title: HctYH_OF3A_1-4-I3-H8


title: HctYH_OF3A_1-4-I3-G20

status: Public on Dec 15 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: OF3A human BA46

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age

tag: Sex

value: Female

tag: molecule subtype

value: nuclear RNA + genomic DNA


title: WT-P10, rep2

city: Adelaide

first: Alison

last: Gardner

state: SA

address: AHMS, Uni of Adelaide, North Terrace

department: Faculty of Health and Medical Sciences

country: Australia

institute: University of Adelaide

library_source: transcriptomic

data_processing:
Aligned RNAseq with hisat2 using grcm38_tran & then ran salmon using Mus_musculus.GRCm38.gencode.vM25.chr_patch_hapl_scaff.annotation.gtf
Please note that sample 06-WT-14 was an outlier and removed from data processing.
Assembly: mm10
Supplementary files format and content: rnaseq gene counts, rnaseq transcript counts

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Total RNAs were extracted from the E14.5, E18.5 and P10 Thoc2Δ/Y and Thoc2+/Y mouse brain dorsal cortices using our in-house protocol that uses combination of TRIzol Reagent (Invitrogen) and RNeasy Mini Kit (Qiagen) and quantified and qualified by NanoDrop (Thermo Fisher Scientific Inc.), Agilent 2100 Bioanalyzer (Agilent Technologies, USA), and 1% agarose gel.
1 μg total RNA from each sample with RNA integrity number (RIN) value ≥7 was used for library preparation. Next generation sequencing libraries were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina as per manufacturer’s protocol (Vazyme Biotech). Briefly, the poly(A) mRNAs were isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). The mRNA fragmentation and priming were performed using NEBNext First Strand Synthesis Reaction Buffer and Random Primer mix. The first strand cDNA was synthesized using NEB ProtoScript II Reverse Transcriptase and the second-strand cDNA using Second Strand Synthesis Enzyme Mix. The double-stranded cDNAs were purified using AxyPrep Mag PCR Clean-up (Axygen) and treated with NEBNext Ultra End Repair/dA-Tailing mix to convert fragmented DNA to repaired DNA and add dA-tails to both ends, followed by T-A ligation using NEBNxt Ultra II Ligation Module to add adaptors to both the ends. The adaptor-ligated DNAs were size selected for fragments of ~360 bp (with ~300 bp inserts) using AxyPrep Mag PCR Clean-Up kit (Axygen). Each sample was amplified by PCR for 11 cycles using P5 and P7 primers; both primers carried sequences that can anneal with flow cell to perform bridge PCR and P7 primer with a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-Up Kit (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, USA). The libraries with different indices were multiplexed and loaded on an Illumina NovaSeq 6000 (Illumina, USA). Strand-specific sequencing at 80 million 2×150bp paired-end reads per sample was carried out.

tag: tissue

value: Brain

tag: strain

tag: genotype

value: WT

value: male


title: Old_1

city: Nashville

first: Ananya

last: Nandy

state: Tennessee

address: 2215 Garland Ave

department: Clinical Pharmacology

institute: VUMC

data_processing:
Cutadapt (https://github.com/marcelm/cutadapt) was used to trim adapters.
STAR was used to map reads to the human reference genome.
DESeq2 was used to detect differential expression between conditions.
Assembly: hg38
Supplementary files format and content: A raw count table that provides complete data with values for all features and all samples

source_name: Femur

extract_protocol:
Femurs were removed, flash frozen on liquid nitrogen, pulverized to powder using Freezer mill and RNA was harvested using Trizol reagent. NovaSeq 6000  (version 2.4.11; Illumina) was used for preparing library
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone

value: 22 months

value: enriched mRNA


title: Old_2


title: HctYH_OF3A_1-4-I3-H7


title: Hemi-P10, rep5


title: Hemi-P10, rep4


title: Young_5

value: 2 months


title: Hemi-P10, rep2


title: Hemi-P10, rep3


title: Young_4


title: HctYH_OF3A_1-4-I3-G8


title: WT-E18, rep5


title: HctYH_OF3A_1-4-I3-F7


title: HctYH_OF3A_1-4-I3-F8


title: Hemi-E14, rep2


title: Young_3


title: HctYH_OF3A_1-4-I3-F20


title: WT-E18, rep4


title: WT-P10, rep3


title: WT-E18, rep2


title: Young_2


title: WT-E18, rep3


title: HctYH_OF3A_1-4-I3-I19


title: WT-P10, rep1


title: WT-E18, rep1


title: HctYH_OF3A_1-4-I3-F19


title: HctYH_OF3A_1-4-I3-G19


title: Hemi-E18, rep4


title: Young_1


title: Hemi-E18, rep5


title: Apoe-/- HFD anti-CVI-mAb, replicate 1, scRNAseq

city: Guangzhou

first: Duan

last: Rui

address: No. 1023-1063, Shatai South Road, Baiyun District, Guangzhou

country: China

institute: Southern Medical University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: peritoneal

extract_protocol:
Peritoneal cells were isolated from C57BL/6 mice or Apoe−/− mice which were injected with 10 ml of cold PBS into the mice peritoneal cavity. Cells were washed and re-suspended in PBS. The cell suspensions obtained individually from the peritoneal cavity were passed through a 100 µm cell strainer and were stained with anti-mouse F4/80-FITC for 30 min. The total viable F4/80+ cells were selected using Beckman Coulter’s MoFlo Astrios EQ for scRNA-sequencing.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

value: peritoneal

value: 24 weeks old

tag: cell type

value: macrophage

tag: treatment

value: high-fat diet with mAb treated

value: ApoE -/-


title: HctYH_OF3A_1-4-I3-E20


title: Apoe-/- HFD, replicate 1, scRNAseq

description: 10x Genomics

value: high-fat diet


title: Hemi-E18, rep2


title: Hemi-E18, rep3


title: Hemi-P10, rep1


title: Apoe-/-, replicate 1, scRNAseq

description: 10x Genomics

value: normal diet


title: snRNA-seq, D. simulans central brain, biol rep6

city: Suwon

first: Daehan

last: Lee

state: Gyeonggi

address: 2066 Seobu-ro

country: South Korea

institute: Sungkyunkwan University

description: 10x Genomics

data_processing:
Raw snRNA-seq data was first processed through Cell Ranger (v6.0.1, default parameters except --include-introns)
Assembly: D. simulans reference genome and transcriptome from FlyBase (release 2.02)
Supplementary files format and content: TSV files and matrix files

organism: Drosophila simulans

source_name: central brain

growth_protocol: Standard fly growth medium

extract_protocol:
Newly-eclosed 30-50 male and female adult flies were collected and placed together for mating, followed by sorting by sex on day 5. The central brains of 20 mated female flies were dissected and collected in 100 μl Schneider’s medium, flash-frozen in liquid nitrogen, and stored at -80ºC for nuclear extraction. Sample homogenization, single-nucleus suspension, and nuclear sorting were performed using the standard protocol described in the Fly Cell Atlas (Li et al. 2022)
To obtain sequencing data from 10,000 nuclei, 15-20,000 nuclei were collected and loaded onto the Chromium Next GEM Chip (10x Genomics). Sequencing libraries were prepared with the Chromium Single Cell 3ʹ reagent kit v3.1 dual index, strictly following the manufacturer’s recommendations.

value: central brain

value: standard fly food


title: Hemi-E18, rep1


title: snRNA-seq, D. simulans central brain, biol rep5

description: 10x Genomics


title: HctYH_OF3A_1-4-I3-E19

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female

value: nuclear RNA + genomic DNA


title: HctYH_OF3A_1-4-I3-D8


title: C57, replicate 1, scRNAseq

description: 10x Genomics

value: WT


title: Hemi-E14, rep1

value: Brain

value: male


title: HctYH_OF3A_1-4-I3-D7


title: Sox2_mzKO_ICM_scRNA_65

city: Beijing

first: Lijia

last: Li

address: Haidian District

department: School of Life Science

institute: Tsinghua University

data_processing:
ChIP-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -t -q -N 1 -L 25. All ummapped reads, non-uniqurely mapped reads and PCR duplicates were removed. For downstream analysis, we computed the numbers of reads per kilobase of bin per million reads sequenced (RPKM) which were further normalized by input. A resolution of 100bp bin in genome was used in the rpkm file.
bulk RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). scRNA-seq reads were mapped to mm9 genome by HISAT2 (version 2.1.0).The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq, ChIP-seq tracks, gene expression table for RNA-seq data

source_name: E3.5 ICM

growth_protocol: Immunosurgery was performed to remove TE and isolate ICM. Briefly, after pronase treatment to remove the zona pellucida, blastocysts were incubated with DMEM containing rabbit anti-mouse serum (1:10) for 30 min and then washed three times in DMEM plus 10% FBS. The resulting embryos were exposed to guinea pig complement (1:5 in DMEM) for 10 min, washed three times, and then pipetted under microscopy to carefully remove TE cells. We separated TE from blastocysts by manual bisection to collect the opposite part of ICM ). Next, we used TrypLE (Invitrogen, Carlsbad, California, USA, Cat. 12605010)  to dissociate embryos into single cells. Incubation time 5 minutes and use a home-made capillary with inner diameter about 20um repeat push-pull the ICM to single cell with oral siphon.

extract_protocol:
Cells or embyos were lysed in lysis buffer containing RNase inhibitor.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before being subjected to sequencing.

value: Sox2 mzKO

value: mix

tag: chip-antibody


title: HctYH_OF3A_1-4-I3-D20


title: ABL group sample 3

city: New York

first: Nicola

last: Partridge

state: NY

address: 345e 24th Street

department: Department of Molecular Pathobiology

institute: New York University

data_processing:
The quality of raw data was checked by FastQC (v. 0.11.9)
Read counts were quantified using Salmon (v. 1.7.0)
Differential expression analysis was performed by DESeq2 R/Bioconductor package
Assembly: GRCm38/mm10
Supplementary files format and content: Salmon Output File Formats
Supplementary files format and content: quant.sf for each sample

source_name: Calvaria

growth_protocol: Primary mouse calvarial osteoblasts were cultured in in αMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated from cells by using TRIzol reagent and purified with Qiagen RNeasy mini kit from Qiagen
Illumina TruSeq Stranded Total RNA library prep with Ribozero Gold

treatment_protocol: Prior to treatment, cells were serum-starved with 0.1% FBS for 16 h. Then, osteoblasts were treated with 1 nM of the peptides for 4 h (n=3 per group).

value: Calvaria

value: osteoblast

value: wild-type

value: ABL


title: HctYH_OF3A_1-4-I3-E8


title: snRNA-seq, D. simulans central brain, biol rep4

description: 10x Genomics


title: Sox2_mzKO_ICM_scRNA_64


title: HctYH_OF3A_1-4-I3-D19


title: ABL group sample 2


title: Sox2_mzKO_ICM_scRNA_63


title: snRNA-seq, D. simulans central brain, biol rep1

description: 10x Genomics


title: Sox2_mzKO_ICM_scRNA_62


title: snRNA-seq, D. simulans central brain, biol rep2

description: 10x Genomics


title: ABL group sample 1


title: HctYH_OF3A_1-4-I3-C8


title: PTHrP 1-36 group sample 3

value: PTHrP 1-36


title: HctYH_OF3A_1-4-I3-C7


title: siCtrl_input_rep2

city: philadelphia

first: Kathy

last: Liu

state: PA

address: 415 curie blvd

institute: University of Pennsylvania

data_processing:
The high throughput sequencing reads were adaptor and quality trimmed using Trimmomatic with following command: trimmomatc SE -phred33 ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:25 TRAILING:25 SLIDINGWINDOW:4:20 MINLEN:30.
Then, the reads were aligned to the mm10 mouse genome reference using HISAT2. Parameters used were: --no-unal (not report the unaligned reads), --known-splicesite-file (generated from the Ensembl mm10 annotation file) and –k 1 (report one alignment).
The exomePeak package was used to call the differentail m6A peaks.
The DEseq2 package was uded to analysis the differential expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: table with differential m6A peaks and table with differential expressed genes

molecule: polyA RNA

growth_protocol: N2a cells were cultured in DMEM + GlutaMAX (GIBCO, 11995065) with 10% FBS (GIBCO, 26140-079) and 1% Pen/Strep (Corning, 30-002-CI) in a humidified incubator with 5% CO2¬ at 37°C.

