele-specific ATAC-seq signal respectively. CSAW (v1.20.0) (Lun and Smyth, 2015) is additionally used to calculate log2FC on peak regions between MSL2 KO and WT or between allele2 and allele1. Bigwig files are created with deepTools bamCoverage (v3.3.2) (Ramirez et al., 2014), using size factor calculated by deepTools multiBamSummary (v3.3.2).
BSseq: Raw fastq files were aligned against the ‘N-masked’ genome and deduplicated using Bismark (v0.22.3) (Krueger and Andreas, 2011). Resulting Alignments were allele-separated using SNPsplit with flags '--paired' and '--bisulfite'. Relevant quality metrics (conversion rates, genome coverage and GC bias) were calculated using MethylDackel version 0.6.0 (https://github.com/dpryan79/MethylDackel) and DeepTools (v3.5.0). Allele-specific differentially CpG methylated sites between MSL2 KO and WT or between allele2 and allele1 were called with DSS version 2.34.0.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files: log2 ratio or subtract value over the input sample (merged replicates) . bed: peak calling from MACS2 (merged replicates). RData: differential peak calling result from CSAW and differential CpG methylation sites from DSS. tsv: differential expression analysis from DESeq2. txt: Differentially expression genes further classification into five cateogories.

molecule: total RNA

source_name: Neural progenitor cells

growth_protocol: Male mouse ES cells, obtained from Anne Ferguson-Smith (University of Cambridge), were cultured in NDiff 227 medium (Takara) supplemented with LIF (Millipore), 2i inhibitors (PD0325901 and CHIR99021, Stemgent). Female mouse ES cells, obtained from Edith Heard (EMBL Heidelberg), were cultured in KnockOut-DMEM (KO-DMEM, Gibco) supplemented with 15% KnockOut Serum Replacement (KOSR, Gibco), GlutaMAX (Gibco), non-essential amino acids (Gibco), sodium pyruvate (Gibco), 2-Mercaptoethanol (Gibco), LIF, and 2i inhibitors. Male and female ES cells were differentiated into NPCs as previously described (Conti et al. 2005; Splinter et al. 2011). In brief, 1 million male or female ES cells were plated on 0.1% gelatin-coated plates in N2B27 medium, consisting of 1:1 DMEM/F-12 (Gibco) and Neurobasal medium (Gibco), supplemented with B27 (Gibco), GlutaMAX, 2-Mercaptoethanol, Apo-transferrin (Sigma), bovine serum albumin (Sigma), insulin (Sigma), putrescine (Sigma), progesterone (Sigma), and sodium selenite (Sigma). After 7 days, cells were dissociated and 3 million cells were plated on non-adherent culture dishes in the presence of 10ng/ml epidermal growth factor (EGF, Peprotech) and 10ng/ml basic fibroblast growth factor (FGF, Peprotech) to induce formation of embryoid bodies. After 3 days, the embryoid bodies were transferred to gelatin-coated plates to allow the expansion of NPCs.

extract_protocol:
RNAseq: Total RNA was extracted using the Direct-zol RNA Miniprep Plus Kit (Zymo Research) according to the manufacturers’ instructions. Maxima First Strand cDNA Synthesis Kit (Thermo Scientific) was used to synthesize cDNA from total RNA according to the manufacturers’ instructions. Quantitative reverse transcription PCR was carried out on Roche LightCycler II using the Faststart SYBR Green Master (Rox) mix (Roche) at a final volume of 10μL.
TT-seq: In brief, 10 million NPCs were incubated with N2B27 medium supplemented with 500 uM 4- thiouridine (4sU, Sigma) for 5 minutes at 37°C. Total RNA was isolated, fragmented using Bioruptor Plus for 1 minute (30s ON, 30s OFF, high setting), and incubated with Biotin-HPDP (Thermo Scientific) for 2 hours. MyOne C1 Streptavidin magnetic beads (Thermo Scientific) were used to immunoprecipitate labelled RNA before elution in 5% beta-mercaptoethanol (Roth). FInal RNA was cleaned up using the Oligo Clean and Concentrator Kit (Zymo Research) according to the manufacturer’s instructions. Libraries were prepared from 100 ng of high quality RNA using the Ovation Universal RNA-Seq System (Nugen) according to the manufacturer’s instructions.
ChIPseq: MSL2 WT and KO NPCs were covered with 1% formaldehyde in culture media on the plate and incubated at room temperature (RT) on a rocking plate for 10 min. Media was removed and cells were washed twice with 1xPBS supplemented with 1x protease inhibitor cocktail (Roche). Cells were scraped off the plate, collected in ice-cold 1xPBS and centrifuged at 500g for 5 minutes. After an additional 1xPBS wash, cell pellets were stored at -80°C until usage. Nuclei were isolated using the NEXSON based nuclei isolation protocol. Cell pellets were thawed on ice and resuspended in ice cold 1ml of lysis buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% Igepal, 1x protease inhibitor cocktail). The cell suspension was then transferred into 1ml milliTUBE (Covaris) and sonicated in Covaris instrument (E220) for 30 sec at peak power 75W, duty factor 2% and 200 cycles/burst. Nuclei were pelleted at 1000g at 20°C for 5min. The cytoplasmic fraction in the supernatant was discarded and nuclear pellets were carefully resuspended in 0.5% SDS and incubated at room temperature for 10min. Sample was diluted 1:5 in the digestion buffer (Final concentration: 1.1% Triton, 1x CutSmart buffer, nuclease free H2O, 1x protease inhibitor cocktail). Chromatin of up to 1 million nuclei were digested in 250ul digestion buffer with Cvik1 (5U/100.000 cells, New England Biolabs) at 20°C for 16hrs, shaking at 800rpm. After the chromatin digestion, the nuclei were pelleted for 5min at 1000g and washed in cold nuclei wash solution (10mM Tris-HCl pH 8, 0.25% Triton, 0.2mg/ml BSA) and stored on ice. To confirm the enzymatic chromatin shearing efficiency, 5% of the nuclei solution was incubated together with a decrosslinking solution consisting of 2ul proteinase K, 1ul RNaseA and 4ul 5M NaCl at 37°C for 30min followed by a 2hr incubation at 65°C. DNA was purified using MinElute PCR purification kit (Qiagen) and analyzed on a Agilent Tapestation system (G2964AA) using the Agilent D1000 Screentape reagents.
ATACseq: In brief, nuclei of 50,000 cells per replicate were isolated in 50 μl of cold ATAC resuspension buffer (0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin (Promega)) by incubating on ice for 3 minutes. After lysis, 1 ml of cold ATAC resuspension buffer containing 0.1% Tween-20 (without NP-40 or digitonin) was added, and nuclei were then centrifuged at 500g for 10 minutes. Transposition was carried out using 50 μl of transposition mix (25 μl 2X TD buffer (Illumina), 2.5 μl transposase (Illumina), 16.5 μl 1X PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) at 37°C for 30 minutes in a thermomixer with shaking at 1000 rpm. Transposed DNA was collected using Zymo DNA Clean and Concentrator (Zymo Research) according to the manufacturer's instructions, and added to the PCR mix containing 25 μl of NEBNext Master Mix (New England Biolabs) and 5 μl of Index adapters (Illumina). Libraries were amplified using the following PCR program: 72°C for 5 minutes, 98°C for 30 seconds, then 10 cycles of: 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. Library quality was analyzed using the Fragment analyzer (Agilent Technologies) prior to sequencing.
BSseq: Bisulfite-Seq was performed using the NEBNext Enzymatic Methyl-seq Kit (E7120S) according to the manufacturer’s instructions. In brief, genomic DNA (gDNA) was extracted from wild-type and MSL2 knockout NPCs using the QIAamp DNA Mini kit (Qiagen) according to the manufacturer’s instructions.Subsequently, 50ng of high quality gDNA was sheared for 120 seconds using an E220 Covaris to obtain fragments between around 300 base pairs in length. Following end prep and EM-seq adapter ligation, DNA was oxidised and denatured using sodium hydroxide. Libraries were amplified for 6 PCR cycles, and sequenced with 2x100bp paired-end reads on an Illumina NovaSeq6000 sequencer.

treatment_protocol: For the MSL2 knockout generation, two guide RNAs (gRNAs) were cloned into a PX-459 derivative (pSpCas9(BB)-2A-Puro) plasmid (Addgene 62988), and a split puromycin resistance or GFP-positive approach for selection was used (Flemr and Bühler 2015). Male and female ES cells and NPCs were transfected using Lipofectamine 3000 (Invitrogen) according to the manufacturer's instructions. After 48 hours, the cells were sorted based on their GFP expression status using a MoFlo XDP Cell Sorter (Beckman Coulter). Genomic DNA from single clones was isolated by resuspending cells in lysis buffer (10 mM Tris pH 8.0, 0.5 mM Ethylenediaminetetraacetic acid (EDTA), 0.5% Triton X-100) supplemented with Proteinase K (Thermo Scientific), and incubated at 55°C for 1 hour. Genomic DNA was collected after centrifugation at 16,000 g for 10 minutes. Polymerase chain reaction (PCR) was carried out using the 2X PCR Master Mix (Qiagen) at a final volume of 10μL. Successful knockout was verified using CloneJet PCR Cloning (Thermo Scientific) and BigDye Direct Sanger Sequencing (Thermo Scientific) kits according to the manufacturer’s instructions.

tag: strain

tag: gender

value: Male

value: WT

tag: library type

value: RNAseq

tag: replicate


title: genomic DNA from CRC-68

type: genomic

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

country: China

institute: The Second Hospital of Shandong University

description: CRC PBMCs sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy3 and Cy5

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Kit according to standard instructions

value: Female

tag: sample type

value: PBMCs

tag: disease state

value: CRC


title: BlCa: NPCs_Control_RNAseq_rep2


title: GC, 0-20 hr, scATAC-seq, ATAC part

description:
10x Genomics
scATAC_ATAC_0-20 hr

library_source: genomic single cell


title: iPCR_EEP_Nanog


title: iPCR_EEP_Lefty1


title: genomic DNA from CRC-63

description: CRC PBMCs sample


title: BlCa: NPCs_Control_KANSL3_rep2

description:
NPCs_Control_KANSL3.bw
NPCs_Control_KANSL3.genome1.bw
NPCs_Control_KANSL3.genome2.bw
NPCs_Control_KANSL3_peaks.bed


title: iPCR_EEP_Fgf5


title: iPCR_EEP_Otx2


title: BlCa: NPCs_Control_KANSL3_rep1


title: genomic DNA from CRC-62

description: CRC PBMCs sample


title: iPCR_EEP_Klf2_run2


title: advanced gastric cancer (NvT1)

city: Seoul

first: EOJIN

last: KIM

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Pathology

country: South Korea

institute: Korea University College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: stomach

