title: Whole Genome Sequencing of HoxA -/- A17iCre mESCs

status: Public on Dec 16 2021

first: Sudarshan

last: Pinglay

address: 3720 15th Ave NE

data_processing:
Library strategy: DNA-seq
Illumina adapter trimming with trimmomatic v0.39
Reads mapped using bowtie2 v2.2.9
Sort bam files using samtools
Make bigwig files using deeptools bamCoverage v3.2.1
Genome_build: mm10_synHoxA custom genome or mm10_synHoxA_delHoxA custom genome, mm10 or rn6
Supplementary_files_format_and_content: bigwig files to normalize coverage

organism:
Mus musculus
Rattus norvegicus

source_name: Parental HoxA -/- mouse ES cell with landing pad at Hprt

growth_protocol: Plasmids were purified from bacterial cultures in Luria Broth (LB) supplemented with the appropriate antibiotic (12.5 µg/mL Chloramphenicol for source BACs, and 25 µg/mL Kanamycin for all assemblons. mESCs were cultured on plastic tissue culture plates coated with 0.1% gelatin (EMD Millipore ES-006-B) at 37°C and 5% CO2 in ‘80/20’ medium comprising 80% 2i medium and 20% mESC medium. mESCs were grown at 37°C and 8% CO2 before differentiation experiments.  2i medium was made from a 1:1 mix of Advanced DMEM/F12 (Gibco 12634010) and Neurobasal-A (Gibco 10888022), containing 1X N-2 supplement (Gibco 17502048), 1X B-27 supplement (Gibco 17504044), 2mM Glutamax (Gibco 35050061), 0.1mM Beta-Mercaptoethanol (Gibco 31350010), 103 units/mL LIF (Millipore, ESG1107), 1 μM MEK1/2 inhibitor (Stemgent, PD0325901), and 3 μM GSK3 inhibitor (R&D Systems, CHIR99021). mESC medium was made from Knockout DMEM (Gibco 10829018), containing 15% Fetal Bovine Serum (Gemini), 0.1 mM Beta-Mercaptoethanol (Gibco 31350010), 1X MEM Non Essential Amino Acids (Gibco 11140050), Glutamax (Gibco 35050061), 1X Nucleosides (Millipore ES-008-D) and LIF (Millipore ESG1107).

extract_protocol:
Plasmids were purified from small scale bacterial cultures (5-10 mL) using alkaline lysis. gDNA was extracted from mESC cell pellets using Qiagen DNA mini kit.
Illumina sequencing libraries for BACs were generated from 100-200 ng BAC DNA using NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs E7805S) according to the manufacturer’s protocol. Whole genome sequencing and capture sequencing libraries were prepared as follows: 1 µg of DNA was sheared to ∼500 to 900 bp in a 96-well microplate using the Covaris LE220 (450 W, 10% Duty Factor, 200 cycles per burst, and 90-s treatment time). Sheared DNA was purified using the DNA Clean and Concentrate-5 Kit (Zymo Research D4013), and the concentration was measured on a NanoDrop instrument (Invitrogen). DNA fragments were end-repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase (New England Biolabs M0203S, M0210S and M0201S, respectively), and A-tailed using Klenow (3′-5′ exo-; New England Biolabs M0212L). Illumina-compatible adapters were subsequently ligated to DNA ends, and DNA libraries were amplified with KAPA 2X Hi-Fi Hotstart Readymix (Roche). Biotinylated baits for capture sequencing were prepared from assemblon BACs using nick translation