extract_protocol:
Total RNA was purified using TRIzol per the manufacturer’s instruction. PolyA RNAs were purified using Dynabeads™ Oligo(dT)25 (Thermo, 61002). m6A IP was performed by using EpiMark® N6-Methyladenosine Enrichment Kit (NEB, E1610S).
Libraries were constructed according to TruSeq Stranded mRNA Kit (Illumina) protocol. The concentrations for all the libraries were determined by KAPA Library Quantification Kit (KAPA Biosystems) following the manufacturer’s protocol, and subjected to Next-generation high-throughput sequewncing using an illumina NextSeq 550 with a single-end 75-bp read length.

treatment_protocol: N2a cells were transfected with siRNA targeting Emg1 or siControl using Lipofectamin RNAimax following the manufacture's instruction. 48 hrs later, the cells were collected.

value: knockdown control


title: HctYH_OF3A_1-4-I3-C20


title: Sox2_mzKO_ICM_scRNA_60


title: PTHrP 1-36 group sample 2


title: siCtrl_input_rep1


title: PTHrP 1-36 group sample 1


title: siEmg1_input_rep2

value: Emg1 knockdown


title: HctYH_OF3A_1-4-I3-C19


title: Sox2_mzKO_ICM_scRNA_59


title: snRNA-seq, D. simulans central brain, biol rep3

description: 10x Genomics

value: central brain


title: siEmg1_input_rep1


title: Sox2_mzKO_ICM_scRNA_58


title: PTH 1-34 group sample 3


title: PTH 1-34 group sample 2


title: HctYH_OF3A_1-4-I3-B7


title: siCtrl_m6AIP-seq_rep2

data_processing:
Library strategy: m6A-Seq
The high throughput sequencing reads were adaptor and quality trimmed using Trimmomatic with following command: trimmomatc SE -phred33 ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:25 TRAILING:25 SLIDINGWINDOW:4:20 MINLEN:30.
Then, the reads were aligned to the mm10 mouse genome reference using HISAT2. Parameters used were: --no-unal (not report the unaligned reads), --known-splicesite-file (generated from the Ensembl mm10 annotation file) and –k 1 (report one alignment).
The exomePeak package was used to call the differentail m6A peaks.
The DEseq2 package was uded to analysis the differential expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: table with differential m6A peaks and table with differential expressed genes


title: PTH 1-34 group sample 1


title: Sox2_mzKO_ICM_scRNA_57


title: Conrol group sample 3

value: no peptide


title: Sox2_mzKO_ICM_scRNA_56


title: HctYH_OF3A_1-4-I3-B20

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: Sox2_mzKO_ICM_scRNA_61


title: siEmg1_m6AIP-seq_rep2


title: Conrol group sample 2


title: siEmg1_m6AIP-seq_rep1


title: Sox2_mzKO_ICM_scRNA_55


title: Conrol group sample 1


title: Sox2_mzKO_ICM_scRNA_54


title: Sox2_mzKO_ICM_scRNA_53


title: HctYH_OF3A_1-4-I3-B8

value: Female


title: 1179

city: Athens

first: Maria

middle: G.

last: Tektonidou

state: Please choose a State

address: Mikras Asias 75

country: Greece

institute: National and Kapodistrian University of Athens

description: Healthy Control

data_processing:
Basecalling on Illumina NextSeq550
Alignement with STAR on hg38 with pipeline provided by Lexogen and BlueBee
Bam used for bedgraph construction
bigWig constructed through bedGraphToBigWig
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Whole Blood

extract_protocol:
Total RNA was isolated from whole blood, stored in paxgene, using the ExtractionMonarch® Total  RNA Miniprep Kit (NEB #T2010). Upon blood isolation, Monarch DNA/RNA Protection Reagent  (supplied as a 2x concentrate) was added undiluted to an equal volume of blood. Addition of the  protection reagent and the following RNA isolation was performed as described in the Kit's manual  for Total RNA Purification from Mammalian Whole Blood Samples.
After quantification on a NanoDrop ND-1000 (Thermofisher) and Bioanalyzer RNA 6000 Nano  assay (Agilent), 140-300ng of total RNA from samples passing quality control were processed  using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen, 015.96) for library  preparation. Libraries were assessed for molarity and median library size using Bioanalyzer High  Sensitivity DNA Analysis (Agilent, 5067-4626)

value: Blood

tag: gender

value: F

tag: diagnosis

value: Healthy Control


title: Sox2_mzKO_ICM_scRNA_52


title: 1180

description: Thrombotic Primary APS

value: M

value: Thrombotic Primary APS


title: HctYH_OF3A_1-4-I3-A20

value: nuclear RNA + genomic DNA


title: HctYH_OF3A_1-4-I3-A19


title: Sox2_mzKO_ICM_scRNA_51

value: Sox2 mzKO

value: mix


title: 1178

description: Healthy Control


title: M-P 4h

city: Charlotte

first: Ehsan

last: Tabari

state: NORTH CAROLINA

address: 9201 University City Blvd

department: Bioinformatics

institute: UNC Charlotte

data_processing:
The genome sequence of E. coli K12 substr. MG1655 (NC_000913.2) was obtained from NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/). The gene annotation file and the experimentally verified operons in the bacterium were downloaded from RegulonDB (Gama-Castro et al., 2011) (http://regulondb.ccg.unam.mx/). A total of 4,501 annotated genes (also including pseudo genes and non-coding small RNAs) are included in this analysis.
As the RNA-seq reads were not size-selected during the library construction to capture short RNAs, we trimmed the 3’ adapters attached to some short insertions. Adapter-free reads with lengths of <10 nucleotides (nt) were discarded, and the remaining reads were mapped to the E. coli K12 genome using Bowtie (Langmead et al., 2009). For the reads of length 10-14, 15-29 and ≥30 nt, up to 1, 2, and 3 mismatches were allowed, respectively. Only uniquely mapped reads were used for further analysis.
We used the assembly tool TruHmm to assemble transcripts in each sample with a window size = 11nt as described earlier (Li et al., 2013) except that we omitted the stitching step in TruHmm to reconstruct the ncRNAs or asRNAs.
In addition, we used DAVID (Dennis et al., 2003) to analyze functional annotation enrichment for groups of genes.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: tab-separated files that each line represent an operon or a gene, columns are titled in the files. logNT and senseLogNT are RKPM values. List items are separated by double dots (..).

organism: Escherichia coli K-12

source_name: M-P 4h

growth_protocol: A frozen stock of Escherichia coli K12 strain MG1655 was thawed, inoculated in LB medium in a test tube by 1:100 dilution and cultured overnight at 37 oC and 250 rpm. The cells were then transferred to fresh LB medium in a flask by 1:100 dilutions, and cultured at 37 oC and 250 rpm. When the cells grew to an optical density at 610 nm (OD610) of 1.0, they were spun down at 3,200g for 25 min.

extract_protocol:
RNA was isolated from the samples using RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10g total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA, and the complete removal of DNA was confirmed  by 35 cycles PCR amplification of a 196 bp fragment of the crp gene (5’-primer:AGCATATTTCGGCAATCCAG;3’-primer:TACAGCGTTTCCGCTTTTTC).  rRNAs were depleted from the total RNA using a MICROBExpress kit (Ambion) to enrich mRNAs.
In our earlier experiments, sequencing was done on an Illumina GAII platform at the sequencing core facility of the University of North Carolina at Chapel Hill, and the directional RNA-seq libraries were constructed using Illumina Small RNA Sample Prep Kit following the vendor’s instruction with some modifications. Briefly, after the purified mRNA was fragmented using a RNA fragmentation kit (Ambion), the fragmented RNA was treated with Antarctic phosphatase (NEB) to remove the 5’-tri-phosphate groups of RNAs with an intact 5’-end. A mono-phosphate group was then added back to the 5’-end of RNAs by polynucleotide kinase (PNK, NEB) in the presence of 10 mM ATP.  The v1.5 sRNA 3’ Adaptor  (5'/5rApp/ ATCTCGTATGCCGTCTTCTGCTTG /3ddC/) was ligated to the 3’-end of fragmented RNAs using truncated T4 ligase 2 (NEB), and the SRA 5’ RNA adaptor (5'GUUCAGAGUUCUACAGUCCGACGAUC) was ligated to the 5’-end of fragmented RNAs using T4 ligase. To preserve short inserts from small RNAs we omitted the size selection step after PCR application of the inserted RNA fragments. For our later experiments, sequencing was done on an Illumina HiSeq 2000 platform at David H. Murdock Research Institute of the North Carolina Research Campus (Kannapolis, NC), and we constructed the directional RNA-seq libraries using Illumina’s TruSeq Small RNA Sample Prep Kit, so that multiplex sequencing can be achieved by using the barcoded PCR primers. The details of the method will be described elsewhere (Dong, Li and Su).  Briefly, after similar treatments as described above, the 5’ Adapter (RA5: 5’ GUUCAGAGUUCUACAGUCCGACGAUC), and 3’ Adapter (RA3: 5’ TGGAATTCTCGGGTGCCAAGG) were ligated to 5’- and 3’-end of fragmented RNAs, respectively. Reverse transcription-PCR (RT-PCR) was performed using SuperScript II Reverse Transcriptase Kit (Invitrogen) using the SRA RT primer, followed by 16 cycles of PCR amplification. Again, the size selection was omitted on PCR products to preserve short inserts from possible small RNAs. Single-end sequencing on the Illumina GA II platform was done with 76 cycles, while that on the HiSeq 2000 platform was done with 100 cycles. Libraries for some samples (M-C1h and M-C2h) were prepared by the two methods and sequenced on the two different platforms.

treatment_protocol: For the minimal medium MOPS culture (MOPS), the cell pellets were resuspended in the same volume of MOPS medium (100 ml of 10X MOPS mixture, 880ml of sterile H2O, 10ml (0.132M) KH2PO4 and 10ml of 20% glucose, Teknova, Hollister, CA). For heat shock treatment (HS), the cell pellets were resuspended in the same volume of MOPS medium, and incubated at 48oC and 250 rpm. For phosphorus-starvation treatment (M-P), the cell pellets were resuspended in the MOPS medium without KH2PO4. For carbon-starvation treatment (M-C), the cell pellets were resuspended in the MOPS medium without glucose. Each culture was done in three replicates in parallel, and an equal volume of cells was collected from each replicate to minimize experimental variations during sampling. Three and 20 ml of the mixed cell suspension were collected for transcriptome and proteome analyses, respectively, at each desired time points (HS:15min, 30min, 1h, 2hrs and 4hrs; MOPS, M-C and M-P: 1hr, 2hrs, 4hrs  6hrs; M-C: 1hr, 2hrs, 4hrs, 6hrs). For the LB culture, samples were collected when the cell suspension OD610 reached to 0.5, 1.0 and 3.  For transcriptome analysis, the collected cells were immediately mixed with 1.5ml RNA Later (Invitrogen) and spun down at 6,000g for 8 min (-4 oC). The pellets were resuspended in 1.5 ml of RNAlater, and stored at -80 oC until use.