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: stomach

value: adenocarcinoma

tag: treatment

value: no


title: iPCR_EEP_Sox2


title: BlCa: NPCs_Control_Input_rep1


title: Plate numbers P189 and P207

city: Parkville

first: Peter

last: Hickey

address: 1G Royal Parade

country: Australia

institute: WEHI

data_processing:
gene and ERCC count matrix generated using scPipe 1.4.1
reads were aligned using Rsubread 1.32.2
Assembly: GRCm38.p6
Supplementary files format and content: CSV, gene count matrix, rows represent genes and each column is a well, values corresponding to UMI counts
Supplementary files format and content: CSV, ERCC count matrix, rows represent ERCC spike-in sequences and each column is a well, values corresponding to UMI counts
Supplementary files format and content: CSV, sample sheet, rows represent a well and columns contain metadata on the sample in the well

source_name: E14.5 fetal liver-derived LSK/SLAM HSCs

extract_protocol:
Cells from E14.5 fetal liver were immunolabeled and subjected to fluorescence activated cell sorting to purify Lin-Sca-1+cKit+CD150+CD48- HSCs. Single cells were deposited into wells of a 384-well plate.
Single cell libraries were generated as follows: Reverse transcription was conducted with a CEL-Seq2 primer containing T7 promoter, partial Illumina 5’ adaptor, unique molecule identifier (UMI), 8bp barcode and polyT stretch followed by second strand synthesis, sample pooling, In vitro transcription, aRNA fragmentation and a final PCR to incorporate full length Illumina P5 and P 7 adaptors.

value: Zbtb11[+/+] Vav-iCre[T/+] / Zbtb11[del/+] Vav-iCre[T/+]; Zbtb11[del/del] Vav-iCre[T/+]


title: RRBS_KO_2

first: Chanhyeok

last: Park

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

institute: KIST (Korea Institute of Science and Technology)

data_processing:
For RRBS data analysis, the sequencing reads were aligned to the mm10 genome after undergoing an in-silico bisulfite transformation.
This alignment was performed using the Bismark aligner tools designed for bisulfite sequencing (ver 0.16.3 with Bowtie ver 2.2.6)
Assembly: mm9
Supplementary files format and content: BEDGRAPH

source_name: Spermatocytes

growth_protocol: Pooled spermatocytes from P21 mice were used for sequencing experiments. The seminiferous tubules of both C57BL/6 and Cfp1Stra8 mice were collected and minced. The minced tissue was incubated with Krebs-Ringer bicarbonate medium (EKRB) containing 0.5 mg/ml collagenase at 33°C for 1 hour to facilitate dissociation. The dissociated seminiferous tubules were further digested with EKRB supplemented with 0.5 mg/ml trypsin and 1 µg/ml DNase I at 33 °C for 15 minutes. Spermatocytes were isolated using the sedimentation velocity method at unit gravity and a temperature of 5°C. (18) The isolated cells, suspended in EKRB containing 0.5% BSA, were placed in a sedimentation chamber and a flow (10 ml/min) was applied. Purified spermatocytes were then subjected to lysis for subsequent sequencing analysis.

extract_protocol:
Genomic DNA (total 500 ng) was first digested with Msp1 (NEB) at 37°C for 7 hours and then with ApeKI (NEB) at 75°C for 16 hours. The digested DNA fragments were purified using the MiniElute PCR Purification Kit (Qiagen).
The reduced-representation bisulfite sequencing libraries were generated using the TruSeq Standed genomic DNA sample preparation kit.

value: Spermatocytes

value: MT


title: RRBS_WT_4


title: genomic DNA from CRC-59

description: CRC PBMCs sample


title: genomic DNA from CRC-56

description: CRC PBMCs sample


title: RRBS_WT_3


title: RRBS_KO_1


title: genomic DNA from CRC-53

description: CRC PBMCs sample


title: BlCa: NPCs_Control_H3_rep2


title: RRBS_WT_2


title: RRBS_WT_1


title: BlCa: NPCs_Control_H3_rep1


title: BlCa: NPCs_Control_BSseq_rep3

description:
NPCs_Control_BSseq.bw
NPCs_Control_BSseq.genome1.bw
NPCs_Control_BSseq.genome2.bw
NPCs_diff.peak.BS.RData

value: BSseq


title: spindrop mouse old RNA 5EU-seq sample 2

city: Cambridge

first: Florian

last: Hollfelder

address: 80 tennis court road

country: United Kingdom

institute: University of Cambridge

description:
old RNA
spinDrop 5EU-seq
EU_E85_old_matrix.csv

data_processing:
FastQC quality control
Pheniqs for demultiplexing
zUMIs to generate gene expression matrices using mouse and human references with Ensembl v99 annotations
Seurat v3 for data integration and analysis
Assembly: GRCm38 genome (Ensembl 99) and GRCh38 genome (Ensembl 99)
Supplementary files format and content: UMI quantified reads mapping to intronic and exonic regions. Downsampled to 20,000 reads per cell when indicated in the file header.

source_name: Embryos at E8.5 whole embryo

extract_protocol:
Live cells were stained with PE-labelled antibodies or Calcein-AM
Bead barcoding: indrop v3 protocol, encapsulation: spinDrop protocol, downstream library preparation: inDrop v3 protocol
inDrop v3 protocol

value: Embryos at E8.5 whole embryo

value: embryos

value: Sample was dissected and cultured for 3 hours in IVC1 with the 5EU analog, cells were then dissociated with TrypLE Express for 15 minutes at 37C,  Click-chemistry was performed as per the scEU-seq protocol and cells were processed using spindrop without sorting. After de-emulsification and clean-up the "old" samples are collected in the supernatant from the streptavidin pull-down before downstream library preparation.


title: genomic DNA from CRC-48

description: CRC PBMCs sample


title: BlCa: NPCs_Control_BSseq_rep2


title: spindrop mouse nascent RNA 5EU-seq sample 2

description:
nascent RNA
spinDrop 5EU-seq
EU_E85_nascent_matrix.csv

value: Sample was dissected and cultured for 3 hours in IVC1 with the 5EU analog, cells were then dissociated with TrypLE Express for 15 minutes at 37C,  Click-chemistry was performed as per the scEU-seq protocol and cells were processed using spindrop without sorting. After de-emulsification and clean-up the "nascent" samples are eliuted from the streptavidin beads before downstream library preparation.


title: spindrop mouse old RNA 5EU-seq sample 1


title: genomic DNA from CRC-47

description: CRC PBMCs sample

value: Male


title: spindrop mouse nascent RNA 5EU-seq sample 1


title: mouse FADS sorted PBMCs

description:
RNA
spindrop
FADS_PBMC_matrix.csv

source_name: mouse splenocytes, frozen

value: mouse splenocytes, frozen

value: splenocytes

value: WT

value: thawed, treated with FC block, stained with fluorescently-labelled antibodies and sequenced using spinDrop


title: genomic DNA from CRC-46

description: CRC PBMCs sample

value: PBMCs

value: CRC


title: BlCa: NPCs_Control_BSseq_rep1


title: BlCa: ESCs_MSL2KO1_RNAseq_rep3

description:
ESCs_DEseq_basic_DEresults.tsv
ESCs_DEseq_allelic_DEresults.tsv
ESCs_DEgenes_classification.txt

source_name: Embryonic stem cells

value: RNAseq


title: rna_cb6f1j_kupffer_f1nsg_rep2

city: La Jolla

first: Hunter

last: Bennett

state: California

address: 9500 Gilman Drive, MC 0651

department: Dept. of Cellular & Molecular Medicine

country: USA

institute: University of California, San Diego

description: F1 data was processed to only consider perfectly aligned reads, then this perfectly aligned reads were filtered for reads overlying mutations to allow us to distinguish reads originating from C57BL/6J or BALB/cJ parental chromosomes. As such each F1 sample was processed into four distinct matrices for both raw and tpm counts. Two matrices were generated for reads that were perfectly aligned to the C57BL/6J genome and BALB/cJ genomes respectively ('perfect_reads'), and two matrices were generated for reads that perfectly aligned AND overlaid a mutation between C57BL/6J and BALB/cJ genomes ("only_muts").

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the strain specific genome, mm10 was used for C57BL/6J (Link et al., 2018). MMARGE was used to shift strain specific alignment to the mm10 genome. STAR was used with default parameters was used to map RNA-seq experiments (Dobin et al., 2013). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
Each experiment was quantified using the “analyzeRepeats” script of HOMER. To generate a table of raw read counts, the parameters -count exons -condenseGenes - noadj were used. To generate a table of TPM values, the parameters -count exons  -tpm were used. Differentially expressed genes were identified using raw sequencing read counts by DESeq2 (Love et al., 2014) analysis through the “getDifferentialExpression” HOMER command. Gene ontology analysis was performed using Metascape (Tripathi et al., 2015).
CB6F1/J data was mapped to both the C57BL/6J and BALB/cJ genome, strain specific mappings were shifted to the reference genome using MMARGE shift (Link et al., 2018). Finally, perfectly aligned reads overlying strain specific mutations were isolated using MMARGE allele specific reads command. As such, the processed data matrices for f1 data include two entries per sample, one initially aligned to the C57BL/6J genome and one initially aligned to the BALB/cJ genome, both then shifted to the mm10 genome.
Assembly: mm10
Supplementary files format and content: Tab delimited text files of the folllowing: Table of unnormalized read counts RNA-seq and table of TPM values for RNA-Seq