value: Parental HoxA -/- A17iCre mESCs

tag: capture bait

value: mESC


title: Whole Genome Sequencing of Parental WT A17iCre mESCs

type: SRA

city: Seattle

state: WA

country: USA

institute: University of Washington

library_source: genomic

molecule: genomic DNA

source_name: Parental mouse ES cell with landing pad at Hprt

tag: strain

value: Parental WT A17iCre mESCs

tag: cell type


title: WTV1

city: Ithaca

first: Brian

last: VanderVen

state: New York

address: 930 Campus Road

department: Microbiology and Immunology

institute: Cornell University

description: 11236_10135_108915_H7Y3TBGXC_1092-3313-KW7-WTV_2_ATGAGC_R1.fastq.gz

library_source: transcriptomic

data_processing:
Basecalling was perfomed on the Illumina NextSeq 500 using RTA 2.0.
Reads were trimmed for low quality and adaptor sequences with TrimGalore v0.6.0, a wrapper for cutadapt and fastQC. Parameters: -j 1 -e 0.1 --nextseq-trim=20 -O 1 -a AGATCGGAAGAGC --length 50 --fastqc
Reads were mapped to the Mycobacterium tuberculosis CDC1551 reference genome using STAR v2.7.0e. Parameters: --outSAMstrandField intronMotif , --outFilterIntronMotifs RemoveNoncanonical ,--outSAMtype BAM SortedByCoordinate, --quantMode GeneCounts
SARTools and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression, upon which conclusions were based.
Genome_build: Mycobacterium tuberculosis CDC1551 reference genome (GCA_000008585.1 )
Supplementary_files_format_and_content: tab-delimited text file containing normalized counts for each sample and each gene

molecule: total RNA

organism: Mycobacterium tuberculosis CDC1551

source_name: Mycobacterium tuberculosis bacteria

growth_protocol: Bacterial strains were pre-grown in 7H9OADC before inoculation into fresh media containing a cAMP-inducing compound (10 µM V-59 or 500 ng/mL Atc) or vehicle control (DMSO or EtOH) at an OD600 of 0.1. The following day, bacteria were inoculated into 7H12+cholesterol media containing fresh compound or vehicle control. After four hours, cultures were pelleted by centrifugation, washed with guanidine thiocyanate-based buffer and stored at -80°C.

extract_protocol:
Trizol LS (Thermo Fisher). Pellets were washed and suspended in Trizol LS (Ambion), 0.1 mmol silicon beads were added, and cells were lysed using a BeadBeater. Total RNA was isolated by chloroform extraction and precipitated in isopropanol with GlycoBlue reagent (Thermo Fisher). RNA was resuspended in nuclease-free water, genomic DNA contamination was removed using the Turbo-DNA free kit (Invitrogen), and rRNA was depleted using the Ribo-Zero Gold rRNA removal kit (Illumina).
Sample quality was determined via Fragment Analyzer (Advanced Analytical) and TruSeq-barcoded RNAseq libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). Sequencing was performed at the Cornell University Transcriptional Regulation and Expression Facility on a NextSeq500 instrument (Illumina) at a depth of 15 M single-end 75 bp reads.

tag: genotype

value: Wild type

tag: compound treatment

value: V-59 (Rv1625c agonist)


title: WTD2

description: 11236_10135_108914_H7Y3TBGXC_1092-3312-KW6-WTD_3_GGTAGC_R1.fastq.gz

value: DMSO (Vehicle)


title: WTV2

description: 11236_10135_108916_H7Y3TBGXC_1092-3314-KW8-WTV_3_ATTCCT_R1.fastq.gz


title: WTD1

description: 11236_10135_108913_H7Y3TBGXC_1092-3311-KW5-WTD_1_GAGTGG_R1.fastq.gz


title: KOD2

description: 11236_10135_108918_H7Y3TBGXC_1092-3316-KW10-KOD_3_CACTCA_R1.fastq.gz

value: Rv1625c Knockout


title: CompD2

description: 11236_10135_108922_H7Y3TBGXC_1092-3320-KW14-CompD_3_CTATAC_R1.fastq.gz

value: Rv1625c Complement


title: CompD1

description: 11236_10135_108921_H7Y3TBGXC_1092-3319-KW13-CompD_1_CATTTT_R1.fastq.gz


title: CompV1

description: 11236_10135_108923_H7Y3TBGXC_1092-3321-KW15-CompV_1_TAATCG_R1.fastq.gz