tag: condition

value: phosphorus-starvation treatment


title: HctYH_OF3A_1-3-I3-P6


title: siCtrl_m6AIP-seq_rep1


title: M-P 2h

source_name: M-P 2h


title: HctYH_OF3A_1-4-I3-B19


title: M-P 1h

source_name: M-P 1h


title: HctYH_OF3A_1-3-I3-P5


title: HctYH_OF3A_1-4-I3-A8


title: Sox2_mzKO_ICM_scRNA_49


title: M-C 6h

source_name: M-C 6h

value: carbon-starvation treatment


title: Sox2_mzKO_ICM_scRNA_48


title: HctYH_OF3A_1-3-I3-P18


title: M-C 4h

source_name: M-C 4h


title: 1175

description: Thrombotic Primary APS


title: 1176

description: Thrombotic Primary APS


title: M-C 2h (paired-end)

source_name: M-C 2h


title: HctYH_OF3A_1-3-I3-P17


title: M-P 6h

source_name: M-P 6h


title: Sox2_mzKO_ICM_scRNA_47


title: 1174

description: Thrombotic Primary APS


title: HctYH_OF3A_1-4-I3-A7


title: HctYH_OF3A_1-3-I3-O6


title: M-C 1h (paired-end)

source_name: M-C 1h


title: Sox2_mzKO_ICM_scRNA_50


title: Sox2_mzKO_ICM_scRNA_46


title: 1177

description: Thrombotic Primary APS


title: 966

description: Healthy Control


title: MOPS 6h

source_name: MOPS 6h

value: minimal medium MOPS culture


title: Sox2_mzKO_ICM_scRNA_44


title: Sox2_mzKO_ICM_scRNA_45


title: 964

description: Healthy Control


title: MOPS 4h

source_name: MOPS 4h


title: HctYH_OF3A_1-3-I3-O17

source_name: OF3A human BA46


title: HctYH_OF3A_1-3-I3-N6


title: 963

description: Healthy Control


title: MOPS 2h

source_name: MOPS 2h


title: HctYH_OF3A_1-3-I3-O18


title: Sox2_mzKO_ICM_scRNA_42


title: HctYH_OF3A_1-3-I3-N5


title: Sox2_mzKO_ICM_scRNA_43


title: 961

description: Healthy Control


title: MOPS 1h

source_name: MOPS 1h


title: Sox2_mzKO_ICM_scRNA_41


title: Sox2_mzKO_ICM_scRNA_40


title: HctYH_OF3A_1-3-I3-N18


title: HS 4h

source_name: HS 4h

value: heat shock in MOPS


title: 969

description: Healthy Control


title: HctYH_OF3A_1-3-I3-O5


title: 960

description: Healthy Control


title: HctYH_OF3A_1-3-I3-M6


title: 959

description: Healthy Control


title: HctYH_OF3A_1-3-I3-N17


title: HctYH_OF3A_1-3-I3-M5


title: Sox2_mzKO_ICM_scRNA_38

source_name: E3.5 ICM


title: HS 30min

source_name: HS 30min


title: Sox2_mzKO_ICM_scRNA_39


title: Sox2_mzKO_ICM_scRNA_37


title: 958

description: Healthy Control

source_name: Whole Blood


title: HS 15min

source_name: HS 15min


title: 957

description: Healthy Control


title: 962

description: Healthy Control


title: HctYH_OF3A_1-3-I3-M18


title: 956

description: Healthy Control


title: LB 3.0

description: stationary phase in the rich medium Luria broth (LB)

value: LB medium OD600=3.0


title: HctYH_OF3A_1-3-I3-M17


title: Sox2_mzKO_ICM_scRNA_35


title: 955

description: Healthy Control


title: HctYH_OF3A_1-3-I3-L6


title: LB 1.0

description: Middle log phasein the rich medium Luria broth (LB)

value: LB medium OD600=1.0


title: HS 2h

source_name: HS 2h


title: LB 0.5

description: Early log phasein the rich medium Luria broth (LB)

value: LB medium OD600=0.5


title: 952

description: Healthy Control


title: Sox2_mzKO_ICM_scRNA_34


title: HS 1h

source_name: HS 1h


title: HctYH_OF3A_1-3-I3-L5

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: Pdr3_3xmyc_IgG

city: Evanston

first: Heather

last: Pinkett

state: IL

address: 2205 Tech Dr, Cook Hall 4161

institute: Northwestern University

data_processing:
Paired-end sequencing reads were trimmed with Trimmomatic v.0.33 to remove adaptor sequences from the 3’ end of each read
Reads were aligned to the reference S. cerevisiae R64 assembly or the E. coli K12 assembly using Bowtie2 with settings --end-to-end,--dove-tail,--phred33
Picard was then used to sort, index and mark as duplicates the alignments using the MarkDuplicate function.
DeepTools was used to filter the resulting BAM files to remove sequences longer than 120bp
Peaks were called using MACS2 v2.1.1 with the settings –c –g ce –q 0.00001 --keep-dup all –f BAMPE –SPMR
Assembly: Saccharomyces cerevisiae R64 (sacCer3)
Supplementary files format and content: BigWig-  pile up generated using the bamCoverage function of deepTools with samples normalized by the reads mapped to the S. cerevisiae genome versus mapped to the E. coli spike in
Supplementary files format and content: NarrowPeak- Peaks generated from the MACS2 call

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: YPD, 30°C

extract_protocol:
CUT&RUN assays were carried out using the Epicypher CUTANA ChIC/CUT&RUN Kit (Epicypher 14-1048). Briefly, 1 million nuclei were thawed, immobilized on concanavalin A beads, and permeabilized in 0.05% digitonin cell permeabilization buffer. For each sample the permeabilized nuclei were divided equally and incubated in 50 µL antibody buffer with either 0.5µg of control rabbit IgG antibody (Epicypher 14-1048) or anti-c-Myc antibody (ThermoFisher Scientific 13-2500) overnight at 4°C. After washing the beads, pAG-MNase (EpiCypher 14-1048) and 100mM CaCl2 was added to the immobilized cells and incubated for 2h at 4°C to digest chromatin DNA. DNA cleavage was terminated by addition of 150 µl of stop buffer and 0.5 ng of E. coli Spike-in DNA (EpiCypher 14-1048). After incubation for 10m at 37°C, the CUT&RUN-enriched DNA was phenol-chloroform precipitated with 80 µg glycogen. The DNA was dissolved in 0.1x TE buffer, followed by DNA quantification using the Quant-iT PicoGreen assay (Thermofisher Scientific P7589).
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645S) following the manufacturer’s instruction with modifications to SPRI bead size selection and library amplification reactions to retain small DNA fragments

value: yeast

tag: cut&run antibody

value: Rabbit IgG (EpiCypher 13-0042k)


title: 951

description: Healthy Control

value: Blood

value: F


title: Sox2_mzKO_ICM_scRNA_33


title: HctYH_OF3A_1-3-I3-L18

value: Female


title: Pdr3_3xmyc_cmyc

value: c-Myc 9E10 (Thermofisher Scientific MA-980)


title: Sox2_mzKO_ICM_scRNA_32


title: HctYH_OF3A_1-3-I3-L17

value: nuclear RNA + genomic DNA


title: Sox2_mzKO_ICM_scRNA_36

value: Sox2 mzKO


title: YRP10_Pdr1_IgG_rep1


title: Sox2_mzKO_ICM_scRNA_31

value: mix


title: YRP10_Pdr1_IgG_rep2


title: 949

description: Thrombotic Primary APS

value: Thrombotic Primary APS


title: Sox2_mzKO_ICM_scRNA_30


title: HctYH_OF3A_1-3-I3-K6


title: HctYH_OF3A_1-3-I3-K5


title: 948

description: Thrombotic Primary APS


title: 00947M

description: Thrombotic Primary APS

value: M


title: YRP10_Pdr1_cmyc_rep2


title: HctYH_OF3A_1-3-I3-K18


title: Sox2_mzKO_ICM_scRNA_29


title: 946

description: Thrombotic Primary APS


title: YRP10_Pdr1_cmyc_rep1


title: Sox2_mzKO_ICM_scRNA_28


title: HctYH_OF3A_1-3-I3-K17


title: Sox2_mzKO_ICM_scRNA_27


title: 945

description: Thrombotic Primary APS


title: HctYH_OF3A_1-3-I3-J6


title: Sox2_mzKO_ICM_scRNA_26


title: 944

description: Thrombotic Primary APS


title: Sox2_mzKO_ICM_scRNA_25


title: 943

description: Thrombotic Primary APS


title: 950

description: Healthy Control

value: Healthy Control


title: Sox2_mzKO_ICM_scRNA_24


title: Sox2_mzKO_ICM_scRNA_23


title: HctYH_OF3A_1-3-I3-I6


title: 942

description: Thrombotic Primary APS


title: IgG ChIP-seq mixed embryos R2

city: Atlanta

first: Leila

middle: E

last: Rieder

state: GA

address: 1510 Clifton Rd

department: Biology

institute: Emory University

data_processing: We directly imported individual FASTQ datasets into the web-based platform Galaxy through the NCBI SRA Run Selector by selecting the desired runs and utilizing the computing Galaxy download feature. We retrieved the FASTQ files from SRA using the “Faster Download and Extract Reads in FASTQ format from NCBI SRA” Galaxy command. We used a custom “genome” that includes a single Drosophila melanogaster histone array (HA) similar to that in Mckay et al. 2015, which we directly uploaded to Galaxy using the “upload data” feature, and normalized using the Galaxy command “NormalizeFasta” specifying an 80 bp line length for the output .fasta file. We aligned ChIP reads to the normalized histone gene array using Bowtie2 to create .bam files using the user built-in index and “very sensitive end-to-end” parameter settings. We converted the .bam files to .bigwig files using the “bamCoverage” Galaxy command in which we set the bin size to 1 bp and set the effective genome size to user specified: 5000 bp (approximate size of l histone array). We also mapped relevant input or IgG datasets.

organism: Drosophila melanogaster

source_name: mixed sex embryos, 0-3 hr

growth_protocol: Embryos were collected on standard grape juice plates with yeast paste.

extract_protocol:
ChIP-seq: Embyros were fixed with 1.8% paraformaldehyde in 1XPBS with 0.5% Triton-X 100 and heptane. Fixed embryos were ground using a pestle in RIPA buffer and chromatin was sonicated using a probe sonicator at 20% output for 9x 20 seconds.
ChIP-seq: Libraries were constructed using the NEBNext ChIP-seq kit (New England Biosystems, E6240L). CUT&RUN: Libraries were constructed using the Kapa HyperPrep Kit (Roche) and IDT Adapters and the NEBNext Ultra II DnA Library Prep Kit.

value: mixed sex embryos, 0-3 hr

value: yw; Df(2L)HisC/CyO twi-GAL4, UAS-EYFP

tag: antibody

value: ChIP-seq with 2 ul rabbit IgG


title: IgG ChIP-seq mixed embryos R1


title: Input mixed embryos R1

value: Input library for R1


title: Mxc ChIP-seq mixed embryos R2

value: ChIP-seq with 2 ul guinea pig anti-Mxc


title: Mxc ChIP-seq mixed embryos R1


title: Sox2_mzKO_ICM_scRNA_22


title: HctYH_OF3A_1-3-I3-I5

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 939

description: Thrombotic Primary APS


title: HctYH_OF3A_1-3-I3-I18


title: Sox2_mzKO_ICM_scRNA_21


title: 00938M

description: Thrombotic Primary APS


title: Sox2_mzKO_ICM_scRNA_20


title: 00937M

description: Thrombotic Primary APS


title: B_CD19mAb_24hr

city: South San Francisco

first: Weilong

last: Zhao

address: 1000 Gateway Blvd

institute: AbbVie Inc.

description: Submitted BAM file for this sample contains reads for both GEX and ADT.

data_processing:
CITE-seq sequencing FASTQ files were processed using cellranger FeatureBarcoding workflow to align reads for both RNA and protein
Uploaded bam files contain reads for both GEX and ADT.
BAM files were generated by 10x cellranger v6.1.2 under FeatureBarcoding mode, and can be converted back to FASTQ by referring to: https://support.10xgenomics.com/docs/bamtofastq?src=distributor&lss=email&cnm=disti-web-website-page-ra_g-apac&cid=NULL. The ADT reads can be identified using Feature Barcode tags as specified here https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/bam?src=distributor&lss=email&cnm=disti-web-website-page-ra_g-apac&cid=NULL and using the uploaded antibody barcode reference file (available on series record).
Assembly: hg38
Supplementary files format and content: Cellranger output files in h5 format: filtered_feature_bc_matrix.h5
Library strategy: CITE-seq

source_name: PBMC

extract_protocol:
Viable cells were washed and resuspended in cell staining buffer (420201, BioLegend). Following 100µm strainer filtration, cells were blockedwith Fc block(422302, BioLegend) in cell staining buffer and stained with TotalSeq Universal antibody cocktail (399904, BioLegend). Cells were washed and loaded into the 10x Chromium controller at16,000 cellsper sample.
Single cell encapsulation was processed according to manufacturer’s protocol using 3’ chemistry version 3.1 (10X Genomics)

value: PBMC


title: B_ABBV319_24hr


title: Sox2_mzKO_ICM_scRNA_19


title: HctYH_OF3A_1-3-I3-I17


title: B_DMSO_24hr


title: HctYH_OF3A_1-3-I3-H6


title: HctYH_OF3A_1-3-I3-J18


title: A_ABBV319_24hr


title: 936

description: Thrombotic Primary APS

value: Blood


title: HctYH_OF3A_1-3-I3-J17


title: 941

description: Thrombotic Primary APS


title: 935

description: Thrombotic Primary APS


title: Sox2_mzKO_ICM_scRNA_18


title: A_CD19mAb_24hr


title: 934

description: Thrombotic Primary APS

value: F


title: Sox2_mzKO_ICM_scRNA_17


title: A_DMSO_24hr


title: HctYH_OF3A_1-3-I3-H17

value: Female


title: HctYH_OF3A_1-3-I3-H18


title: 933

description: Thrombotic Primary APS


title: Sox2_mzKO_ICM_scRNA_16


title: Input mixed embryos R2

value: Input library for R2


title: HctYH_OF3A_1-3-I3-J5

value: nuclear RNA + genomic DNA


title: 932

description: Thrombotic Primary APS


title: Sox2_mzKO_ICM_scRNA_15

value: Sox2 mzKO


title: SUDHL6_ADC_24hr

data_processing:
FASTQ files were aligned to hg38 using STAR and then quantified for gene and transcript reads counts using Salmon, using the reference transcriptome of Ensembl v93.
Assembly: hg38
Supplementary files format and content: Salmon gene quantification output file: SAMPLE.quant.genes.sf

extract_protocol:
RNA was isolated from frozen cell pellet using Qiagen RNAeasy kit (Hilden, Germany) according to manufacturer protocol.
Whole-transcriptome sequencing (RNA-sequencing) was performed using TruSeq™ Stranded Total RNA With IlluminaÒ Ribo-ZeroTM Plus rRNA Depletion kit according to manufacturer protocol (Illumina, Inc. San Diego, California).