source_name: Kupffer Cells, CB6F1/J, Control

extract_protocol:
Mice were humanely euthanized by exposure to CO2 and liver non-parenchymal cells processed for fluorescence activated cell sorting of Kupffer cells, with modifications from published methodology (Seidman et al., 2020; Sakai et al., 2019). In brief, livers were retrograde perfused for 3 min at a rate of 5-7 ml/min through the inferior vena cava with HBSS without Ca++ or Mg++ supplemented with 0.5 mM EGTA, 0.5 mM EDTA, and 20 mM HEPES. Perfusions were then switched to 40 ml of a digestion buffer, held at 37C, comprised of HBSS with Ca++ and Mg++ supplemented with 0.033 mg/ml of Liberase TM (Roche), 20 μg/ml DNaseI (Worthington), and 20 mM HEPES. Livers were then excised, minced, and digested for an additional 20 minutes in vitro at 37C with gentle rotation in 20 ml of fresh digestion buffer. The perfusion and digestion steps were performed in the presence of 1 μM flavopiridol to offset transcriptional changes associated with digestion. After tissue digestion, cells were passed through a 70-micron cell strainer and hepatocytes removed by 2 low-speed centrifugation steps at 50 X G for 2 min. Nonparenchymal cells in the supernatant were further separated from debris by pelleting for 15 min at 600 X G in 50 ml of 20% isotonic Percoll (Sigma Aldrich) at room temperature. Cells were then washed from Percoll containing buffer and suspended in 10 ml 28% OptiPrep (Sigma Aldrich) and carefully underlaid beneath 3 ml of wash buffer. The resulting gradient was centrifuged at 1,400 X G for 25 minutes at 4C with no break and cells enriched at the interface were saved and subjected to isotonic erythrocyte lysis. Enriched non-parenchymal cells were then washed, suspended in PBS, then stained for 10 minutes with Zombie NIR (BioLegend) and purified anti-CD16/32 (93, BioLegend) to label dead cells and block Fc receptors. Cells were then immunolabeled with specific antibodies of interest, washed, and sorted using a Beckman Coulter MoFlo Astrios EQ configured with spatially separated 355 nm, 405 nm, 488 nm, 561 nm, and 642 nm lasers.
Hepatocytes were prepared by perfusion digestion in a retrograde fashion through the inferior vena cava to the portal vein. In brief, livers were blanched with clearing buffer, then digested with a collagenase solution at 39C. Livers were perfused for 18 minutes at 5 ml/min. The perfusion and digestion steps were performed in the presence of 1 mM flavopiridol to offset transcriptional changes associated with digestion. After digestion, individual livers were gently dissociated using forceps in Medium 199 supplemented with 5% FBS and penicillin/streptomycin/gentamycin. Crude hepatocyte preps were carefully strained through a 100-micron strainer into and isolated using a Percoll gradient.
Mice were humanely euthanized by exposure to CO2 and bone marrow from femur, tibia, and iliac bones was isolated as described previously (Link et al., 2018). Bone marrow cells were seeded innon- tissue culture plates in m-CSF enriched media. After an additional 4-5 days of culture, non-adherent cells were washed off with room temperature PBS, and adherent macrophages were obtained by scraping.
Performed as published previously (Gosselin et al., 2017; Oishi et al., 2016). Isolated cells were pelleted and put into 150 μl lysis/Oligo d(T) Magnetic Beads binding buffer and stored at -80°C until processing. mRNAs were enriched by incubation with Oligo d(T) Magnetic Beads (NEB, S1419S) and then fragmented/eluted by incubation at 94°C for 9 min. Poly A enriched mRNA was fragmented, in 2x Superscript III first-strand buffer with 10mM DTT (Invitrogen), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 μL of fragmented mRNA, 0.5 μL of Random primer (Invitrogen), 0.5 μL of Oligo dT primer (Invitrogen), 0.5 μL of SUPERase-In (Ambion), 1 μL of dNTPs (10 mM) and 1 μL of DTT (10 mM) were heated at 50°C for three minutes. At the end of incubation, 5.8 μL of water, 1 μL of DTT (100 mM), 0.1 μL Actinomycin D (2 μg/μL), 0.2 μL of 1% Tween-20 (Sigma) and 0.2 μL of Superscript III (Invitrogen) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads according to manufacturer's instruction and eluted with 10 μL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 μL of Blue Buffer (Enzymatics), 1.1 μL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 μL of RNAse H (5 U/μL), 1.05 μL of water, 1 μL of DNA polymerase I (Enzymatics) and 0.15 μL of 1% Tween-20. The mixture was incubated at 16°C for 1 hour. The resulting dUTP-marked dsDNA was purified using 28 μL of Sera-Mag Speedbeads (Thermo Fisher Scientific), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 μL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen at -80°C. The purified dsDNA (40 μL) underwent end repair by blunting, A-tailing and adapter ligation as previously described (Heinz et al., 2010) using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 9-14 cycles, size selected by gel extraction, quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and sequenced on a Hi-seq 4000 or a NextSeq 500 (Illumina, San Diego, CA) according to the manufacturer's instructions.

treatment_protocol: For in vivo LPS experiments male mice were fasted overnight and treated for 2 hours by intraperitoneal injection of 0.1 mg/kg E. coli O114:B4 lipopolysaccharide. Control mice were equivalently fasted but uninjected. For in vitro BMDM LPS experiments macrophages were treated with 100 ng/ml Kdo2-lipid A (Avanti lipids), a highly purified E. coli lipopolysaccharide or an equivalent volume of PBS.

tag: source

value: Sorted non-parenchymal cells

value: Kupffer cell

value: Control


title: rna_cb6f1j_kupffer_f1nsg_rep3


title: ILC2s, Compound 5D 2

city: Los Angeles

first: Emily

last: Howard

state: Ca

address: 1450 Biggy St

department: MMI

institute: University of Southern California

data_processing:
Image analysis and base calling was carried out using RTA 1.13.48.0.  Final file formatting, demultiplexing and fastq generation were carried out using CASAVA v 1.8.2.
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25 nt were excluded from downstream analyses)
Trimmed reads were then mapped to the mouse genome mm10 using STAR (v2.6.1) with default parameter settings
Gencode M23 annotation was used to quantify the aligned reads to genes/transcripts using Partek E/M method.
read counts per gene/transcript in all samples were normalized using Upper Quartile normalization and analyzed for differential expression using Partek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
Assembly: mm10
Supplementary files format and content: tab-delimited file with raw read counts for genes

source_name: lung

extract_protocol:
Total RNA was isolated using MicroRNAeasy (Qiagen, Valencia, California). 10ng of input RNA was used to produce cDNA for downstream library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly isolated lung ILC2s  were isolated and cultured overnight with IL-2, IL-7, IL-33 and compound 5D or vehicle.

value: sorted ILC2s

value: BALB/c

value: lung

tag: age

value: 6 weeks

value: Compound 5D


title: genomic DNA from CRC-44

description: CRC PBMCs sample

value: Female


title: genomic DNA from CRC-42

description: CRC PBMCs sample


title: genomic DNA from CRC-41

description: CRC PBMCs sample

value: Male


title: ILC2s, Compound 5D 1


title: BlCa: ESCs_MSL2KO1_RNAseq_rep2


title: ILC2s, Control 2


title: BlCa: ESCs_MSL2KO1_RNAseq_rep1


title: ILC2s, Control 1


title: rna_cb6f1j_kupffer_f1nsg_rep1


title: genomic DNA from CRC-39

description: CRC PBMCs sample


title: BlCa: ESCs_Control_RNAseq_rep3


title: atac_BALBcJ_Kupffer_LPS_2hr_rep1

description:
atac_BALBcJ_Kupffer_LPS_2hr_rep1.peaks
atac_BALBcJ_Kupffer_LPS_2hr.idr
atac_f0_raw.txt

data_processing:
FASTQ files: Sequencing data were assessed for quality using fastqc. ATAC-seq data was mapped using Bowtie2 (Langmead and Salzberg, 2012). ATAC-seq data were trimmed to 30 bp to remove sequencing adapters, which improved mapping efficiency.  Strain specific genomes for BALB/cJ and A/J were generated from by replacing invariant positions of mm10 sequence with alleles reported in the Mouse Genome Project strain specific VCF files. mm10 was used as the C57BL/6J strain specific genome. Samples from parental strains of mice were mapped to the strain specific genome.  Mapped reads were shifted to the chromosome coordinates of the mm10 genome build using MARGE.pl shift with -ind set to balbcj or aj for reads mapped to the BALB/cJ or A/J genome, respectively (Link et al., 2018b)
F1 Hybrid: For samples from CB6F1/J samples, reads were mapped to the mm10 and BALB/cJ genome builds. Then the BALB/cJ mapped reads were shifted to the mm10 build with MMARGE as above. Perfectly mapped reads spanning genetic mutations between BALB/cJ and mm10 were identified using the MMARGE.pl allele_specific_reads command with -ind set to BALB/cJ and a second time with -ind set to mm10 resulting in two SAM files for each biological sample: one SAM file containing reads perfectly mapped to the mm10 genome that spanned known DNA sequence differences relative to the BALB/cJ genome; and a second SAM file containing reads perfectly mapped to the BALB/cJ genome that spanning known DNA sequence differences relative to the reference mm10 genome.
IDR: Strain specific ATAC-seq SAM files were used to generate HOMER tag directories and allelic IDR peaks were identified using each biological replicate. Alterations in allelic signals from pooled IDR peaks were detected using DeSeq2 and required the following thresholds: minimum normalized average tag depth > 16; absolute log2 fold-change > 1; and adjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: Tab delimited file of IDR peaks
Supplementary files format and content: Tab delimited file of normalized and raw tag counts over IDR peaks.

source_name: Kupffer Cells, BALB/cJ, LPS 2 hours

extract_protocol:
Mice were humanely euthanized by exposure to CO2 and liver non-parenchymal cells processed for fluorescence activated cell sorting of Kupffer cells, with modifications from published methodology (Seidman et al., 2020; Sakai et al., 2019). In brief, livers were retrograde perfused for 3 min at a rate of 5-7 ml/min through the inferior vena cava with HBSS without Ca++ or Mg++ supplemented with 0.5 mM EGTA, 0.5 mM EDTA, and 20 mM HEPES. Perfusions were then switched to 40 ml of a digestion buffer, held at 37C, comprised of HBSS with Ca++ and Mg++ supplemented with 0.033 mg/ml of Liberase TM (Roche), 20 μg/ml DNaseI (Worthington), and 20 mM HEPES. Livers were then excised, minced, and digested for an additional 20 minutes in vitro at 37C with gentle rotation in 20 ml of fresh digestion buffer. The perfusion and digestion steps were performed in the presence of 1 μM flavopiridol to offset transcriptional changes associated with digestion. After tissue digestion, cells were passed through a 70-micron cell strainer and hepatocytes removed by 2 low-speed centrifugation steps at 50 X G for 2 min. Nonparenchymal cells in the supernatant were further separated from debris by pelleting for 15 min at 600 X G in 50 ml of 20% isotonic Percoll (Sigma Aldrich) at room temperature. Cells were then washed from Percoll containing buffer and suspended in 10 ml 28% OptiPrep (Sigma Aldrich) and carefully underlaid beneath 3 ml of wash buffer. The resulting gradient was centrifuged at 1,400 X G for 25 minutes at 4C with no break and cells enriched at the interface were saved and subjected to isotonic erythrocyte lysis. Enriched non-parenchymal cells were then washed, suspended in PBS, then stained for 10 minutes with Zombie NIR (BioLegend) and purified anti-CD16/32 (93, BioLegend) to label dead cells and block Fc receptors. Cells were then immunolabeled with specific antibodies of interest, washed, and sorted using a Beckman Coulter MoFlo Astrios EQ configured with spatially separated 355 nm, 405 nm, 488 nm, 561 nm, and 642 nm lasers.
Transposase reactions and sequencing libraries were generated as described previously (Buenrostro et al., 2013; Sakai et al., 2019; Seidman et al., 2020) using 25,000 to 50,000 FACS purified Kupffer cells. Tagmented DNA was cleaned up using Zymo ChIP Clean & Concentrate columns and PCR amplified for 14 cycles using barcoding primers. Libraries were size selected to 175-225 bp using gel excision and purified as described (Texari et al., 2021). For F1 samples, dual indexed libraries were pooled for a targeted depth of 100 million reads per sample.

treatment_protocol: Male mice were fasted overnight and treated for 2 hours by intraperitoneal injection of 0.1 mg/kg E. coli O114:B4 lipopolysaccharide. Control mice were equivalently fasted but uninjected.