title: KOV2

description: 11236_10135_108920_H7Y3TBGXC_1092-3318-KW12-KOV_3_CATGGC_R1.fastq.gz


title: KOV1

description: 11236_10135_108919_H7Y3TBGXC_1092-3317-KW11-KOV_1_CAGGCG_R1.fastq.gz


title: CompV2

description: 11236_10135_108924_H7Y3TBGXC_1092-3322-KW16-CompV_3_TACAGC_R1.fastq.gz


title: EtOH2

description: 11236_10135_108910_H7Y3TBGXC_1092-3308-KW2-EtOH_3_ATGTCA_R1.fastq.gz

value: TetOn-cAMP

value: EtOH (Vehicle)


title: Atc2

description: 11236_10135_108912_H7Y3TBGXC_1092-3310-KW4-Atc_3_CGTACG_R1.fastq.gz

value: Atc (Rv1264cat Inducer)


title: KOD1

description: 11236_10135_108917_H7Y3TBGXC_1092-3315-KW9-KOD_2_CACGAT_R1.fastq.gz


title: 5WTe14

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: 2 μg

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Mus musculus

source_name: Brain microglia

extract_protocol:
The microglia was  purified from  Arid1acKO and Arid1afl/fl  mice cortex by fluorescence activated cell sorting.  Total RNA was immediately extracted by using the RNAeasy Mini kit (QIAGEN). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage


title: Atc1

description: 11236_10135_108911_H7Y3TBGXC_1092-3309-KW3-Atc_2_GTGGCC_R1.fastq.gz


title: EtOH1

description: 11236_10135_108909_H7Y3TBGXC_1092-3307-KW1-EtOH_2_AGTTCC_R1.fastq.gz


title: Peritoneal macrophages, WT_1

status: Public on Dec 17 2021

city: Nanjing

first: Yuyu

last: Zhu

address: Xianlin

institute: Nanjing University of Chinese Medicine

data_processing:
Basecalls performed using Illumina Casava 1.8
Index of the reference genome was built using Hisat2 v2.0.4 and pairedend clean reads were aligned to the reference genome using Hisat2 v2.0.4.
Data were filtered using the following specifications…
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Mus_musculus_Ensemble_92
Supplementary_files_format_and_content: fpkm.txt includes FPKMs for each Sample

source_name: Peritoneal macrophages

growth_protocol: Wild-type and SHP2lyz2-/- mice were intraperitoneally injected with 1 ml starch broth per mice, after 3 days, peritoneal cells were harvested by lavaging the peritoneal cavity . Adherent peritoneal macrophages were cultured in DMEM media containing 10% FBS and  at 37°C.

extract_protocol:
Peritoneal macrophages were used for total RNA isolation with Trizol (TaKaRa)
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H ）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: peritoneal macrophages

tag: age

value: 8 weeks

value: wild type


title: 6WTe14

description: 2 μg


title: 2KOe14

description: 2 μg


title: Smad3 binding region in HaCaT cells stimulated with TGF-beta, replicate 2

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description: anti-Smad3 ChIP-seq data

data_processing:
Reference files of the human reference sequence assembly (hg19) were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html)
ChIP-seq reads were aligned using Bowtie2 (Langmead et al., 2009).
Smad3 binding reagions were identified using MACS2 software (Model based analysis of ChIP-seq) (Zhang et al, 2008) with the command "callpeak --bdg --SPMR --keep-dup auto" and a q-value threshold of 0.0001 (two sample analysis using input genomic data).
control_HaCaT sample was used as input for peak calling and processed data are not available.
Genome_build: hg19
Supplementary_files_format_and_content: BED and bdg files were generated using MACS2.

organism: Homo sapiens

source_name: A human epidermal keratinocyte cell line

growth_protocol: HaCaT is a spontaneously immortalized human epidermal keratinocyte cell line that was established previously (Boukamp et al, JCB 1988, 106, 761-771). HaCaT cells were maintained in Dulbecco's modified Eagle's medium (DMEM #11965; Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin G, and 100 µg/ml streptomycin.