tag: cell line

value: ABBV-319 treated


title: Sox2_mzKO_ICM_scRNA_14

value: mix


title: Farage_ADC_24hr

source_name: Farage

value: Farage


title: HctYH_OF3A_1-3-I3-G6


title: DOHH2_ADC_24hr


title: Sox2_mzKO_ICM_scRNA_13


title: HctYH_OF3A_1-3-I3-G18


title: HctYH_OF3A_1-3-I3-G5


title: Sox2_mzKO_ICM_scRNA_12


title: OCILY19_ADC_24hr


title: 931

description: Thrombotic Primary APS

value: Thrombotic Primary APS


title: 927

description: Thrombotic Primary APS

value: M


title: HctYH_OF3A_1-3-I3-G17


title: SUDHL6_SM_24hr

value: GRM small molecular treated


title: HctYH_OF3A_1-3-I3-H5


title: 928

description: Thrombotic Primary APS


title: Sox2_mzKO_ICM_scRNA_11


title: 926

description: Thrombotic Primary APS


title: HctYH_OF3A_1-3-I3-F6


title: Sox2_mzKO_ICM_scRNA_10


title: DOHH2_SM_24hr


title: Farage_SM_24hr


title: HctYH_OF3A_1-3-I3-F5


title: 925

description: Thrombotic Primary APS


title: 924

description: Thrombotic Primary APS


title: HctYH_OF3A_1-3-I3-F18


title: Sox2_mzKO_ICM_scRNA_9


title: OCILY19_SM_24hr


title: Sox2_mzKO_ICM_scRNA_8


title: 923

description: Thrombotic Primary APS


title: HctYH_OF3A_1-3-I3-F17


title: Sox2_mzKO_ICM_scRNA_7


title: SUDHL6_unstim_24hr

value: DMSO


title: 922

description: Thrombotic Primary APS


title: Sox2_mzKO_ICM_scRNA_6


title: HctYH_OF3A_1-3-I3-E6


title: HctYH_OF3A_1-3-I3-E5


title: Farage_unstim_24hr


title: Sox2_mzKO_ICM_scRNA_5


title: DOHH2_unstim_24hr


title: OCILY19_unstim_24hr


title: Sox2_mzKO_ICM_scRNA_4


title: 921

description: Thrombotic Primary APS


title: 00896M

description: Thrombotic Primary APS


title: HctYH_OF3A_1-3-I3-E18


title: 00895M

description: Thrombotic Primary APS


title: HctYH_OF3A_1-3-I3-E17


title: 894

description: Thrombotic Primary APS


title: HctYH_OF3A_1-3-I3-D6


title: W12E_Prol_DMSO_CUT&RUN_S_2

city: Dallas

first: Cheng-Ming

last: Chiang

state: Texas

address: 6001 Forest Park Road

department: Simmons Comprehensive Cancer Center

institute: UT Southwestern Medical Center

data_processing:
150 bp paired-end reads in Fastq files were checked for quality using FastQC (v0.11.2). Adaptors were removed using TrimGalore.
Trimmed reads were mapped to human genome hg38 using BWA, followed by Samtools to sort and convert the mapped reads to bam files. Duplicate reads in the resulting bam files were marked with Sambamba and subsequently removed by Samtools.
BRD4-L and BRD4-S peak calling was done by MACS2 with IgG as control using the following configurations: effective genome size 2.70e+09, band width 300, model fold [5, 50], q-value cutoff 0.01, larger dataset scaled towards smaller dataset, range for calculating regional lambda 1000 bps and 10000 bps
Assembly: hg38
Supplementary files format and content: tab delimited txt file including normalized read counts logCPM
Supplementary files format and content: CUT&RUN bigwig files containing relative signal fold change (fc) of BRD4 IP vs. IgG IP.
Library strategy: CUT&RUN

growth_protocol: Proliferating W12E cells were cultured without feeder cells at sub-confluence in low-calcium (0.05 mM) F-medium. Differentiated W12E cells were cultured in EGF-free high-calceium (1.4 mM) F-medium upon confluence.

extract_protocol:
DNA fragments were isolated following proteinase K treatment, phenol/chloroform extraction, and ethanol precipitation.
DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: Cells were treated by 5 µM of pNPS14, 1 µM of pNPS90 or JQ1, or DMSO-only for 4 hours before harvest.

value: HPV16-positive cervical keratinocyte

value: wildtype

value: Proliferation, DMSO, BRD4-S(a) antibody (Chiang)


title: W12E_Prol_DMSO_CUT&RUN_S_1


title: Sox2_mzKO_ICM_scRNA_3


title: Sox2_mzKO_ICM_scRNA_2


title: 893

description: Thrombotic Primary APS


title: HctYH_OF3A_1-3-I3-D5

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 00892M

description: Thrombotic Primary APS

value: Blood


title: W12E_Prol_DMSO_CUT&RUN_L_2

value: Proliferation, DMSO, BRD4-L antibody (Bethyl)


title: HctYH_OF3A_1-3-I3-D18

value: Female


title: Sox2_control_ICM_scRNA_44

value: Sox2 control


title: 891

description: Thrombotic Primary APS

value: F


title: HctYH_OF3A_1-3-I3-D17

value: nuclear RNA + genomic DNA


title: W12E_Prol_DMSO_CUT&RUN_Ig_2

value: Proliferation, DMSO, IgG


title: Sox2_control_ICM_scRNA_43

value: mix


title: W12E_Prol_DMSO_CUT&RUN_Ig_1


title: HctYH_OF3A_1-3-I3-C6


title: 890

description: Thrombotic Primary APS


title: Sox2_control_ICM_scRNA_42


title: HctYH_OF3A_1-3-I3-C5


title: W12E_Diff_JQ1_CUT&RUN_S_2

description: W12E_Diff_JQ1_CUT&RUN_BRD4_S_fc_signal.bw

value: Differentiation, JQ1, BRD4-S(a) antibody (Chiang)


title: 00889M

description: Thrombotic Primary APS

value: Thrombotic Primary APS


title: Sox2_control_ICM_scRNA_41


title: HctYH_OF3A_1-3-I3-C18


title: W12E_Diff_JQ1_CUT&RUN_S_1


title: 887

description: Thrombotic Primary APS


title: 886

description: Thrombotic Primary APS


title: HctYH_OF3A_1-3-I3-B6


title: HctYH_OF3A_1-3-I3-C17


title: W12E_Diff_JQ1_CUT&RUN_L_2

description: W12E_Diff_JQ1_CUT&RUN_BRD4_L_fc_signal.bw

value: Differentiation, JQ1, BRD4-L antibody (Bethyl)


title: W12E_Diff_JQ1_CUT&RUN_L_1


title: Sox2_control_ICM_scRNA_40


title: W12E_Prol_DMSO_CUT&RUN_L_1


title: Sox2_control_ICM_scRNA_39


title: 885

description: Thrombotic Primary APS


title: Sox2_mzKO_ICM_scRNA_1

value: Sox2 mzKO


title: Sox2_control_ICM_scRNA_38


title: HctYH_OF3A_1-3-I3-B18


title: 883

description: Thrombotic Primary APS


title: W12E_Diff_90_CUT&RUN_S_2

description: W12E_Diff_90_CUT&RUN_BRD4_S_fc_signal.bw

value: Differentiation, pNPS90, BRD4-S(a) antibody (Chiang)


title: 882

description: Thrombotic Primary APS


title: 888

description: Thrombotic Primary APS


title: Sox2_control_ICM_scRNA_35


title: W12E_Diff_90_CUT&RUN_S_1

value: HPV16-positive cervical keratinocyte


title: HctYH_OF3A_1-3-I3-A6


title: 880

description: Thrombotic Primary APS

value: M


title: 879

description: Thrombotic Primary APS


title: HctYH_OF3A_1-3-I3-B17


title: HctYH_OF3A_1-3-I3-A5


title: W12E_Diff_90_CUT&RUN_L_2

description: W12E_Diff_90_CUT&RUN_BRD4_L_fc_signal.bw

value: wildtype

value: Differentiation, pNPS90, BRD4-L antibody (Bethyl)


title: W12E_Diff_JQ1_CUT&RUN_Ig_2

value: Differentiation, JQ1


title: Sox2_control_ICM_scRNA_32


title: Sox2_control_ICM_scRNA_33


title: W12E_Diff_90_CUT&RUN_L_1


title: HctYH_OF3A_1-3-I3-B5

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: HctYH_OF3A_1-3-I3-A18

value: Female


title: HctYH_OF3A_1-3-I3-A17


title: Sox2_control_ICM_scRNA_37

value: Sox2 control


title: W12E_Diff_JQ1_CUT&RUN_Ig_1


title: W12E_Diff_90_CUT&RUN_Ig_2

value: Differentiation, pNPS90, IgG


title: Sox2_control_ICM_scRNA_31


title: 876

description: Thrombotic Primary APS

value: Blood


title: Sox2_control_ICM_scRNA_30


title: 875

description: Thrombotic Primary APS

value: F


title: Sox2_control_ICM_scRNA_34

value: mix


title: 874

description: Thrombotic Primary APS


title: HctYH_OF3A_1-2-I3-P4

value: nuclear RNA + genomic DNA


title: W12E_Diff_90_CUT&RUN_Ig_1


title: W12E_Diff_DMSO_CUT&RUN_S_2

value: Differentiation, DMSO, BRD4-S(a) antibody (Chiang)


title: 878

description: Thrombotic Primary APS

value: Thrombotic Primary APS


title: HctYH_OF3A_1-2-I3-P3


title: Sox2_control_ICM_scRNA_36


title: HctYH_OF3A_1-2-I3-P16


title: 873

description: Thrombotic Primary APS


title: W12E_Diff_DMSO_CUT&RUN_S_1


title: 877

description: Thrombotic Primary APS


title: W12E_Diff_DMSO_CUT&RUN_L_2

value: Differentiation, DMSO, BRD4-L antibody (Bethyl)


title: Sox2_control_ICM_scRNA_27


title: Sox2_control_ICM_scRNA_28


title: Sox2_control_ICM_scRNA_29


title: Sox2_control_ICM_scRNA_26


title: 872

description: Thrombotic Primary APS


title: HctYH_OF3A_1-2-I3-P15


title: Sox2_control_ICM_scRNA_25


title: HctYH_OF3A_1-2-I3-O4


title: W12E_Diff_DMSO_CUT&RUN_L_1


title: W12E_Diff_DMSO_CUT&RUN_Ig_2

value: Differentiation, DMSO, IgG


title: 00869M

description: Thrombotic Primary APS


title: 870

description: Thrombotic Primary APS


title: HctYH_OF3A_1-2-I3-O3


title: Sox2_control_ICM_scRNA_24


title: W12E_Diff_DMSO_CUT&RUN_Ig_1

value: HPV16-positive cervical keratinocyte


title: 868

description: Thrombotic Primary APS


title: HctYH_OF3A_1-2-I3-O15


title: W12E_Prol_JQ1_RNA_3

data_processing:
150 bp paired-end reads in Fastq files were checked for quality using FastQC (v0.11.2). Reads were trimmed using Samtools.
Trimmed fastq files were mapped to human genome hg38 using HiSAT2. Duplicates were marked using SAMBAMBA and removed.
Read counts were generated using featureCounts and StringTie.
Normalized read counts and differentially expressed genes were generated using edgeR.
Assembly: hg38
Supplementary files format and content: tab delimited txt file including normalized read counts logCPM
Supplementary files format and content: CUT&RUN bigwig files containing relative signal fold change (fc) of BRD4 IP vs. IgG IP.