value: BALB/cJ

value: LPS 2 hours


title: atac_C57_Kupffer_LPS_2hr_rep2

description:
atac_C57_Kupffer_LPS_2hr_rep2.peaks
atac_C57_Kupffer_LPS_2hr.idr
atac_f0_raw.txt

source_name: Kupffer Cells, C57BL6/J, LPS 2 hours


title: BlCa: ESCs_Control_RNAseq_rep2

value: WT


title: atac_C57_Kupffer_LPS_2hr_rep1

description:
atac_C57_Kupffer_LPS_2hr_rep1.peaks
atac_C57_Kupffer_LPS_2hr.idr
atac_f0_raw.txt


title: atac_C57_Kupffer_LPS_2hr_rep3

description:
atac_C57_Kupffer_LPS_2hr_rep3.peaks
atac_C57_Kupffer_LPS_2hr.idr
atac_f0_raw.txt


title: BlCa: ESCs_Control_RNAseq_rep1


title: genomic DNA from CRC-38

description: CRC PBMCs sample


title: genomic DNA from CRC-37

description: CRC PBMCs sample


title: 9sCa: NPCs_MSL2KO2_unlabeledTTseq_rep3

data_processing:
Library strategy: TT-Seq
RNAseq and TTseq: The data are processed via snakePipes mRNA-seq pipeline (developing branch) (Bhardwaj et al., 2019). SnakePipes removed adapters and low quality bases (< Q20) using TrimGalore (v0.6.5) with parameters '-q 20 --trim-n'. The trimmed reads are aligned with STAR (v2.7.4) (Dobin et al., 2013) to an ‘N-masked’ genome, which is a version of the mouse reference genome mm10 where all the polymorphicsites (SNPs) for Mus musculus CAST/EiJ and Mus musculus C57BL/6 (or 129S1/SvImJ) are masked by ambiguity nucleobase ‘N’ (Keane et al., 2011). The mapped reads are then passed to SNPSplit (0.3.4) (Krueger and Andrews, 2016) to generate allele-specific BAM files by separating the alignment into two distinct alleles (CAST/EiJ and C57BL/6 or 129S1/SvImJ) based on SNPs information downloaded from Mouse Genome Database (Keane et al., 2011). The aligned reads of standard and allele specific level are counted separately on Gencode GTF (m9) via featureCounts (v2.0.0) (Yang et al., 2014).
ChIPseq: The data are processed via snakePipes DNA-mapping and ChIP-seq pipeline (developing branch) (Bhardwaj et al., 2019). Adapters and low quality bases (< Q20) are removed using TrimGalore (v0.6.5) with parameters '-q 20 --trim-n'. For all samples, reads are then mapped to the ‘N-masked’’ genome with Bowtie2 (2.3.5) (Langmead and Salzberg, 2012). Reads mapped on blacklisted regions from Encode Consortium are discarded. Duplicated reads are also filtered with Picard MarkDuplicates (1.65) (https://broadinstitute.github.io/picard/). In the end, only properly paired mapped reads and reads with mapping quality over 3 are kept for further analysis. SNPSplit (0.3.4) (Krueger and Andrews, 2016) is then used to generate allele-specific BAM files and deepTools (v3.3.2) (Ramirez et al., 2014) is used to check data quality. In the ChIP-seq part, peak calling is performed with MACS2 (v2.2.6) (Zhang et al., 2008) with options [--qvalue 0.001]. It is done with input as control on total and allele specific ChIP-seq signals respectively. CSAW (v1.20.0) (Lun and Smyth, 2015) is additionally used to calculate log2FC on peak regions between MSL2 KO and WT or between allele2 and allele1. Bigwig files are created with deepTools bamCompare (v3.3.2) (Ramirez et al., 2014), using input normalization method and log2ratio and subtract option.
ATACseq: The data are processed via snakePipes DNA-mapping and ATAC-seq pipeline (developing branch) (Bhardwaj et al., 2019). In the DNA-mapping part, adapters and low quality bases (< Q20) are removed using TrimGalore (v0.6.5) with parameters '-q 20 --trim-n'. For all samples, reads are then mapped to the ‘N-masked’’ genome with Bowtie2 (v2.3.5) (Langmead and Salzberg, 2012). Reads mapped on blacklisted regions from Encode Consortium are discarded. Duplicated reads are also filtered with Picard MarkDuplicates (v1.65) (https://broadinstitute.github.io/picard/). In the end, only properly paired mapped reads and reads with mapping quality over 3 are kept for further analysis. SNPSplit (0.3.4) (Krueger and Andrews, 2016) is then used to generate allele-specific BAM files and deepTools (v3.3.2) (Ramirez et al., 2014) is used to check data quality. In the ATAC-seq part, the BAM files are filtered to include only properly paired reads with appropriate fragment sizes (<150 bases). To identify open/accessible regions, peak calling is done with MACS2 (v2.2.6) (Zhang et al., 2008) with options [--qvalue 0.001], on total and allele-specific ATAC-seq signal respectively. CSAW (v1.20.0) (Lun and Smyth, 2015) is additionally used to calculate log2FC on peak regions between MSL2 KO and WT or between allele2 and allele1. Bigwig files are created with deepTools bamCoverage (v3.3.2) (Ramirez et al., 2014), using size factor calculated by deepTools multiBamSummary (v3.3.2).
BSseq: Raw fastq files were aligned against the ‘N-masked’ genome and deduplicated using Bismark (v0.22.3) (Krueger and Andreas, 2011). Resulting Alignments were allele-separated using SNPsplit with flags '--paired' and '--bisulfite'. Relevant quality metrics (conversion rates, genome coverage and GC bias) were calculated using MethylDackel version 0.6.0 (https://github.com/dpryan79/MethylDackel) and DeepTools (v3.5.0). Allele-specific differentially CpG methylated sites between MSL2 KO and WT or between allele2 and allele1 were called with DSS version 2.34.0.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files: log2 ratio or subtract value over the input sample (merged replicates) . bed: peak calling from MACS2 (merged replicates). RData: differential peak calling result from CSAW and differential CpG methylation sites from DSS. tsv: differential expression analysis from DESeq2. txt: Differentially expression genes further classification into five cateogories.

value: unlabeledTTseq


title: rna_BALBcJ_Kupffer_AMLN_30weeks_rep3

description:
f0_tpm.txt
f0_raw.txt

source_name: Kupffer Cells, BALB/cJ, AMLN 30 weeks

extract_protocol:
extract protocol, non-parenchymal cells (Kupffer cells, Stellate cells, liver sinusoidal endoethelial cells)
Mice were humanely euthanized by exposure to CO2 and liver non-parenchymal cells processed for fluorescence activated cell sorting of Kupffer cells, with modifications from published methodology (Seidman et al., 2020; Sakai et al., 2019). In brief, livers were retrograde perfused for 3 min at a rate of 5-7 ml/min through the inferior vena cava with HBSS without Ca++ or Mg++ supplemented with 0.5 mM EGTA, 0.5 mM EDTA, and 20 mM HEPES. Perfusions were then switched to 40 ml of a digestion buffer, held at 37C, comprised of HBSS with Ca++ and Mg++ supplemented with 0.033 mg/ml of Liberase TM (Roche), 20 μg/ml DNaseI (Worthington), and 20 mM HEPES. Livers were then excised, minced, and digested for an additional 20 minutes in vitro at 37C with gentle rotation in 20 ml of fresh digestion buffer. The perfusion and digestion steps were performed in the presence of 1 μM flavopiridol to offset transcriptional changes associated with digestion. After tissue digestion, cells were passed through a 70-micron cell strainer and hepatocytes removed by 2 low-speed centrifugation steps at 50 X G for 2 min. Nonparenchymal cells in the supernatant were further separated from debris by pelleting for 15 min at 600 X G in 50 ml of 20% isotonic Percoll (Sigma Aldrich) at room temperature. Cells were then washed from Percoll containing buffer and suspended in 10 ml 28% OptiPrep (Sigma Aldrich) and carefully underlaid beneath 3 ml of wash buffer. The resulting gradient was centrifuged at 1,400 X G for 25 minutes at 4C with no break and cells enriched at the interface were saved and subjected to isotonic erythrocyte lysis. Enriched non-parenchymal cells were then washed, suspended in PBS, then stained for 10 minutes with Zombie NIR (BioLegend) and purified anti-CD16/32 (93, BioLegend) to label dead cells and block Fc receptors. Cells were then immunolabeled with specific antibodies of interest, washed, and sorted using a Beckman Coulter MoFlo Astrios EQ configured with spatially separated 355 nm, 405 nm, 488 nm, 561 nm, and 642 nm lasers.
extract protocol, hepatocyes
Hepatocytes were prepared by perfusion digestion in a retrograde fashion through the inferior vena cava to the portal vein. In brief, livers were blanched with clearing buffer, then digested with a collagenase solution at 39C. Livers were perfused for 18 minutes at 5 ml/min. The perfusion and digestion steps were performed in the presence of 1 mM flavopiridol to offset transcriptional changes associated with digestion. After digestion, individual livers were gently dissociated using forceps in Medium 199 supplemented with 5% FBS and penicillin/streptomycin/gentamycin. Crude hepatocyte preps were carefully strained through a 100-micron strainer into and isolated using a Percoll gradient.
extract protocol, BMDMs
Mice were humanely euthanized by exposure to CO2 and bone marrow from femur, tibia, and iliac bones was isolated as described previously (Link et al., 2018). Bone marrow cells were seeded innon- tissue culture plates in m-CSF enriched media. After an additional 4-5 days of culture, non-adherent cells were washed off with room temperature PBS, and adherent macrophages were obtained by scraping.
Performed as published previously (Gosselin et al., 2017; Oishi et al., 2016). Isolated cells were pelleted and put into 150 μl lysis/Oligo d(T) Magnetic Beads binding buffer and stored at -80°C until processing. mRNAs were enriched by incubation with Oligo d(T) Magnetic Beads (NEB, S1419S) and then fragmented/eluted by incubation at 94°C for 9 min. Poly A enriched mRNA was fragmented, in 2x Superscript III first-strand buffer with 10mM DTT (Invitrogen), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 μL of fragmented mRNA, 0.5 μL of Random primer (Invitrogen), 0.5 μL of Oligo dT primer (Invitrogen), 0.5 μL of SUPERase-In (Ambion), 1 μL of dNTPs (10 mM) and 1 μL of DTT (10 mM) were heated at 50°C for three minutes. At the end of incubation, 5.8 μL of water, 1 μL of DTT (100 mM), 0.1 μL Actinomycin D (2 μg/μL), 0.2 μL of 1% Tween-20 (Sigma) and 0.2 μL of Superscript III (Invitrogen) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads according to manufacturer's instruction and eluted with 10 μL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 μL of Blue Buffer (Enzymatics), 1.1 μL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 μL of RNAse H (5 U/μL), 1.05 μL of water, 1 μL of DNA polymerase I (Enzymatics) and 0.15 μL of 1% Tween-20. The mixture was incubated at 16°C for 1 hour. The resulting dUTP-marked dsDNA was purified using 28 μL of Sera-Mag Speedbeads (Thermo Fisher Scientific), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 μL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen at -80°C. The purified dsDNA (40 μL) underwent end repair by blunting, A-tailing and adapter ligation as previously described (Heinz et al., 2010) using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 9-14 cycles, size selected by gel extraction, quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and sequenced on a Hi-seq 4000 or a NextSeq 500 (Illumina, San Diego, CA) according to the manufacturer's instructions.