extract_protocol:
Total RNA was isolated by miRNeasy Mini Kit (Qiagen).
RNA-seq cDNA libraries were constructed using NEBNext Ultra II directional RNA Library Prep Kit with Illumina Ribo-zero Plus.

value: Proliferation, JQ1


title: Sox2_control_ICM_scRNA_23


title: HctYH_OF3A_1-2-I3-N4

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq


title: Sox2_control_ICM_scRNA_21


title: W12E_Prol_JQ1_RNA_2

value: wildtype


title: 00865M

description: Thrombotic Primary APS

value: M


title: HctYH_OF3A_1-2-I3-N16


title: W12E_Prol_JQ1_RNA_1


title: HctYH_OF3A_1-2-I3-O16


title: Sox2_control_ICM_scRNA_22


title: W12E_Prol_90_RNA_3

value: Proliferation, pNPS90


title: 863

description: Thrombotic Primary APS


title: Sox2_control_ICM_scRNA_20


title: Sox2_control_ICM_scRNA_19


title: HctYH_OF3A_1-2-I3-M3

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: HctYH_OF3A_1-2-I3-M4

value: Female


title: Sox2_control_ICM_scRNA_18

value: Sox2 control


title: 862

description: Thrombotic Primary APS


title: W12E_Prol_90_RNA_2


title: HctYH_OF3A_1-2-I3-M16


title: 860

description: Thrombotic Primary APS


title: W12E_Prol_14_RNA_3

value: Proliferation, pNPS14


title: W12E_Prol_14_RNA_2


title: 859

description: Healthy Control

value: Blood

value: Healthy Control


title: 866

description: Healthy Control

value: F


title: HctYH_OF3A_1-2-I3-L4

value: nuclear RNA + genomic DNA


title: 858

description: Healthy Control


title: W12E_Prol_14_RNA_1


title: W12E_Prol_DMSO_RNA_3

description:
W12E_Prol_Cpd_RNA_countTable.logCPM.txt
W12E_Prol_vs_Diff_RNA_countTable.logCPM.txt

value: Proliferation, DMSO


title: 867

description: Healthy Control


title: HctYH_OF3A_1-2-I3-N15


title: HctYH_OF3A_1-2-I3-L3


title: W12E_Prol_DMSO_RNA_2


title: HctYH_OF3A_1-2-I3-L16


title: 857

description: Healthy Control


title: Sox2_control_ICM_scRNA_15

value: mix


title: 861

description: Thrombotic Primary APS

value: Thrombotic Primary APS


title: Sox2_control_ICM_scRNA_13


title: W12E_Prol_90_RNA_1


title: 856

description: Healthy Control


title: Sox2_control_ICM_scRNA_16


title: Sox2_control_ICM_scRNA_11


title: Sox2_control_ICM_scRNA_12


title: W12E_Prol_DMSO_RNA_1


title: W12E_Diff_JQ1_RNA_3

value: Differentiation, JQ1


title: HctYH_OF3A_1-2-I3-M15


title: 855

description: Healthy Control


title: Sox2_control_ICM_scRNA_10


title: HctYH_OF3A_1-2-I3-K3


title: 854

description: Healthy Control


title: W12E_Diff_JQ1_RNA_2

value: HPV16-positive cervical keratinocyte


title: Sox2_control_ICM_scRNA_9


title: Sox2_control_ICM_scRNA_14


title: 853

description: Healthy Control


title: W12E_Diff_JQ1_RNA_1


title: Sox2_control_ICM_scRNA_8


title: Sox2_control_ICM_scRNA_7


title: W12E_Diff_90_RNA_3

value: Differentiation, pNPS90


title: HctYH_OF3A_1-2-I3-L15


title: 852

description: Healthy Control


title: HctYH_OF3A_1-2-I3-J4


title: HctYH_OF3A_1-2-I3-K15


title: Sox2_control_ICM_scRNA_6


title: 850

description: Healthy Control


title: HctYH_OF3A_1-2-I3-K16


title: HctYH_OF3A_1-2-I3-J3


title: 851

description: Healthy Control


title: HctYH_OF3A_1-2-I3-K4


title: W12E_Diff_90_RNA_2

value: wildtype


title: HctYH_OF3A_1-2-I3-J16


title: Male_IVF_9R318

city: Madison

last: Ortega

state: Wisconsin

address: 1675 Observatory Drive

department: Department of Animal and DairySciences

institute: University of Wisconsin

description: bovine placenta day 32 from aritificial insemination

data_processing:
The quality of fastq files of sequences data was checked with a FastQC tool
Illumina adapters were trimmed
Reads were mapped to the bovine reference genome using the Hisat2
Read counts were determined using FeatureCounts program
Differentially expressed genes (DEGs) between sample groups were determined by edgeR-robust
Genome_build: Bos_taurus.ARS-UCD1.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: Placenta

extract_protocol:
Placentas were collected, flash frozen on liquid nitrogen, and RNA was harvested using ALLprep or Trizol reagent.
poly-A containing mRNA is purified from total RNA(1 ug), RNA is fragmented, double-stranded cDNA is generated from fragmented RNA, and the index containing adapters are ligated to the ends.  The amplified cDNA constructs were purified by addition of Axyprep Mag PCR Clean-up beads.  The final construct of each purified library was evaluated using the Fragment Analyzer automated electrophoresis system, quantified with the Qubit flourometer using the Qubit HS dsDNA assay kit, and diluted according to Illumina’s standard sequencing protocol for sequencing on the NovaSeq 6000

treatment_protocol: Placentas from embryos produced using different assisted reproductive techniques, Artificial insemination vs In vitro produced embryos.

value: In vitro produced embryos

value: bovine placenta

value: Male


title: W12E_Diff_14_RNA_3

value: Differentiation, pNPS14


title: Sox2_control_ICM_scRNA_5

value: Sox2 control


title: Male_IVF_6R432

description: bovine placenta day 32 from in vitro derived embryo


title: HctYH_OF3A_1-2-I3-J15

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: Sox2_control_ICM_scRNA_4


title: W12E_Diff_14_RNA_2


title: Sox2_control_ICM_scRNA_3


title: Male_IVF_51R318


title: W12E_Diff_14_RNA_1


title: Sox2_control_ICM_scRNA_2


title: Male_IVF_47R318

description: bovine placenta day 18 from in vitro derived embryo


title: W12E_Diff_DMSO_RNA_3

description:
W12E_Diff_Cpd_RNA_countTable.logCPM.txt
W12E_Prol_vs_Diff_RNA_countTable.logCPM.txt

value: Differentiation, DMSO


title: HctYH_OF3A_1-2-I3-I3


title: Male_IVF_28R432


title: W12E_Diff_DMSO_RNA_2


title: W12E_Diff_90_RNA_1


title: Male_AI_4R232

value: Artificial insemination embryos


title: HctYH_OF3A_1-2-I3-I15

value: nuclear RNA + genomic DNA


title: W12E_Diff_DMSO_RNA_1


title: Sox2FKBP_D3_EpiLC_dTAG_RNA_rep1

source_name: mESC-derived D3 EpiLC

growth_protocol: 2i ESC cells were plated on TC dishes pretreated with 1:100 matrigel in N2B27-based medium supplemented with 1% KSR (Invitrogen), 12 mg/ml bFGF (Peprotech) and 20 ng/ml Activin A (R&D Scientific) was added to induce EpiLCs.


title: HctYH_OF3A_1-2-I3-I16


title: Male_IVF_17R432


title: HctYH_OF3A_1-2-I3-H4


title: Sox2FKBP_D3_EpiLC_DMSO_RNA_rep2


title: CBX405 human-derived xenograft

city: Chicago

first: Mohamed

last: Abazeed

address: 303 E Superior St Lurie

department: Radiation Oncology

description:
CBX405
single tumor, homogenized
replicate1

data_processing:
Reads were aligned to a genome assembly using STAR and aligned reads were assigned.
Gene read counts were normalized by calculating transcripts per million (TPM)
Assembly: hg19
Supplementary files format and content: Normalized and total counts for all samples are included in spreadsheet Counts_GEO.xlsx

source_name: human-derived xenograft

growth_protocol: Tumors were grown in NSG mice.

extract_protocol:
RNA was isolated using the Rneasy Plus Mini Kit.
Samples were checked using BioA and libraries were prepared using the TruSeq Stranded mRNA kit. Each library was quantified using Qubit and then pooled toether. Library pool was quantified using qPCR. Pool was then diluted to 4 nM and loaded on the HiSeq High Output Mode. Run was performed using a full flow cell (8 lanes) PE 100. 5% PhiX was spiked in to check run qaulity.

value: human-derived xenograft

tag: passages


title: HctYH_OF3A_1-2-I3-H3

source_name: OF3A human BA46

tag: brain region


title: CCX280 human-derived xenograft

description:
CCX280
single tumor, homogenized
replicate1


title: Male_AI_4R132


title: Sox2FKBP_D3_EpiLC_DMSO_RNA_rep1


title: HctYH_OF3A_1-2-I3-I4

tag: age


title: HctYH_OF3A_1-2-I3-H16

tag: Sex


title: Sox2FKBP_D2_EpiLC_dTAG_RNA_rep2

source_name: mESC-derived D2 EpiLC


title: Male_AI_25R218


title: Male_AI_21R218

description: bovine placenta day 18 from aritificial insemination


title: CCX13 human-derived xenograft

description:
CCX13
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-2-I3-H15

tag: molecule subtype


title: Sox2_control_ICM_scRNA_1

value: mix


title: Sox2FKBP_D2_EpiLC_dTAG_RNA_rep1


title: Male_AI_1R132

tag: tissue


title: Sox2FKBP_D3_EpiLC_dTAG_RNA_rep2

tag: strain


title: Male_AI_1R118


title: Sox2FKBP_D2_EpiLC_DMSO_RNA_rep2

tag: genotype


title: CCX1 human-derived xenograft

description:
CCX1
single tumor, homogenized
replicate1


title: CBX99 human-derived xenograft

description:
CBX99
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-2-I3-G3


title: CBX96 human-derived xenograft

description:
CBX96
single tumor, homogenized
replicate1


title: Sox2FKBP_D2_EpiLC_DMSO_RNA_rep1


title: HctYH_OF3A_1-2-I3-G16


title: Sox2FKBP_D1_EpiLC_dTAG_RNA_rep2

source_name: mESC-derived D1 EpiLC

growth_protocol: 2i ESCs were cultured on 0.1% gelatin pre-coated dishes in DMEM medium (Gibco, 11995-065) containing leukemia-inhibiting factor (LIF) (Millipore, ESG1107), 15% fetal bovine serum (FBS; Hyclone, SH30396.03), GlutaMAX (Gibco, 35050-061), penicillin/ streptomycin (Millipore, TMS-AB2-C), nucleosides (Millipore, ES-008-D), non-essential amino acids (Gibco, 25-025-CIR), and β-mercaptoethanol (Gibco, 21985- 023). Naïve mESCs (2i) mESCs were cultured on feeder-free dishes coated with 0.1% gelatin in the N2B27 medium supplemented with 1 μM PD035901, 3 μM Chir99021, and 1 × 103 units/mL LIF. The cells were passaged 1:10-1:30.


title: CBX94 human-derived xenograft

description:
CBX94
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-2-I3-G15


title: CCX250 human-derived xenograft

description:
CCX250
single tumor, homogenized
replicate1


title: Sox2FKBP_D1_EpiLC_dTAG_RNA_rep1


title: HctYH_OF3A_1-2-I3-F4


title: Fem_IVF_d32_30R4


title: Fem_IVF_d32_12R4


title: CBX88 human-derived xenograft

description:
CBX88
single tumor, homogenized
replicate1


title: Fem_IVF_d18_3R3


title: Sox2FKBP_D1_EpiLC_DMSO_RNA_rep2


title: HctYH_OF3A_1-2-I3-F3


title: CBX59 human-derived xenograft

description:
CBX59
single tumor, homogenized
replicate1


title: Sox2FKBP_D1_EpiLC_DMSO_RNA_rep1


title: Fem_IVF_d18_34R3


title: HctYH_OF3A_1-2-I3-F16


title: HctYH_OF3A_1-2-I3-G4


title: Fem_IVF_d18_2R3


title: Sox2FKBP_12h_EpiLC_dTAG_RNA_rep2

source_name: mESC-derived 12h EpiLC


title: CBX54 human-derived xenograft

description:
CBX54
single tumor, homogenized
replicate1


title: CBX52 human-derived xenograft

description:
CBX52
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-2-I3-F15


title: Sox2FKBP_12h_EpiLC_dTAG_RNA_rep1


title: Fem_IVF_d32_32R4

description: bovine placenta day 32 from aritificial insemination


title: CBX502 human-derived xenograft

description:
CBX502
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-2-I3-E4


title: CBX49 human-derived xenograft

description:
CBX49
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-2-I3-E3


title: Sox2FKBP_12h_EpiLC_DMSO_RNA_rep2


title: HctYH_OF3A_1-2-I3-E16


title: Fem_AI_d32_6R1


title: CBX488 human-derived xenograft

description:
CBX488
single tumor, homogenized
replicate1


title: Sox2FKBP_12h_EpiLC_DMSO_RNA_rep1


title: Fem_AI_d18_1R2


title: Sox2FKBP_D0_EpiLC_DMSO_RNA_rep1

source_name: mESC-derived D0 EpiLC


title: HctYH_OF3A_1-2-I3-E15


title: CBX466 human-derived xenograft

description:
CBX466
single tumor, homogenized
replicate1


title: Fem_AI_d18_13R1


title: HctYH_OF3A_1-2-I3-D4


title: CBX464 human-derived xenograft

description:
CBX464
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-2-I3-D3


title: Fem_AI_d18_12R1

description: bovine placenta day 18 from aritificial insemination


title: Sox2FKBP_2iESC_dTAG_96h_RNA_rep2

source_name: 2i mESC


title: CBX46 human-derived xenograft

description:
CBX46
single tumor, homogenized
replicate1


title: c1128_STIM_canine_PHA

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

description:
c1128_STIM
Partek_Canine_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt

data_processing:
Partek Flow software, version 10.0
Raw data were filtered by removing reads containing adapters and reads containing N > 10% and for Phred scores >30
Filtered reads were aligned with STAR 2.7.3a, using either CanFam3.1 genome assembly or GRCh38 human genome assembly
Aligned reads were annotated and counted using HT-seq  with Ensembl 104 for CanFam3.1 and release 107 for GRCh38
differentially expressed genes were identified using DEseq2
Assembly: CanFam3.1 genome assembly or GRCh38 human genome assembly
Supplementary files format and content: tab-delimited text files include CPM normalized counts

organism: Canis lupus familiaris

source_name: Blood

growth_protocol: Following Ficoll separation, PBMC for both species were washed with PBS, counted and added to 24-well plates in triplicate cultures, at a cell density of 2 X 10^6 cells per mL in complete culture medium.  Cell culture medium consisted of DMEM supplemented with amino acids (essential and non-essential), 1% penicillin-streptomycin, Glutamax (ThermoFisher Scientific, Waltham, MA) and 10% fetal bovine serum (Peak Serum, Inc, Wellington, CO).  For T cell activation, phytohemagglutinin (PHA) (Sigma-Aldrich, St. Louis, MO) was added to cultures at a concentration of 5 ug/ml for 24h (RNA sequencing).

extract_protocol:
RNA was extracted from cells using Qiagen RNeasy mini kit
the mRNA was purified using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was completed following end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Blood

value: primary tissue

tag: cell type

value: PBMC

value: PHA


title: Sox2FKBP_2iESC_dTAG_96h_RNA_rep1


title: CBX445 human-derived xenograft

description:
CBX445
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-2-I3-D16

city: La Jolla

last: Ecker

address: 10010 North Torrey Pines Road


title: Fem_AI_d32_6R2

tag: treatment


title: Sox2FKBP_2iESC_dTAG_72h_RNA_rep2

tag: chip-antibody


title: HctYH_OF3A_1-2-I3-D15


title: CBX440 human-derived xenograft

description:
CBX440
single tumor, homogenized
replicate1


title: Fem_AI_d32_2R2


title: CBX438 human-derived xenograft

description:
CBX438
single tumor, homogenized
replicate1


title: Sox2FKBP_2iESC_dTAG_72h_RNA_rep1


title: c1829_STIM_canine_PHA

description:
c1829_STIM
Partek_Canine_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt

treatment_protocol: phytohemagglutinin (PHA) (Sigma-Aldrich, St. Louis, MO) was added to cultures at a concentration of 5 ug/ml


title: HctYH_OF3A_1-2-I3-C4


title: Sox2FKBP_D0_EpiLC_DMSO_RNA_rep2


title: c1962_STIM_canine_PHA

description:
c1962_STIM
Partek_Canine_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt


title: HctYH_OF3A_1-2-I3-C3


title: CBX428 human-derived xenograft

description:
CBX428
single tumor, homogenized
replicate1


title: CBX419 human-derived xenograft

description:
CBX419
single tumor, homogenized
replicate1


title: c1962_canine_ctrl

description:
c1962
Partek_Canine_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt

value: untreated


title: Sox2FKBP_2iESC_dTAG_48h_RNA_rep2


title: c1829_canine _ctrl

description:
c1829
Partek_Canine_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt


title: Sox2FKBP_2iESC_dTAG_48h_RNA_rep1


title: Sox2FKBP_2iESC_dTAG_24h_RNA_rep2


title: HctYH_OF3A_1-2-I3-C15


title: HctYH_OF3A_1-2-I3-C16


title: CBX412 human-derived xenograft

description:
CBX412
single tumor, homogenized
replicate1


title: Sox2FKBP_2iESC_dTAG_24h_RNA_rep1


title: c1646_canine_ctrl

description:
c1646
Partek_Canine_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt


title: Sox2FKBP_2iESC_dTAG_12h_RNA_rep2

extract_protocol:
Cells or embyos were lysed in lysis buffer.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before being subjected to sequencing.


title: HctYH_OF3A_1-2-I3-B4


title: c1646_STIM_canine_PHA

description:
c1646_STIM
Partek_Canine_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt


title: CBX411 human-derived xenograft

description:
CBX411
single tumor, homogenized
replicate1


title: Sox2FKBP_2iESC_dTAG_12h_RNA_rep1


title: CBX410 human-derived xenograft

description:
CBX410
single tumor, homogenized
replicate1


title: CBX41 human-derived xenograft

description:
CBX41
single tumor, homogenized
replicate1


title: Sample_b_HFD4

first: Xi

address: 2929 N Stemmons Fwy

data_processing:
Data was processed by UT Southwestern Next Generation Sequencing Core facility.
Assembly: mm10
Supplementary files format and content: Raw reads were processed to counts per million (CPM) and differentially expressed (DE) genes were initially determined by using the edgeR package.

source_name: pancreatic islet

extract_protocol:
Total RNA was isolated from sorted β-cells using TRIzol reagent (Invitrogen).
cDNA libraries were prepared using Illumina’s TruSeq Stranded mRNA Library Prep kit.

value: pancreatic islet

value: Islet beta cell

value: 2-day high fat diet


title: c1128_canine_ctrl

description:
c1128
Partek_Canine_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt


title: Sample_b_HFD3


title: Sox2FKBP_2iESC_dTAG_0h_RNA_rep2

data_processing:
ChIP-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -t -q -N 1 -L 25. All ummapped reads, non-uniqurely mapped reads and PCR duplicates were removed. For downstream analysis, we computed the numbers of reads per kilobase of bin per million reads sequenced (RPKM) which were further normalized by input. A resolution of 100bp bin in genome was used in the rpkm file.
bulk RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). scRNA-seq reads were mapped to mm9 genome by HISAT2 (version 2.1.0).The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq, ChIP-seq tracks, gene expression table for RNA-seq data

extract_protocol:
Cells or embyos were lysed in lysis buffer containing RNase inhibitor.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before being subjected to sequencing.


title: CBX401 human-derived xenograft

description:
CBX401
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-2-I3-B3

first: Joseph


title: HctYH_OF3A_1-2-I3-B16


title: Sample_b_HFD2


title: HctYH_OF3A_1-2-I3-A3


title: Sox2FKBP_2iESC_dTAG_0h_RNA_rep1


title: CBX382 human-derived xenograft

description:
CBX382
single tumor, homogenized
replicate1


title: Sample_b_CD4

value: chow diet


title: Sox2FKBP_D3_EpiLC_dTAG_H3K27ac_rep1

extract_protocol:
Cells or embyos were lysed in lysis buffer.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: H3K27ac (Active Motif, 39133)


title: Sample_b_CD3


title: HctYH_OF3A_1-2-I3-A15

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: CBX365 human-derived xenograft

description:
CBX365
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-2-I3-A16

value: Female


title: CBX371 human-derived xenograft

description:
CBX371
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-2-I3-A4


title: Sox2FKBP_D3_EpiLC_DMSO_H3K27ac_rep1


title: Sox2FKBP_D2_EpiLC_dTAG_H3K27ac_rep1


title: Sample_b_CD1


title: Sample_b_CD2


title: HctYH_OF3A_1-1-I3-P1


title: CBX354 human-derived xenograft

description:
CBX354
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-1-I3-P2


title: Sox2FKBP_D2_EpiLC_DMSO_H3K27ac_rep1


title: CBX346 human-derived xenograft

description:
CBX346
single tumor, homogenized
replicate1


title: CBX351 human-derived xenograft

description:
CBX351
single tumor, homogenized
replicate1


title: Sox2FKBP_D1_EpiLC_dTAG_H3K27ac_rep1


title: Sox2FKBP_D1_EpiLC_DMSO_H3K27ac_rep1


title: Sox2FKBP_12h_EpiLC_dTAG_H3K27ac_rep1


title: HctYH_OF3A_1-1-I3-P14


title: HctYH_OF3A_1-1-I3-P13


title: KO, 7dpi, rep2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: Lung

extract_protocol:
Total RNA was isolated from whole lung using Qiagen RNeasy kit.
Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and converted to cDNA via reverse transcription. First strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 12 cycles using barcoded primers such that each sample carries a specific combination of eight base Illumina P5 and P7 barcodes and pooled together prior to sequencing. Smart-seq paired-end sequencing is performed on an Illumina NextSeq500 (two full NextSeq runs per batch of 96 samples, for 10M raw reads/sample on average) using 2 x 38bp reads with no further trimming.

value: Lung

value: Osm-/-

value: Influenza A virus, strain WSN infected

tag: time point

value: 7 days post infection


title: CBX340 human-derived xenograft

description:
CBX340
single tumor, homogenized
replicate1

value: human-derived xenograft


title: HctYH_OF3A_1-1-I3-O2

institute: HHMI-Salk-Institute

value: nuclear RNA + genomic DNA


title: CBX334 human-derived xenograft

description:
CBX334
single tumor, homogenized
replicate1


title: WT, 7dpi, rep2

value: Osm+/+


title: KO, 7dpi, rep1


title: CBX330A human-derived xenograft

description:
CBX330A
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-1-I3-O1


title: WT, 7dpi, rep1


title: Sox2FKBP_D0_EpiLC_DMSO_H3K27ac_rep1


title: KO, 3dpi, rep2

value: 3 days post infection


title: Sox2FKBP_12h_EpiLC_DMSO_H3K27ac_rep1


title: HctYH_OF3A_1-1-I3-O14


title: Sox2FKBP_2iESC_dTAG_12h_H3K27ac_rep1


title: KO, 3dpi, rep1


title: Sox2FKBP_2iESC_dTAG_0h_H3K27ac_rep1


title: CBX295 human-derived xenograft

description:
CBX295
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-1-I3-N1


title: CBX280 human-derived xenograft

description:
CBX280
single tumor, homogenized
replicate1


title: CBX281 human-derived xenograft

description:
CBX281
single tumor, homogenized
replicate1


title: WT, 3dpi, rep2


title: WT, 3dpi, rep1


title: Sox2FKBP_D3_EpiLC_DMSO_ATAC_rep1

extract_protocol:
Cells or embyos were lysed in lysis buffer.
The ATAC-seq procedure was performed as previously described (Wu et al. 2018). Briefly, cells were transferred into 6 μl of lysis buffer [10 mM tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.02% digitonin) in ice for 10 min. The ATAC reaction was performed by adding 4 μl of ddH2O, 4 μl of 5× TTBL, and 5 μl TTE mix V5 (Vazyme Biotech Co.,Ltd, catalog no. TD502) at 37°C for 30 min and then stopped by adding 5 μl of 5× TS stop buffer at room temperature for 5 min. DNA was extracted by phenol chloroform and ethanol purification after adding 40 ng of carrier RNA and 103 μl of tris-EDTA. Then, DNA was PCR-amplified with 10 μl of index (Vazyme Biotech Co.,Ltd, catalog no. TD202), 10 μl of 5× TAB and 1 μl tris-acetate-EDTA (Vazyme Biotech Co.,Ltd, catalog no. TD502) with the program of 72°C for 3 min, 98°C for 30 s, (98°C for 15 s, 60°C for 30 s, and 72°C for 3 min) with 18 cycles, and 72°C for 5 min.