value: AMLN Diet 30 weeks


title: rna_BALBcJ_Kupffer_AMLN_30weeks_rep1

description:
f0_tpm.txt
f0_raw.txt


title: rna_BALBcJ_Kupffer_AMLN_30weeks_rep2

description:
f0_tpm.txt
f0_raw.txt


title: 9sCa: NPCs_MSL2KO2_unlabeledTTseq_rep2


title: genomic DNA from CRC-36

description: CRC PBMCs sample

value: PBMCs

value: CRC


title: rna_AJ_Kupffer_AMLN_30weeks_rep3

description:
f0_tpm.txt
f0_raw.txt

source_name: Kupffer Cells, A/J, AMLN 30 weeks

value: Sorted non-parenchymal cells

value: A/J


title: genomic DNA from CRC-40

description: CRC PBMCs sample


title: atac_BALBcJ_Kupffer_LPS_2hr_rep2

description:
atac_BALBcJ_Kupffer_LPS_2hr_rep2.peaks
atac_BALBcJ_Kupffer_LPS_2hr.idr
atac_f0_raw.txt

value: Kupffer cell


title: rna_AJ_Kupffer_AMLN_30weeks_rep2

description:
f0_tpm.txt
f0_raw.txt


title: 9sCa: NPCs_MSL2KO2_unlabeledTTseq_rep1


title: 9sCa: NPCs_MSL2KO2_labeledTTseq_rep3

value: labeledTTseq


title: 9sCa: NPCs_MSL2KO2_labeledTTseq_rep2


title: rna_C57_Kupffer_LPS_2hr_rep1

description:
f0_tpm.txt
f0_raw.txt

source_name: Kupffer Cells, C57BL/6J, LPS 2 hours


title: rna_C57_Kupffer_LPS_2hr_rep2

description:
f0_tpm.txt
f0_raw.txt


title: rna_AJ_Kupffer_AMLN_30weeks_rep1

description:
f0_tpm.txt
f0_raw.txt


title: genomic DNA from CRC-30

description: CRC PBMCs sample


title: rna_BALBcJ_Kupffer_LPS_2hr_rep2

description:
f0_tpm.txt
f0_raw.txt


title: rna_BALBcJ_Kupffer_LPS_2hr_rep1

description:
f0_tpm.txt
f0_raw.txt


title: 9sCa: NPCs_MSL2KO2_RNAseq_rep3

description:
NPCs_MSL2KO2_RNAseq.bw
NPCs_MSL2KO2_RNAseq.genome1.bw
NPCs_MSL2KO2_RNAseq.genome2.bw

value: RNAseq


title: genomic DNA from CRC-26

description: CRC PBMCs sample


title: genomic DNA from CRC-25

description: CRC PBMCs sample


title: Heart, K6

city: Newark

first: Michinari

last: Nakamura

state: NJ

address: 185 South Orange Ave, Medical Science Building G609

department: Cell Biology and Molecular Medicine

institute: Rutgers New Jersey Medical School

data_processing:
Raw reads were quality trimmed using Trimmomatic-0.39 with leading and trailing Q score 20, minimum length 35 bp.
The cleaned reads were mapped to Mus musculus genome GRCm38 using HISAT2 (Version 2.2.1). The reference genome sequence and annotation files were downloaded from ENSEMBLE, release.97 (Mus_musculus.GRCm38.101fa and Mus_musculus.GRCm38.101.gtf).
The aligned read counts were obtained using htseq-count as part of the package HTSeq-0.6.1. The Bioconductor package edgeR (Version 3.18.1 with limma 3.32.10) was used to perform the differential gene expression analysis under R environment, R version 4.1.1.
Assembly: grcm38
Supplementary files format and content: comma separated spreadsheet file includes RPKM values for each Sample

source_name: Heart

extract_protocol:
Total RNA was isolated from the hearts of the indicated mice 9 hours after TAC or Sham using TRIzol (Invitrogen).
Isolated RNA was checked for integrity on an Agilent Bioanalyzer 2100; samples with RNA integrity number (RIN) >7.0 were used for subsequent processing. Total RNA was subjected to two rounds of poly(A) selection using oligo-d(T)25 magnetic beads (New England Biolabs). A paired-end (strand specific) cDNA library was prepared using the NEB Next Ultra-directional RNA-seq protocol. Briefly, poly(A)+ RNA was fragmented by heating at 94°C for 10 min followed by reverse transcription and second strand cDNA synthesis using the reagents provided in the NEB Next kit. End-repaired cDNA was then ligated with double stranded DNA adapters, followed by purification of ligated DNA with AmpureXP beads. cDNA was then amplified by PCR for 15 cycles with a universal forward primer and a reverse primer with bar code. The sequencing of the cDNA libraries was performed on the Illumina NextSeq 500 platform (Illumina, San Diego, CA) using the single-read 1x75 cycles configuration.

treatment_protocol: Transverse aortic constriction (TAC) or Sham surgery for 9 hours

value: Heart

value: Bcl-xL S14A KI mutant

value: TAC


title: rna_AJ_Kupffer_AMLN_30weeks_rep4

description:
f0_tpm.txt
f0_raw.txt


title: 9sCa: NPCs_MSL2KO2_labeledTTseq_rep1

value: Female


title: Heart, K5


title: Heart, K3

value: Sham


title: genomic DNA from CRC-23

description: CRC PBMCs sample

value: Male


title: Heart, K1


title: 9sCa: NPCs_MSL2KO2_RNAseq_rep1


title: Heart, W10

value: Wild-type


title: genomic DNA from CRC-35

description: CRC PBMCs sample


title: 9sCa: NPCs_MSL2KO2_RNAseq_rep2


title: genomic DNA from CRC-21

description: CRC PBMCs sample


title: Heart, K2


title: genomic DNA from CRC-34

description: CRC PBMCs sample


title: Heart, W9


title: 9sCa: NPCs_MSL2KO2_Pol2_rep2

description:
NPCs_MSL2KO2_Pol2.bw
NPCs_MSL2KO2_Pol2.genome1.bw
NPCs_MSL2KO2_Pol2.genome2.bw


title: genomic DNA from CRC-20

description: CRC PBMCs sample


title: Heart, W3


title: 9sCa: NPCs_MSL2KO2_Pol2_rep1


title: Heart, W2


title: Heart, W7


title: Heart, W1


title: Heart, K7


title: genomic DNA from CRC-15

description: CRC PBMCs sample


title: 9sCa: NPCs_MSL2KO2_MSL2_rep2

description:
NPCs_MSL2KO2_MSL2.bw
NPCs_MSL2KO2_MSL2.genome1.bw
NPCs_MSL2KO2_MSL2.genome2.bw


title: 9sCa: NPCs_MSL2KO2_MSL2_rep1


title: 9sCa: NPCs_MSL2KO2_Input3_rep1

description: Same batch as H3K4me1, H3K4me3, H3K27ac, H3K36me3, H3K27me3, H3K9me3, H4K16ac


title: genomic DNA from CRC-12

description: CRC PBMCs sample


title: 9sCa: NPCs_MSL2KO2_Input3_rep2


title: 9sCa: NPCs_MSL2KO2_MOF_rep2

description:
NPCs_MSL2KO2_MOF.bw
NPCs_MSL2KO2_MOF.genome1.bw
NPCs_MSL2KO2_MOF.genome2.bw
NPCs_MSL2KO2_MOF_peaks.bed


title: 9sCa: NPCs_MSL2KO2_MOF_rep1


title: 9sCa: NPCs_MSL2KO2_H3K4me3_rep2

description:
NPCs_MSL2KO2_H3K4me3.bw
NPCs_MSL2KO2_H3K4me3.genome1.bw
NPCs_MSL2KO2_H3K4me3.genome2.bw


title: genomic DNA from CRC-10

description: CRC PBMCs sample


title: 9sCa: NPCs_MSL2KO2_H3K4me1_rep2

description:
NPCs_MSL2KO2_H3K4me1.bw
NPCs_MSL2KO2_H3K4me1.genome1.bw
NPCs_MSL2KO2_H3K4me1.genome2.bw


title: 9sCa: NPCs_MSL2KO2_H3K9me3_rep1

description:
NPCs_MSL2KO2_H3K9me3.bw
NPCs_MSL2KO2_H3K9me3.genome1.bw
NPCs_MSL2KO2_H3K9me3.genome2.bw


title: 9sCa: NPCs_MSL2KO2_H3K4me3_rep1


title: 9sCa: NPCs_MSL2KO2_H3K36me3_rep1

description:
NPCs_MSL2KO2_H3K36me3.bw
NPCs_MSL2KO2_H3K36me3.genome1.bw
NPCs_MSL2KO2_H3K36me3.genome2.bw


title: 9sCa: NPCs_MSL2KO2_H3K4me1_rep1


title: 9sCa: NPCs_MSL2KO2_H3K36me3_rep2


title: genomic DNA from CRC-16

description: CRC PBMCs sample


title: genomic DNA from CRC-9

description: CRC PBMCs sample


title: 9sCa: NPCs_MSL2KO2_H3K27me3_rep2

description:
NPCs_MSL2KO2_H3K27me3.bw
NPCs_MSL2KO2_H3K27me3.genome1.bw
NPCs_MSL2KO2_H3K27me3.genome2.bw


title: genomic DNA from CRC-11

description: CRC PBMCs sample


title: 9sCa: NPCs_MSL2KO2_KANSL1_rep2

description:
NPCs_MSL2KO2_KANSL1.bw
NPCs_MSL2KO2_KANSL1.genome1.bw
NPCs_MSL2KO2_KANSL1.genome2.bw
NPCs_MSL2KO2_KANSL1_peaks.bed


title: 9sCa: NPCs_MSL2KO2_H3K27me3_rep1


title: 9sCa: NPCs_MSL2KO2_H3K27ac_rep2

description:
NPCs_MSL2KO2_H3K27ac.bw
NPCs_MSL2KO2_H3K27ac.genome1.bw
NPCs_MSL2KO2_H3K27ac.genome2.bw


title: genomic DNA from CRC-13

description: CRC PBMCs sample


title: genomic DNA from CRC-6

description: CRC PBMCs sample


title: 9sCa: NPCs_MSL2KO2_KANSL3_rep1

description:
NPCs_MSL2KO2_KANSL3.bw
NPCs_MSL2KO2_KANSL3.genome1.bw
NPCs_MSL2KO2_KANSL3.genome2.bw
NPCs_MSL2KO2_KANSL3_peaks.bed


title: 9sCa: NPCs_MSL2KO2_H3K9me3_rep2


title: 9sCa: NPCs_MSL2KO2_KANSL1_rep1


title: 9sCa: NPCs_MSL2KO2_H3K27ac_rep1


title: genomic DNA from CRC-5

description: CRC PBMCs sample


title: 9sCa: NPCs_MSL2KO1_H3K9me3_rep1

description:
NPCs_MSL2KO1_H3K9me3.bw
NPCs_MSL2KO1_H3K9me3.genome1.bw
NPCs_MSL2KO1_H3K9me3.genome2.bw


title: 9sCa: NPCs_MSL2KO1_H3K9me3_rep2


title: 9sCa: NPCs_MSL2KO1_Input3_rep1


title: 9sCa: NPCs_MSL2KO2_KANSL3_rep2


title: 9sCa: NPCs_MSL2KO2_Input4_rep1

description: Same batch as H4K5ac, H4K12ac


title: genomic DNA from CRC-3

description: CRC PBMCs sample


title: 9sCa: NPCs_MSL2KO1_H3K4me3_rep1

description:
NPCs_MSL2KO1_H3K4me3.bw
NPCs_MSL2KO1_H3K4me3.genome1.bw
NPCs_MSL2KO1_H3K4me3.genome2.bw