title: Sox2FKBP_D3_EpiLC_dTAG_ATAC_rep1


title: KO, uninfected, rep1

value: Uninfected control


title: HctYH_OF3A_1-1-I3-N14


title: CBX286 human-derived xenograft

description:
CBX286
single tumor, homogenized
replicate1


title: KO, uninfected, rep2


title: CBX298 human-derived xenograft

description:
CBX298
single tumor, homogenized
replicate1


title: Sox2FKBP_D2_EpiLC_dTAG_ATAC_rep1


title: CBX278 human-derived xenograft

description:
CBX278
single tumor, homogenized
replicate1


title: CBX277B human-derived xenograft

description:
CBX277B
single tumor, homogenized
replicate1


title: WT, uninfected, rep2


title: Sox2FKBP_D2_EpiLC_DMSO_ATAC_rep1


title: HctYH_OF3A_1-1-I3-M2


title: HctYH_OF3A_1-1-I3-O13


title: WT, uninfected, rep1


title: CBX277A human-derived xenograft

description:
CBX277A
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-1-I3-N2


title: Sox2FKBP_D1_EpiLC_DMSO_ATAC_rep1


title: CBX269 human-derived xenograft

description:
CBX269
single tumor, homogenized
replicate1


title: Phf6 cKO LIC-e cells ATAC-Seq Rep4

city: Philadelphia

first: Vikram

last: Paralkar

address: 421 Curie Boulevard

department: Division of Hematology and Oncology, Department of Medicine

institute: University of Pennsylvania Perelman School of Medicine

description: sorted for GFP+, c-Kit+, Ly6C- cells

data_processing:
Sequence reads were trimmed for low quality/adapter sequence using Trimmomatic.
Trimmed reads were mapped to mm10 genome using Bowtie2.
Peaks were called using MACS2.
Differential peak analyses was performed using DiffBind.
Assembly: mm10
Supplementary files format and content: bigwigs file include individual sample tracks, tab-delimited text file includes peak signal on all samples

source_name: Bone marrow

growth_protocol: 50,000 LIC-e cells were sort purified 4 days after transduction with HoxA9 transgene

extract_protocol:
50,000 LIC-e cells were collected for each sample, lysed and their nuclei were isolated. Tagmentation was performed using Nextera Tn5 transposase (Illumina Nextera ATAC seq kit, 20034197). Libraries were prepared using dual end indexing using NEBNext Ultra II DNA Library Prep Kit (E7645L) using the manufacturer's protocol, quantified using KAPA library quantification kit (Roche KK4824) and equimolar libraries were pooled.
Libraries were prepared using dual end indexing with NEBNext Ultra II DNA Library Prep Kit (E7645L) using the manufacturer's protocol. Concentrations and sizes of libraries were determined using Agilent 2200 Tapestation and KAPA library quantification kit (Roche KK4824).
LIbraries from all samples were pooled in equimolar concentrations and denatured along with 1% of PhiX for paired-end sequencing. Pooled library quantification was determined using  KAPA library quantification kit (Roche KK4824).

value: Bone marrow

value: HoxA9-transduced marrow (c-Kit+, Ly6C- cells)

value: Hematopoietic

value: Vav-Cre/+, Phf6 flox/Y


title: Sox2FKBP_12h_EpiLC_dTAG_ATAC_rep1


title: Phf6 cKO LIC-e cells ATAC-Seq Rep3

description: sorted for GFP+, c-Kit+, Ly6C- cells


title: HctYH_OF3A_1-1-I3-N13


title: CBX259B human-derived xenograft

description:
CBX259B
single tumor, homogenized
replicate1


title: CBX259A human-derived xenograft

description:
CBX259A
single tumor, homogenized
replicate1


title: Sox2FKBP_12h_EpiLC_DMSO_ATAC_rep1


title: CBX246 human-derived xenograft

description:
CBX246
single tumor, homogenized
replicate1


title: Phf6 cKO LIC-e cells ATAC-Seq Rep2

description: sorted for GFP+, c-Kit+, Ly6C- cells


title: Phf6 cKO LIC-e cells ATAC-Seq Rep1

description: sorted for GFP+, c-Kit+, Ly6C- cells


title: Sox2FKBP_D0_EpiLC_DMSO_ATAC_rep1


title: HctYH_OF3A_1-1-I3-L2


title: Sox2FKBP_D1_EpiLC_dTAG_ATAC_rep1


title: HctYH_OF3A_1-1-I3-L14


title: Sox2FKBP_2iESC_dTAG_12h_ATAC_rep1


title: HctYH_OF3A_1-1-I3-L13


title: HctYH_OF3A_1-1-I3-M1


title: Ctrl LIC-e cells ATAC-Seq Rep2

description: sorted for GFP+, c-Kit+, Ly6C- cells

value: Vav-Cre/+, Phf6 +/Y


title: CBX24 human-derived xenograft

description:
CBX24
single tumor, homogenized
replicate1


title: Ctrl LIC-e cells ATAC-Seq Rep3

description: sorted for GFP+, c-Kit+, Ly6C- cells


title: HctYH_OF3A_1-1-I3-M14


title: Sox2_mzKO_ICM_SOX2_CR_rep2

source_name: E3.5 ICM

growth_protocol: For collection of wildtypes E3.5 ICM, 4–6-week-old C57BL/6J female mice were injected with pregnant mare serum gonadotropin followed by human chorionic gonadotropin (hCG; Ningbo Hormone Product Co., Cat # 110251283 Ltd., China 10 IU) 48 hours before being mated with PWK/PhJ mice. Fertilized 8 cell were flushed out from the oviduct with HEPES-buffered CZB medium at E2.5 (68-70h). In vitro cultured was carried out for one day with the 8-cell embryo in KSOM medium to get blastocyst.

extract_protocol:
Cells or embyos were lysed in wash buffer.
CUT&RUN was performed as previously reported (Skene et al., 2018; Skene and Henikoff, 2017) with modifications. Briefly, after removing the zona pellucida with Tyrode’s solution (Sigma-Aldrich, T1788) or 0.5% (m/v) Protease from Streptomyces griseus (Sigma-Aldrich, P8811), early embryos were incubated with Concanavalin-coated magnetic beads (Polyscience, 86057) for 10 min at room temperature on a thermomixer at 400 rpm. Samples were then incubated with primary antibody at a ratio of 1:100 at 4℃ for 3-5 hours on a thermomixer at 400 rpm. After washing for one time, beads were incubated with pA-MNase (to a final concentration of 400-700ng/mL) (a gift from Steven Henikoff lab) at 4℃ for 1 hours on a thermomixer at 400 rpm. After two times of washing, targeted digestion was performed by adding 2μL of 100mM CaCl2 for 30 mins on ice, followed by termination by adding an equal volume of 2  × stop buffer. Samples were then incubated at 37℃ for 20 mins for fragment releasing. The total samples or supernatants were digested with Proteinase K (NEB, P8107S) and purified using phenol:chloroform:isoamyl alcohol (25:24:1, v/v) followed by ethanol purification at -80℃ overnight. The next day, DNA was purified and subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Sequencing was done using the HiSeq X Ten system or  NovaSeq (Illumina) according to the manufacturer’s protocol.

value: Sox2 mzKO

value: mix

value: Sox2 (Abclonal, A11936)


title: CBX232A human-derived xenograft

description:
CBX232A
single tumor, homogenized
replicate1


title: Sox2FKBP_2iESC_dTAG_0h_ATAC_rep1


title: CBX191 human-derived xenograft

description:
CBX191
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-1-I3-K2

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: Ctrl LIC-e cells ATAC-Seq Rep1

description: sorted for GFP+, c-Kit+, Ly6C- cells


title: Sox2_mzKO_ICM_SOX2_CR_rep1


title: HctYH_OF3A_1-1-I3-K1


title: Phf6 cKO Committed cells RNA-Seq Rep4

description: sorted for GFP+, c-Kit+, Ly6C+ cells

data_processing:
Sequence reads were trimmed for low quality/adapter sequence using Trimmomatic.
Trimmed reads were mapped to mm10 genome using STAR.
read quantification and feature annotation were performed using featureCounts.
Differential expression analysis was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw read counts on all samples

growth_protocol: Cells were directly sorted from mouse bone marrow and used for RNA-extraction, without ex vivo growth.

extract_protocol:
150,000 GFP+ committed leukemic cells were sort purified into TRIzol LS reagent (Thermo Fisher Scientific, 10296010). Total RNA was isolated using RNeasy mini kit (Qiagen 74106) by following manufacturer recommended protocol. RNA concentration was determined by using Agilent 2200 TapeStation and a high sensitivity RNA Screentape (Agilent 5067-5579). Samples with a RIN greater than or equal to 8 were used to construct RNA-Seq libraries. RNA libraries were prepared using Smarter Stranded Total RNA-Seq Kit - Pico Input Mammalian (Takara Bio 635005) using the manufacturer recomended protocol. Concentration and the size of the libraries were detremined using Agilent 2200 TapeStation and KAPA library quantification kit (Roche KK4824).
RNA libraries were prepared using NEBNext® Ultra™ II directional RNA library prep kit (New England Biolabs, E7530L) using the manufacturer recommended protocol. Concentrations and sizes of libraries were determined using Agilent 2200 Tapestation and KAPA library quantification kit (Roche KK4824).
Libraries from all samples were pooled in equimolar concentrations and denatured along with 1% PhiX for paired-end sequencing. Pooled libraries were quantified using KAPA library quantification kit (Roche KK4824).

value: Transplanted retroviral HoxA9 AML (c-Kit+, Ly6C+ cells)

value: Committed leukemic cells


title: HctYH_OF3A_1-1-I3-M13


title: CBX180 human-derived xenograft

description:
CBX180
single tumor, homogenized
replicate1

value: human-derived xenograft


title: HctYH_OF3A_1-1-I3-L1

value: nuclear RNA + genomic DNA


title: Sox2_control_ICM_SOX2_CR_rep2

value: Sox2 control


title: HctYH_OF3A_1-1-I3-K14


title: Phf6 cKO Committed cells RNA-Seq Rep3

description: sorted for GFP+, c-Kit+, Ly6C+ cells


title: CBX175 human-derived xenograft

description:
CBX175
single tumor, homogenized
replicate1


title: Phf6 cKO Committed cells RNA-Seq Rep2

description: sorted for GFP+, c-Kit+, Ly6C+ cells


title: Sox2_control_ICM_SOX2_CR_rep1


title: CBX167 human-derived xenograft

description:
CBX167
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-1-I3-K13


title: EpiLCs_SOX2_CR_rep2

source_name: EpiLC

value: wild type


title: CBX140 human-derived xenograft

description:
CBX140
single tumor, homogenized
replicate1


title: CBX163 human-derived xenograft

description:
CBX163
single tumor, homogenized
replicate1


title: Ctrl Committed cells RNA-Seq Rep3

description: sorted for GFP+, c-Kit+, Ly6C+ cells


title: EpiLCs_SOX2_CR_rep1


title: HctYH_OF3A_1-1-I3-J2


title: PolII-3T3-L1-CTL

city: xiamen

first: Guosheng

last: Hu

state: fujian

address: Xiang'an South Road, Xiang'an District

department: school of life sciences

institute: xiamen university

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the mm10 genome assembly using Bowtie version 2.2.6 with the default options.
The bigwig files were generated by using HOMER 4.9, in which the total tags are normalized to 1.00e+07.
Peaks are called by using Homer findPeaks script
Genome_build: mm10

growth_protocol: 3T3-L1 cells,obtained from American Type Culture Collection, were cultured in Medium B (Dulbecco's modified Eagle's medium (1 g/L glucose)  supplemented with 10% (v/v) NCS (Thermo Fisher Scientific), 100 U/ml penicillin, and 100 mg/ml streptomycin) at 37 C in an  atmosphere of 8.8% CO2 and maintained in less than 50% confluence.

extract_protocol:
3T3-L1 preadipocytes with indicated treatments were used for ChIP-Seq analysisFor ChIP with Pol II (Bethyl, A300-653A) andC/EBPβ (Santa Cruz, sc-150) antibodies, cells were fixed with 1% formaldehyde for 15 min at RT. For ChIP with HA antibody (Abcam, ab9110), cells were fixed with disuccinimidyl glutarate (DSG) (5 mM) for 45 min at RT, washed twice with PBS and fixed with 1% formaldehyde for another 15 min at RT. Fixation was stopped by 0.14 M glycine at RT for 10 min, followed by two washes with PBS. For each ChIP, 1×107 cells were resuspended in Lysis Buffer A (50 mM Tris-cl, pH7.8, 10 mM EDTA, 1% SDS ) supplemented with protease inhibitors (Roche). Chromatin was fragmented to 150-300 bp on a Bioruptor for 30 cycles of 30 s on and 30 s off. Chromatin lysates were then diluted 10-fold with Buffer D (20 mM Tris, pH7.8, 150 mM NaCl, 2 mM EDTA and 1% Triton X-100) supplemented with protease inhibitors, incubated with 5 μg anti-HA (Abcam, ab9110), 5 μg anti-C/EBPβ (Santa Cruz, sc-150), 5 μg anti-Pol II (Bethyl, A300-653A)antibodies overnight at 4oC, and then immunoprecipitated with Protein G magnetic beads (Biorad, 161-4023) with rotation at 4oC for 4 hr. Immunoprecipitations were washed once with Buffer E (20 mM Tris, pH8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS and 1% Triton X-100) for 15 min at 4oC, once with Buffer E containing 400 mM NaCl for 15 min at 4oC, and twice with Buffer F (50 mM Tris, pH8.0, 1 mM EDTA). Formaldehyde crosslinked chromatin was reversed in Buffer G (50 mM Tris, pH8.0, 10 mM EDTA, 1% SDS) at 65oC overnight. DNA was isolated using Qiagen PCR product purification kit (#28104).
Library was generated using a KAPA Hyper Prep Kit (Roche, KK8503) following manufacturer’s instructions. Adaptors and primer sequences from Roche were used for library construction and amplification. After PCR amplification, the 250-450 bp fragments were purified using KAPA pure beads (Roche, KK8000) following manufacturer’s instructions.

treatment_protocol: On day 0 (2 days after confluence), 3T3-L1 preadipocytes were treated with Induction Medium (Dulbecco’s modified Eagle’s medium  (1 g/L glucose) supplemented with 10% (v/v) FCS, 100 U/ml penicillin, and 100 mg/ml streptomycin) containing 5 mg/ml insulin,  0.5 mM IBMX, 1 mM Dexamethasone and 1 mM pioglitazone.

tag: chip antibody

value: anti-Pol II (Bethyl, A300-653A)

value: 3T3-L1 preadipocytes harvested  with differentiation medium treatment


title: CBX130B human-derived xenograft

description:
CBX130B
single tumor, homogenized
replicate1


title: Phf6 cKO Committed cells RNA-Seq Rep1

description: sorted for GFP+, c-Kit+, Ly6C+ cells

value: Bone marrow


title: CBX119 human-derived xenograft

description:
CBX119
single tumor, homogenized
replicate1


title: Ctrl Committed cells RNA-Seq Rep2

description: sorted for GFP+, c-Kit+, Ly6C+ cells


title: Ctrl Committed cells RNA-Seq Rep1

description: sorted for GFP+, c-Kit+, Ly6C+ cells


title: PolII-3T3-L1-KD-MED20


title: HctYH_OF3A_1-1-I3-J14


title: HctYH_OF3A_1-1-I3-J1


title: CBX113 human-derived xenograft

description:
CBX113
single tumor, homogenized
replicate1


title: HctYH_OF3A_1-1-I3-I2


title: Phf6 cKO LIC-e cells RNA-Seq Rep4

description: sorted for GFP+, c-Kit+, Ly6C- cells

extract_protocol:
50,000 GFP+ LIC-e cells were sort purified into TRIzol LS reagent
RNA libraries were prepared using Smarter Stranded Total RNA-Seq Kit - Pico Input Mammalian
Libraries from all samples were pooled in equimolar concentrations and denatured along with 1% PhiX for paired-end sequencing. Pooled libraries were quantified using KAPA library quantification kit

value: Transplanted retroviral HoxA9 AML

value: Hematopoietic


title: HctYH_OF3A_1-1-I3-J13


title: CEBPbeta-3T3-L1

value: anti-C/EBPβ (Santa Cruz, sc-150)


title: CBX110 human-derived xenograft

description:
CBX110
single tumor, homogenized
replicate1


title: Phf6 cKO LIC-e cells RNA-Seq Rep3

description: sorted for GFP+, c-Kit+, Ly6C- cells

value: Vav-Cre/+, Phf6 flox/Y


title: CBX107 human-derived xenograft

description:
CBX107
single tumor, homogenized
replicate1


title: 3XHA-MED20-3T3-L1

value: anti-HA (Abcam, ab9110)


title: Phf6 cKO LIC-e cells RNA-Seq Rep2

description: sorted for GFP+, c-Kit+, Ly6C- cells


title: HctYH_OF3A_1-1-I3-I1


title: 2iESC_SOX2_CR_rep2

address: Haidian District

value: Sox2 (Abclonal, A11936)


title: Phf6 cKO LIC-e cells RNA-Seq Rep1

description: sorted for GFP+, c-Kit+, Ly6C- cells


title: CBX102A human-derived xenograft

description:
CBX102A
single tumor, homogenized
replicate1


title: 3XHA-MED20-3T3-L1-KD-CEBPbeta


title: Ctrl LIC-e cells RNA-Seq Rep3

description: sorted for GFP+, c-Kit+, Ly6C- cells

value: Vav-Cre/+, Phf6 +/Y


title: 2iESC_SOX2_CR_rep1


title: Ctrl LIC-e cells RNA-Seq Rep2

description: sorted for GFP+, c-Kit+, Ly6C- cells


title: HctYH_OF3A_1-1-I3-H2

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: HctYH_OF3A_1-1-I3-H14


title: E75_ectoderm_SOX2_CR_rep2

source_name: E7.5 ectoderm

growth_protocol: To dissect the E7.5 embryo, endoderm at E7.5 was first isolated similarly as that to obtain TE. Mesoderm was then collected by making a cut parallel to the PS. After cutting the ‘J-shaped’ PS where the mesoderm was attached, the rest of the embryo was collected as ectoderm.

value: C57BL/6J x  PWK/PhJ


title: HctYH_OF3A_1-1-I3-H1


title: E75_ectoderm_SOX2_CR_rep1


title: Ctrl LIC-e cells RNA-Seq Rep1

description: sorted for GFP+, c-Kit+, Ly6C- cells


title: ZsGreen- Tumor Infiltrating T cells

city: Amherst

first: Leonid

last: Pobezinsky

address: 661 N Pleasant St

department: Veterinary and Animal Sciences

institute: University of Massachusetts Amherst

description: G158-cnt-minus_S1, CD45+TCRb+TILs_ZsG+S1_ZsG-S2

data_processing:
The 10x Cloud Analysis Cell Ranger Pipeline (Cellranger version 6.1.2) was used to align reads and generate feature-barcode matrices. Reads were aligned to Mus musculus reference genome (Mouse mm10 v3.0.0). The aggr pipeline was used to combine data from multiple samples into an experiment-wide feature-barcode matrix and analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated vales files and matrix files

source_name: Tumor

extract_protocol:
Mice were injected subcutaneously in the right flank (or both flanks) with 2.5 x 10^5 B16 ZsGreen+ tumor cells. 8 days after injection, tumors were minced and digested with 1 mg/mL collagenase D and 200 μg/mL DNase mix (Roche) by incubating at 37°C for 30 min with mixing every 5 min. The digestants were then passed through 40-micron filter, spun at 1250 rpm for 5 min and resuspended in FACS buffer. Cells were stained and sorted on ZsG+ and ZsG- cells using a BD FACSAria Fusion instrument (BD Biosciences). After sorting, cells were counted using a Cellometer K2 cell counter (Nexcelom Bioscience) and by manual counting via hemocytometer.
Single cell gene expression profiling was performed using the Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) kit. Each cell suspension was loaded onto a well of Chip G on the 10x Genomics Chromium Controller System following the manufacturer's user manual (10x Genomics). Barcoding and cDNA synthesis were performed according to the manufacturer's instructions. Qualitative analysis of cDNA was performed using the 2100 Agilent Bioanalyzer High Sensitivity assay. The cDNA libraries were constructed using the 10x Chromium Single cell 3’ Library Kit v3.1 (dual index) according to the manufacturer’s protocol. Quality assessment of final libraries was done on Qubit fluorometer using a DNA High Sensitivity assay (Thermo Scientific) and a 2100 Agilent Bioanalyzer High Sensitivity assay (Agilent Technologies). Libraries were sequenced on an Illumina NextSeq 500 using the NextSeq 500/550 Mid Output Kit v2.5 (150 Cycles) sequencing kit, with the following read length: 28 bp Read1 for the 10x cell barcode and UMI, 90 bp Read 2 for the insert, and 10 bp I7 and I5 for the sample index. Phix (Illumina) was spiked in at 1% as per kit manual recommendation (10x Genomics).

value: Tumor

tag: group

value: CD45+ TCRb+ TILs

value: Tumor infiltrating lymphocytes


title: E55_epiblast_SOX2_CR_rep2

city: Beijing

first: Lijia

last: Li

source_name: E5.5 epiblast

growth_protocol: E5.5 -E7.5 embryo tissues were collected via previously described (Harrison et al. 1995). Briefly, female mice (C57BL/6J) and male mice (PWK/Phj) were mated naturally, and the time when the vaginal plug was observed the next day was considered E0.5. To dissect the E5.5 Epi, we first collected embryos by removing decidua and Reichert’s membrane. Then embryonic regions were dissected away from extra-embryonic tissues (ExE) in Dulbecco’s modified Eagle medium containing 10% fetal bovine serum and incubated in pancreatic and trypsin enzyme solution for 2 min at room temperature.

value: wild type


title: SW480R544Q3,biol rep 3

city: beijing

first: wenjie

last: liu

address: No. 17 Nanli, Panjiayuan, Chaoyang District

institute: National Cancer Center/National Clinical  Research Center for Cancer/Cancer  Hospital

data_processing:
Illumina NovaSeq platform
RNA-seq raw reads were trimmed by Skewer (v0.2.2) to remove adapter sequences
then aligned to the human hg19 reference genome by STAR (v2.4.2a)
RSEM (1.2.29) were used to determine expression abundance quantification.
Differentially expressed genes (DEGs) were selected based on |fold change| >=2 and adjusted P-value < 0.05 thresholds by edge R.
Assembly: GENCODE(v19)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: HCT116 and SW480 were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA from HCT116 and SW480 cells was extracted by Trizol reagent. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared by TruSeq Ribozero kit following manufacturer's protocols.

treatment_protocol: TRPS1 overexpressed stable cells (empty vector, Con; wild type, WT; and R544Q mutant, MT) using these two cell lines were constructed and confirmed by Western blot

value: epithelial

value: TRPS1-MT overexpression


title: SW480trps1_2,biol rep 2

value: TRPS1-WT overexpression


title: ZsGreen+ Tumor Infiltrating T cells

description: G158-exp-plus_S2, CD45+TCRb+TILs_ZsG+S1_ZsG-S2


title: HctYH_OF3A_1-1-I3-I13

value: nuclear RNA + genomic DNA


title: HctYH_OF3A_1-1-I3-I14


title: SW480R544Q1,biol rep 1


title: E65_epiblast_SOX2_CR_rep1

institute: Tsinghua University

source_name: E6.5 epiblast

growth_protocol: Epi was obtained by pipetting embryonic regions through a capillary to detach each other.


title: SW480trps1_3,biol rep 3


title: HctYH_OF3A_1-1-I3-G2


title: ZsGreen+ Tumor Infiltrating Lymphocytes

description: G177_S2_Plus_Expt, All_CD45+TILs_ZsG-S1_ZsG+S2

value: CD45+ TILs


title: SW480R544Q2,biol rep 2


title: E55_epiblast_SOX2_CR_rep1


title: ZsGreen- Tumor Infiltrating Lymphocytes

description: G177_S1_minus_Control, All_CD45+TILs_ZsG-S1_ZsG+S2


title: ICM_SOX2_CR_rep2


title: HctYH_OF3A_1-1-I3-G13


title: CBX102B human-derived xenograft

description:
CBX102B
single tumor, homogenized
replicate1

source_name: human-derived xenograft

value: human-derived xenograft


title: E65_epiblast_SOX2_CR_rep2


title: SW480Control2,biol rep 2

value: WT