title: 9sCa: NPCs_MSL2KO1_H3K36me3_rep2

description:
NPCs_MSL2KO1_H3K36me3.bw
NPCs_MSL2KO1_H3K36me3.genome1.bw
NPCs_MSL2KO1_H3K36me3.genome2.bw


title: 9sCa: NPCs_MSL2KO2_Input2_rep2

description: Same batch as MSL2, DNMT3A, DNMT3B


title: 9sCa: NPCs_MSL2KO1_H3K4me1_rep2

description:
NPCs_MSL2KO1_H3K4me1.bw
NPCs_MSL2KO1_H3K4me1.genome1.bw
NPCs_MSL2KO1_H3K4me1.genome2.bw


title: 9sCa: NPCs_MSL2KO1_H3K4me1_rep1


title: 9sCa: NPCs_MSL2KO1_H3K36me3_rep1


title: genomic DNA from CRC-8

description: CRC PBMCs sample


title: 9sCa: NPCs_MSL2KO1_Input3_rep2


title: 5m_dNTP_transcriptome-4

city: Xiamen

first: Xi

last: Zeng

state: Fujian

address: No.422, Siming South Road

institute: Xiamen University

data_processing:
The original sequence data obtained contain 150bp paired-end sequences. Before alignment, Trim Galore version 0.6.7 was used for adapter removal. Trimmed clean sequences were aligned and de-duplicated with hg19/mm10 by the bisulfite alignment tool Bismark version v0.15.0. The obtained bam files were converted into sam files using samtools version 1.3.1.
For the sam files, after the initial comparison using Bismark, we obtained the methylation information of each read based on the XM-tag (methylation call string) in the sam files. We calculated the methylation levels of CHH and CHG for each read and distinguished the reads into methylomic reads and transcriptomic reads by the methylation levels. When the methylation level of the reads was greater than 90%, they were classified as transcriptomic reads, and when the methylation level of the reads was less than 50%, they were classified as methylomic reads. For the analysis of methylomic reads, we extracted CpG methylation site information using the common methylation analysis pipeline and the R package methylKit version 1.22.0. For the isolated transcriptomic reads, the transcriptome analysis pipeline was used, which mainly included realignment using STAR version 2.7.3a and obtaining the expression profiles of the cells using htseq version 0.12.4.
For clustering using transcriptome data, the expression matrix of cells was obtained from expression profiles and then clustered using R package SC3 version 1.24.0. For the clustering of the methylome data, the Pearson correlation coefficients for the methylation levels of the commonly covered methylation sites were calculated and clearer clusters could be seen on the correlation matrix.
We used the methylome data as DNA data to perform copy number variation analysis. We used the bwa tool version 0.7.17 to perform genomic alignment and analysis. The bam files after alignment were converted to bed files for input into ginkgo for copy number variation analysis. The length of a bin was set to the default of 1M. The cell copy number variance profiles were obtained by feeding the bed files to ginkgo.
We input the gene expression matrix obtained from the transcriptome analysis pipeline into the R package DESeq2 version 1.36.0, and obtained the differentially expressed genes. For the enriched pathway analysis, we input the gene list into the enrichGO function in the R package clusterProfiler version 4.4.4 to obtain the enriched pathways. The Gene Set Enrichment Analysis (GSEA) was performed using the python package gseapy version 1.0.5.
Assembly: hg19, mm10
Supplementary files format and content: CpG.txt file containing methylation information for CpG sites.
Supplementary files format and content: counts.txt file containing gene expression information.

growth_protocol: All cultures were maintained at 37ºC in a humidified incubator with 5% CO2. The human chronic myeloid leukemia cell line K562 and acute myeloid leukemia cell line HL60 were cultured in IMDM, supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin-Glutamine.

extract_protocol:
Single cells were isolated with the Digital microfluidics chip. By incorporating 2'-deoxy-5-methylcytidine 5'-triphosphate (5-methyl dCTP) during reverse transcription and cDNA amplification, the resulting library of RNA and gDNA sequencing reads exhibit drastically different methylation patterns. Single-cell DNA methylation and gene expression information were obtained simultaneously, without the need to physically separate DNA and RNA.
After single-cell isolation, droplets of lysis buffer are introduced to lyse the cells. The lysates are then subjected to RT and cDNA amplification using 5’-methyl-dCTP instead of dCTP, so that all cytosines in the synthesized cDNA are methylcytosines, while the genomic DNA remains unchanged during the process. Subsequently, both the cDNA and gDNA undergo bisulfite conversion concurrently, during which normal cytosines are converted to uracil, while methylated cytosines remain unchanged. Consequently, fully cytosine-methylated cDNA produced from RNA remains unaffected by the C-U transition. In contrast, less than 10% of mammalian genomic cytosines are endogenously methylated, resulting in a substantial conversion of gDNA cytosines to uracil, which will be identified as thymine in sequencing. After scBS-seq-based library construction, the DNA reads are distinguished from RNA reads based on the methylated cytosine density in reads, and thus both DNA methylation and gene expression information are obtained from a single-cell library.
smart-seq2 and scBS

treatment_protocol: Mouse embryonic stem cells (mESCs; E14, 129/Ola) were grown on 6-cm culture dishes with MEF feeder cells and cultured in a complete medium supplemented with leukemia inhibitory factor (LIF) to prevent differentiation. To induce undirectional differentiation, mESCs were dissociated and replated onto 0.1% gelatin-coated dishes, and cultured without LIF in a feeder-free manner for two passages.

value: chronic myeloid leukemia cells


title: 9sCa: NPCs_MSL2KO2_Input2_rep1

description: Same batch as MSL2, DNMT3A, DNMT3B


title: 9sCa: NPCs_MSL2KO1_H3K27me3_rep2

description:
NPCs_MSL2KO1_H3K27me3.bw
NPCs_MSL2KO1_H3K27me3.genome1.bw
NPCs_MSL2KO1_H3K27me3.genome2.bw


title: 5m_dNTP_transcriptome-2


title: 9sCa: NPCs_MSL2KO1_H3K27ac_rep2

description:
NPCs_MSL2KO1_H3K27ac.bw
NPCs_MSL2KO1_H3K27ac.genome1.bw
NPCs_MSL2KO1_H3K27ac.genome2.bw


title: 5m_dNTP_transcriptome-1


title: 9sCa: NPCs_MSL2KO2_Input1_rep1

description: Same batch as NRF1, BRD4, KANSL1, KANSL3, MOF, Pol2


title: 9sCa: NPCs_MSL2KO1_H3K27ac_rep1


title: 9sCa: NPCs_MSL2KO1_H3K27me3_rep1


title: 9sCa: NPCs_Control_Input3_rep3

description: Same batch as H3K4me1, H3K4me3, H3K27ac, H3K36me3, H3K27me3, H3K9me3, H4K16ac

value: WT


title: 9sCa: NPCs_MSL2KO2_Input4_rep2

description: Same batch as H4K5ac, H4K12ac


title: 9sCa: NPCs_MSL2KO2_H4K5ac_rep2

description:
NPCs_MSL2KO2_H4K5ac.bw
NPCs_MSL2KO2_H4K5ac.genome1.bw
NPCs_MSL2KO2_H4K5ac.genome2.bw


title: normal_transcriptome-4


title: 9sCa: NPCs_Control_Input3_rep2


title: 9sCa: NPCs_MSL2KO1_H3K4me3_rep2


title: 9sCa: NPCs_MSL2KO2_H4K5ac_rep1


title: 9sCa: NPCs_Control_Input3_rep1


title: 9sCa: NPCs_Control_H3K9me3_rep3

description:
NPCs_Control_H3K9me3.bw
NPCs_Control_H3K9me3.genome1.bw
NPCs_Control_H3K9me3.genome2.bw
NPCs_diff.peak.histone.RData


title: normal_transcriptome-3


title: 5m_dNTP_transcriptome-3


title: 9sCa: NPCs_MSL2KO2_H4K16ac_rep2

description:
NPCs_MSL2KO2_H4K16ac.bw
NPCs_MSL2KO2_H4K16ac.genome1.bw
NPCs_MSL2KO2_H4K16ac.genome2.bw


title: 9sCa: NPCs_MSL2KO2_Input1_rep2


title: 9sCa: NPCs_Control_H3K9me3_rep1


title: 9sCa: NPCs_Control_H3K9me3_rep2


title: normal_transcriptome-2


title: 9sCa: NPCs_Control_H3K4me3_rep3

description:
NPCs_Control_H3K4me3.bw
NPCs_Control_H3K4me3.genome1.bw
NPCs_Control_H3K4me3.genome2.bw
NPCs_diff.peak.histone.RData


title: normal_transcriptome-1


title: 9sCa: NPCs_Control_H3K4me3_rep2


title: 9sCa: NPCs_Control_H3K4me3_rep1


title: scBS-K562-3

data_processing:
The original sequence data obtained contain 150bp paired-end sequences. Before alignment, Trim Galore version 0.6.7 was used for adapter removal. Trimmed clean sequences were aligned and de-duplicated with hg19/mm10 by the bisulfite alignment tool Bismark version v0.15.0. The obtained bam files were converted into sam files using samtools version 1.3.1.
For the sam files, after the initial comparison using Bismark, we obtained the methylation information of each read based on the XM-tag (methylation call string) in the sam files. We calculated the methylation levels of CHH and CHG for each read and distinguished the reads into methylomic reads and transcriptomic reads by the methylation levels. When the methylation level of the reads was greater than 90%, they were classified as transcriptomic reads, and when the methylation level of the reads was less than 50%, they were classified as methylomic reads. For the analysis of methylomic reads, we extracted CpG methylation site information using the common methylation analysis pipeline and the R package methylKit version 1.22.0. For the isolated transcriptomic reads, the transcriptome analysis pipeline was used, which mainly included realignment using STAR version 2.7.3a and obtaining the expression profiles of the cells using htseq version 0.12.4.
For clustering using transcriptome data, the expression matrix of cells was obtained from expression profiles and then clustered using R package SC3 version 1.24.0. For the clustering of the methylome data, the Pearson correlation coefficients for the methylation levels of the commonly covered methylation sites were calculated and clearer clusters could be seen on the correlation matrix.
We used the methylome data as DNA data to perform copy number variation analysis. We used the bwa tool version 0.7.17 to perform genomic alignment and analysis. The bam files after alignment were converted to bed files for input into ginkgo for copy number variation analysis. The length of a bin was set to the default of 1M. The cell copy number variance profiles were obtained by feeding the bed files to ginkgo.
We input the gene expression matrix obtained from the transcriptome analysis pipeline into the R package DESeq2 version 1.36.0, and obtained the differentially expressed genes. For the enriched pathway analysis, we input the gene list into the enrichGO function in the R package clusterProfiler version 4.4.4 to obtain the enriched pathways. The Gene Set Enrichment Analysis (GSEA) was performed using the python package gseapy version 1.0.5.
Assembly: hg19, mm10
Supplementary files format and content: CpG.txt file containing methylation information for CpG sites.
Supplementary files format and content: counts.txt file containing gene expression information.
Library strategy: scBS-seq


title: 9sCa: NPCs_MSL2KO2_H4K12ac_rep1

description:
NPCs_MSL2KO2_H4K12ac.bw
NPCs_MSL2KO2_H4K12ac.genome1.bw
NPCs_MSL2KO2_H4K12ac.genome2.bw


title: 9sCa: NPCs_Control_H3K4me1_rep3

description:
NPCs_Control_H3K4me1.bw
NPCs_Control_H3K4me1.genome1.bw
NPCs_Control_H3K4me1.genome2.bw
NPCs_diff.peak.histone.RData


title: 9sCa: NPCs_MSL2KO2_H4K12ac_rep2


title: 9sCa: NPCs_Control_H3K4me1_rep2


title: 9sCa: NPCs_MSL2KO2_H3-4_rep2

description: Same batch as H4K5ac, H4K12ac


title: scBS-K562-1


title: scBS-K562-2


title: 9sCa: NPCs_MSL2KO2_H3-4_rep1

description: Same batch as H4K5ac, H4K12ac


title: 9sCa: NPCs_Control_H3K4me1_rep1


title: 9sCa: NPCs_Control_H3K36me3_rep2

description:
NPCs_Control_H3K36me3.bw
NPCs_Control_H3K36me3.genome1.bw
NPCs_Control_H3K36me3.genome2.bw
NPCs_diff.peak.histone.RData


title: DIRECT-HL60-6

description: DIRECT: single-cell DNA methylation and gene expression co-analysis in a single library

library_source: other

data_processing:
The original sequence data obtained contain 150bp paired-end sequences. Before alignment, Trim Galore version 0.6.7 was used for adapter removal. Trimmed clean sequences were aligned and de-duplicated with hg19/mm10 by the bisulfite alignment tool Bismark version v0.15.0. The obtained bam files were converted into sam files using samtools version 1.3.1.
For the sam files, after the initial comparison using Bismark, we obtained the methylation information of each read based on the XM-tag (methylation call string) in the sam files. We calculated the methylation levels of CHH and CHG for each read and distinguished the reads into methylomic reads and transcriptomic reads by the methylation levels. When the methylation level of the reads was greater than 90%, they were classified as transcriptomic reads, and when the methylation level of the reads was less than 50%, they were classified as methylomic reads. For the analysis of methylomic reads, we extracted CpG methylation site information using the common methylation analysis pipeline and the R package methylKit version 1.22.0. For the isolated transcriptomic reads, the transcriptome analysis pipeline was used, which mainly included realignment using STAR version 2.7.3a and obtaining the expression profiles of the cells using htseq version 0.12.4.
For clustering using transcriptome data, the expression matrix of cells was obtained from expression profiles and then clustered using R package SC3 version 1.24.0. For the clustering of the methylome data, the Pearson correlation coefficients for the methylation levels of the commonly covered methylation sites were calculated and clearer clusters could be seen on the correlation matrix.
We used the methylome data as DNA data to perform copy number variation analysis. We used the bwa tool version 0.7.17 to perform genomic alignment and analysis. The bam files after alignment were converted to bed files for input into ginkgo for copy number variation analysis. The length of a bin was set to the default of 1M. The cell copy number variance profiles were obtained by feeding the bed files to ginkgo.
We input the gene expression matrix obtained from the transcriptome analysis pipeline into the R package DESeq2 version 1.36.0, and obtained the differentially expressed genes. For the enriched pathway analysis, we input the gene list into the enrichGO function in the R package clusterProfiler version 4.4.4 to obtain the enriched pathways. The Gene Set Enrichment Analysis (GSEA) was performed using the python package gseapy version 1.0.5.
Assembly: hg19, mm10
Supplementary files format and content: CpG.txt file containing methylation information for CpG sites.
Supplementary files format and content: counts.txt file containing gene expression information.
Library strategy: DIRECT

molecule: other

value: promyelocytic leukemia cells


title: 9sCa: NPCs_Control_H3K36me3_rep1


title: 9sCa: NPCs_MSL2KO2_H3-2_rep2

description: Same batch as MSL2, DNMT3A, DNMT3B


title: 9sCa: NPCs_Control_H3K27me3_rep2

description:
NPCs_Control_H3K27me3.bw
NPCs_Control_H3K27me3.genome1.bw
NPCs_Control_H3K27me3.genome2.bw
NPCs_diff.peak.histone.RData


title: 9sCa: NPCs_Control_H3K27me3_rep3


title: 9sCa: NPCs_Control_H3K27me3_rep1


title: 9sCa: NPCs_MSL2KO2_H4K16ac_rep1


title: DIRECT-HL60-5


title: DIRECT-HL60-4


title: DIRECT-HL60-3


title: 9sCa: NPCs_Control_H3K36me3_rep3


title: 9sCa: NPCs_Control_H3K27ac_rep3

description:
NPCs_Control_H3K27ac.bw
NPCs_Control_H3K27ac.genome1.bw
NPCs_Control_H3K27ac.genome2.bw
NPCs_diff.peak.histone.RData


title: 9sCa: NPCs_Control_H3K27ac_rep2


title: 9sCa: NPCs_MSL2KO2_H3-2_rep1

description: Same batch as MSL2, DNMT3A, DNMT3B


title: Ampk InsMet input rep1

city: San Diego

first: April

middle: Elizabeth

last: Williams

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
First, adapter trimming was performed with cutadapt (v1.14).
Next, reads were mapped with STAR (v2.4.0i) against a database of repetitive elements, with mapping reads discarded from further analysis.
Remaining reads were then mapped to the mouse genome (mm10) with STAR (v2.4.0i)
Stranded reads mapping to GENCODE (vM20) genes were quantified with featureCounts (subread-1.6.4). Mitochondrial genes were discarded, and only genes with at least 0.5 reads per million across all datasets were kept for further analysis.
Differential expression in polysome versus input was quantified with edgeR (v3.26.8) with dispersion = 0.06 estimated from the subset of experiments with multiple replicates.
Genome_build: mm10
Supplementary_files_format_and_content: EdgeR output files (*.txt.gz*) contain gene identifier, log(fold-change in polysome versus input), log(counts per million), and p-value (polysome versus input)

source_name: Primary Hepatocytes

growth_protocol: Primary hepatocytes were isolated from mice 8-16 weeks of age following Tamoxifen treatment to induce deletion of Tsc2 and AMPK, cells were plated in serum for 3-4 hours then moved to serum free media for 16h prior to treatment

extract_protocol:
Cells were snap frozen, lysed in polysome buffer, put through sucrose gradient and fractionated (ribosome associated only), RNA isolated using Trizol LS and zymo direct-zol RNA purification kit
mRNA-seq libraries were prepared using the TruSeq RNA library preparation kit (version 2)

treatment_protocol:
Cells in serum-free media were treated with metformin or Ink in the presence or absence of Insulin 15' pretreatment
Cells were treated with cyclohexamide 10' prior to collection

value: C57BL/6 (F3 generation)

value: primary hepatocytes

value: 8-16 weeks old

value: Ampka1 fl/fl; Ampka2 fl/fl; AlbCreER

tag: tamoxifen treatment

value: Tamoxifen treatment 3x 14-17 days prior to hepatocyte isolation

tag: metformin treatment

value: 2mM Metformin for 2h serum-starved

tag: insulin treatment

value: 15 minute pre-treatment with 1nM Insulin

tag: rna fraction

value: polyA RNA


title: 9sCa: NPCs_Control_H3K27ac_rep1


title: Ampk Ins input rep1

tag: tissue

value: untreated - serum starved


title: 9sCa: NPCs_MSL2KO2_H3-1_rep1

tag: genotype


title: DIRECT-HL60-2

tag: cell line


title: AATsc Ins input rep1

value: Raptor - S722A; S792A; Tsc2 fl/fl; AlbCreEr


title: DIRECT-HL60-1

tag: cell type


title: 9sCa: NPCs_MSL2KO2_DNMT3B_rep2

description:
NPCs_MSL2KO2_DNMT3B.bw
NPCs_MSL2KO2_DNMT3B.genome1.bw
NPCs_MSL2KO2_DNMT3B.genome2.bw

tag: strain

value: Female


title: Bulk-K562-2


title: Tsc Ins input rep1

value: Tsc2 fl/fl; AlbCreEr


title: 9sCa: NPCs_MSL2KO2_DNMT3B_rep1

tag: gender


title: Tsc InsMet input rep1


title: AA InsMet input rep1

value: Raptor - S722A; S792A


title: 9sCa: NPCs_MSL2KO2_DNMT3A_rep2

description:
NPCs_MSL2KO2_DNMT3A.bw
NPCs_MSL2KO2_DNMT3A.genome1.bw
NPCs_MSL2KO2_DNMT3A.genome2.bw

tag: library type


title: WT InsInk input rep1

value: wild type

value: 0.1uM INK-128 for 2h serum-starved


title: Bulk-K562-1

value: chronic myeloid leukemia cells


title: WT InsMet input rep1


title: WT Ins input rep1


title: 9sCa: NPCs_MSL2KO2_H3-1_rep2

tag: replicate


title: Tube-K562-3


title: 9sCa: NPCs_MSL2KO2_BSseq_rep2

description:
NPCs_MSL2KO2_BSseq.bw
NPCs_MSL2KO2_BSseq.genome1.bw
NPCs_MSL2KO2_BSseq.genome2.bw

value: BSseq


title: Tube-K562-2


title: 9sCa: NPCs_MSL2KO2_BSseq_rep1


title: AATsc InsMet input rep1

value: C57BL/6 (F3 generation)


title: Tube-K562-1


title: 9sCa: NPCs_MSL2KO2_BRD4_rep2

description:
NPCs_MSL2KO2_BRD4.bw
NPCs_MSL2KO2_BRD4.genome1.bw
NPCs_MSL2KO2_BRD4.genome2.bw


title: DIRECT-K562-13


title: 9sCa: NPCs_MSL2KO2_DNMT3A_rep1


title: 9sCa: NPCs_MSL2KO2_BRD4_rep1


title: AA Ins input rep1

value: primary hepatocytes


title: DIRECT-K562-10


title: DIRECT-K562-11


title: Cultured Normal ovarian stromal cells rep3

type: RNA

city: Dummerstorf

first: Vijay simha

last: Baddela

address: Wilhelm-Stahl-Allee 2

department: Reproductive biology

institute: Leibniz institute for farm animal biology

hyb_protocol: The RNA was hybridized overnight (45°C) in the GeneChipR Hybridization Oven (Affymetrix) to the Affymetrix Bovine Gene 1.0 ST arrays. Washing and staining were performed according to the Affymetrix standard protocol.

scan_protocol: The scanning of the microarray was done with the GeneChip Scanner 3000 HR (Affymetrix) and image processing was done with the software AGCC (Affymetrix).

data_processing: Data analysis was performed with TAC 4.0 software (Affymetrix) and RMA method was used for normalization

label: Biotin

organism: Bos taurus

source_name: Cultured stromal cells, Normal

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol (GeneChip® Expression 3’Amplification One-Cycle Target Labeling and Control Reagents).

growth_protocol: Normal and tumor ovarian stromal cells were cultured in DMEM/F12ꓼ10% FKS media

extract_protocol: Total RNA was prepared using innuPREP RNA Mini Kit (Analytik Jena, Germany)

treatment_protocol: No specific treatments were given

value: cultured stromal fibroblast cells


title: iPCR_EEP_Klf2_run1

data_processing:
Basecalling, filtering and demultiplexing were performed using standard software of the Illumina MiSeq, NextSeq or NovaSeq platforms
For cDNA and pDNA samples, the barcode sequence was extracted from the read (using a custom python scripts) and counted.
For iPCR samples the insert sequence was aligned to a custom genome (using bowtie2) containing only the target sequences extracted from the mm10 genome, and the barcode was extracted from the ead using a custom python script.
Barcodes were clustered using Starcode (version 1.1) {Zorita, 2015, 25638815} to remove errors from barcode sequencing.
barcodes  matched with multiple element combinations were removed from the data
Per  combination an activity value was calculated as the ratio of the mean readcount in the RNA samples and the mean readcount in the pDNA library samples across all barcodes assigned to the singlet or combination.
Baselines were calculated across control-control combinations and then used to calculate boost indices as the log2 ratio between the activity of a combination and the baseline
Assembly: mm10
Supplementary files format and content: tsv format, each row contains a unique EEP combination, with fragment identifiers, calculated activities, baselines and Boost indices

value: mESCs


title: DIRECT-K562-9


title: 9sCa: NPCs_MSL2KO2_ATACseq_rep3

description:
NPCs_MSL2KO2_ATACseq.bw
NPCs_MSL2KO2_ATACseq.genome1.bw
NPCs_MSL2KO2_ATACseq.genome2.bw

data_processing:
RNAseq and TTseq: The data are processed via snakePipes mRNA-seq pipeline (developing branch) (Bhardwaj et al., 2019). SnakePipes removed adapters and low quality bases (< Q20) using TrimGalore (v0.6.5) with parameters '-q 20 --trim-n'. The trimmed reads are aligned with STAR (v2.7.4) (Dobin et al., 2013) to an ‘N-masked’ genome, which is a version of the mouse reference genome mm10 where all the polymorphicsites (SNPs) for Mus musculus CAST/EiJ and Mus musculus C57BL/6 (or 129S1/SvImJ) are masked by ambiguity nucleobase ‘N’ (Keane et al., 2011). The mapped reads are then passed to SNPSplit (0.3.4) (Krueger and Andrews, 2016) to generate allele-specific BAM files by separating the alignment into two distinct alleles (CAST/EiJ and C57BL/6 or 129S1/SvImJ) based on SNPs information downloaded from Mouse Genome Database (Keane et al., 2011). The aligned reads of standard and allele specific level are counted separately on Gencode GTF (m9) via featureCounts (v2.0.0) (Yang et al., 2014).
ChIPseq: The data are processed via snakePipes DNA-mapping and ChIP-seq pipeline (developing branch) (Bhardwaj et al., 2019). Adapters and low quality bases (< Q20) are removed using TrimGalore (v0.6.5) with parameters '-q 20 --trim-n'. For all samples, reads are then mapped to the ‘N-masked’’ genome with Bowtie2 (2.3.5) (Langmead and Salzberg, 2012). Reads mapped on blacklisted regions from Encode Consortium are discarded. Duplicated reads are also filtered with Picard MarkDuplicates (1.65) (https://broadinstitute.github.io/picard/). In the end, only properly paired mapped reads and reads with mapping quality over 3 are kept for further analysis. SNPSplit (0.3.4) (Krueger and Andrews, 2016) is then used to generate allele-specific BAM files and deepTools (v3.3.2) (Ramirez et al., 2014) is used to check data quality. In the ChIP-seq part, peak calling is performed with MACS2 (v2.2.6) (Zhang et al., 2008) with options [--qvalue 0.001]. It is done with input as control on total and allele specific ChIP-seq signals respectively. CSAW (v1.20.0) (Lun and Smyth, 2015) is additionally used to calculate log2FC on peak regions between MSL2 KO and WT or between allele2 and allele1. Bigwig files are created with deepTools bamCompare (v3.3.2) (Ramirez et al., 2014), using input normalization method and log2ratio and subtract option.
ATACseq: The data are processed via snakePipes DNA-mapping and ATAC-seq pipeline (developing branch) (Bhardwaj et al., 2019). In the DNA-mapping part, adapters and low quality bases (< Q20) are removed using TrimGalore (v0.6.5) with parameters '-q 20 --trim-n'. For all samples, reads are then mapped to the ‘N-masked’’ genome with Bowtie2 (v2.3.5) (Langmead and Salzberg, 2012). Reads mapped on blacklisted regions from Encode Consortium are discarded. Duplicated reads are also filtered with Picard MarkDuplicates (v1.65) (https://broadinstitute.github.io/picard/). In the end, only properly paired mapped reads and reads with mapping quality over 3 are kept for further analysis. SNPSplit (0.3.4) (Krueger and Andrews, 2016) is then used to generate allele-specific BAM files and deepTools (v3.3.2) (Ramirez et al., 2014) is used to check data quality. In the ATAC-seq part, the BAM files are filtered to include only properly paired reads with appropriate fragment sizes (<150 bases). To identify open/accessible regions, peak calling is done with MACS2 (v2.2.6) (Zhang et al., 2008) with options [--qvalue 0.001], on total and allele-specific ATAC-seq signal respectively. CSAW (v1.20.0) (Lun and Smyth, 2015) is additionally used to calculate log2FC on peak regions between MSL2 KO and WT or between allele2 and allele1. Bigwig files are created with deepTools bamCoverage (v3.3.2) (Ramirez et al., 2014), using size factor calculated by deepTools multiBamSummary (v3.3.2).
BSseq: Raw fastq files were aligned against the ‘N-masked’ genome and deduplicated using Bismark (v0.22.3) (Krueger and Andreas, 2011). Resulting Alignments were allele-separated using SNPsplit with flags '--paired' and '--bisulfite'. Relevant quality metrics (conversion rates, genome coverage and GC bias) were calculated using MethylDackel version 0.6.0 (https://github.com/dpryan79/MethylDackel) and DeepTools (v3.5.0). Allele-specific differentially CpG methylated sites between MSL2 KO and WT or between allele2 and allele1 were called with DSS version 2.34.0.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files: log2 ratio or subtract value over the input sample (merged replicates) . bed: peak calling from MACS2 (merged replicates). RData: differential peak calling result from CSAW and differential CpG methylation sites from DSS. tsv: differential expression analysis from DESeq2. txt: Differentially expression genes further classification into five cateogories.

source_name: Neural progenitor cells

value: ATACseq


title: Cultured Tumor ovarian stromal cells rep3

source_name: Cultured stromal cells, Tumor


title: 9sCa: NPCs_MSL2KO2_ATACseq_rep2


title: Cultured Tumor ovarian stromal cells rep1


title: Cultured Tumor ovarian stromal cells rep2


title: 9sCa: NPCs_MSL2KO2_ATACseq_rep1


title: Cultured Normal ovarian stromal cells rep2


title: Jurkat-SCML4-2

first: Maoxiao

last: Feng

address: Beiyuan Street 247

institute: Department of Clinical Laboratory

data_processing:
CLC Genomics Workbench v 11.0.1
RNA-seq libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB)
Sequenced on an Illumina platform with 125bp/150bp paired-end reads
FastQC initially processed raw sequence reads for quality control, and then adapter sequences and poor-quality reads were removed. Quality filtered reads were then mapped to reference genome using STAR, and only uniquely mapped reads were kept. Sam files were converted to Bam format using Samtools.
Assembly: hg19
Supplementary files format and content: csv file includes FPKM values for each Sample

source_name: Jurkat

growth_protocol: Jurkat cells stably overexpressing SCML4 or control (EV) were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics at 37°C and 5% CO in a humidified atmosphere.

extract_protocol:
RNA was extracted using TRIzol from the Jurkat cells
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Jurkat cells were induced with PMA (100 ng/ml) plus ionomycin (1 μM) for 6 h.

value: Jurkat

value: Ouabain-induced leukemia cell line

value: PMA plus ionomycin

tag: time


title: Jurkat-SCML4-1


title: Cultured Normal ovarian stromal cells rep1


title: DIRECT-K562-12


title: Jurkat-EV-3

value: EV


title: DIRECT-K562-8


title: 9sCa: NPCs_MSL2KO1_unlabeledTTseq_rep3

value: unlabeledTTseq


title: 9sCa: NPCs_MSL2KO1_unlabeledTTseq_rep2

value: Female


title: Jurkat-EV-2


title: DIRECT-K562-7


title: 9sCa: NPCs_MSL2KO1_unlabeledTTseq_rep1


title: Jurkat-EV-1


title: DIRECT-K562-6


title: Jurkat-SCML4-3


title: shKRAS_2_S21

city: Pamplona

first: Silvestre

last: Vicent

state: Outside the US or Canada

address: 55 PIO XII Ave

department: Oncology

country: Spain

institute: Center for Applied Medical Research (CIMA)

data_processing:
The quality of the samples was verified using FastQC v0.11.3 software.
FASTQ files were mapped to hg19 human assembly using STAR v2.5.2b with default parameters.
featureCounts v1.5.0 software and Gencode v19 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: H358 cell line

growth_protocol: Cells were grown in RPMI1640 (10% FBS and 1% antibiotics)

extract_protocol:
RNA was processed using Trizol and cleaned using Qiagen columns. RNA quality was analysed using Experion™ (Bio-Rad) and only RNAs with RQI>7 were included in the experiment.
Library construction was done as reported in Jaitin, D.A., et al., Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science, 2014. 343(6172): p. 776-9.
Low input RNA-seq (mars-seq)

treatment_protocol: Cells were infected with 3 different shRNAs (GFPsh, FOSL1sh or KRASsh) for 2 days, then selected with puromycin for 3 days. Upon expansion of selected cells, shRNAs were induced by addition of 1 ug/ml doxycycline for 4 days, then trypsinized and plated for 24 h before RNA was harvested

value: shKRAS


title: shKRAS_3_S24


title: Mouse lung adenocarcinoma cell line in 2D cell culture

city: Zhunan, Miaoli County

first: Chia-Chi

last: Chang

address: 35 Keyan Road

department: Institute of Cellular and System Medicine

institute: National Health Research Institutes

hyb_protocol: Samples were hybridized with Mouse Gene 2.0 ST Array (Affymetrix) and scanned at the NHRI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: The data were analyzed using Affymetrix Expression Console™ Software (version 1.4) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options.

label: biotin

source_name: LLC, 72 h after 2D culture

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: LLC are cultured in DMEM with 10% FBS, 100 U/ml antibiotics. Cells were sub-cultured at the dilution of 1:3 to 1:4 at 80-90% conﬂuence.

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. Inclusion of 1 U/ µL of the RiboLock RNase Inhibitor (Thermo) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with RQ1 RNase-Free DNasee (Peomega) to remove trace amounts of genomic DNA.

treatment_protocol: 2D culture condition: seeded 10^6 cells on cell culture dish for 3 days.

value: Lung cancer cell

tag: culture condition