extract_protocol:
ChIP of HaCaT cells were performed using 10 μg of anti-Smad3 antibody (Isogaya et al, Cell Res 2011) or 10 ug of anti-Smad2 antibody (abcam, EP567Y), as described previously (Koinuma D et al, Mol cell biol, 2009).
The libraries were constructed as described (Morikawa et al, Nuc Acids Res 2011). Adaptor-ligated samples were amplified by 15 cycles of PCR.

treatment_protocol: Cells were treated with 1 ng/ml of TGF-beta for 1.5 h before fixation.

tag: ChIP

value: anti-Smad3 ChIP

tag: stimulation

value: TGF-beta, 1 ng/ml, 1.5h

tag: cell line

value: HaCaT


title: Smad2 binding region in HaCaT cells stimulated with TGF-beta, replicate 1

description: anti-Smad2 ChIP-seq data

value: anti-Smad2 ChIP


title: Smad2 binding region in HaCaT cells stimulated with TGF-beta, replicate 2

description: anti-Smad2 ChIP-seq data


title: Smad3 binding region in HaCaT cells stimulated with TGF-beta, replicate 1

description: anti-Smad3 ChIP-seq data


title: IRF3 binding region in BT549-caSmad3 cells transfected with polyI:C (Smad3 gene inactivation, gRNA#1)

description: anti-IRF3 ChIP-seq, BT549, Smad3 gRNA#1, polyI:C-transfected

data_processing:
Reference files of the human reference sequence assembly (UCSC hg38) were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html)
ChIP-seq reads were trimmed down to 50 bp and were aligned using Bowtie2 (version 2.2.2.6) (Langmead et al., 2009) with the command “-q --local”.
IRF3 binding regions were identified using MACS2 software (Model based analysis of ChIP-seq) (version 2.1.0.20151222) (Zhang et al, 2008) with the command "callpeak --bdg --SPMR --keep-dup auto" and a q-value threshold of 0.0001 (two sample analysis using GSM2795975 mapped to hg 38 as an input DNA).
bdg files were sorted using sort command  (sort -k1,1 -k2,2n).
bdg to wig conversion was performed  using bedClip, bedGraphToBigWig, bigWigToWig (ENCODE programs).
Genome_build: hg38
Supplementary_files_format_and_content: BED and WIG files were generated using MACS2 (version 2.1.0) and ENCODE programs as described above.

source_name: A basal-like breast cancer cell line, BT549

growth_protocol: BT-549 cells were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA) and cultured in RPMI1640 medium (#11875, Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS; #SH30910.03, Thermo Fisher Scientific, #10270-106, Gibco), 50 U/mL penicillin, 50 μg/mL streptomycin, and 0.95 μg/mL insulin. The cells were maintained in a 5% CO2 atmosphere at 37°C.

extract_protocol:
ChIP-seq of BT549 cells were performed using 10 μg of anti-IRF3 antibody (#655704, Biolegend, San Diego, CA, USA, lot number unavailable) as described previously (Koinuma D et al, Mol cell biol, 2009).
The libraries were constructed as described (Murai et al, Cell Discov, 2015), using IonXpress Plus Fragment Library Kit (Thermo Fisher Scientific). Adaptor-ligated samples were amplified by 15 cycles of PCR and purified by E-Gel SizeSelect (Thermo Fisher Scientific).

treatment_protocol: BT549 cells were infected with lentiviral vectors (made from lentiCRISPR v2 plasmid obtained from Feng Zhang (#52961; Addgene, Watertown, MA, USA)) to stably express Cas9 and gRNAs. Cells were transfected with polyI:C. Target genomic sequences without PAM are as follows: Smad3 gRNAs #1: GTTCGCCTTCAATATGAAGA and #2: ATGTCATCTACTGCCGCCTG, control gRNA: ATCGTTTCCGCTTAACGGCG.

tag: gene inactivation by crispr/cas9

value: Smad3 gRNA #1

tag: transfection

value: polyI:C transfection

value: no

tag: antibody


title: IRF3 binding region in BT549-caSmad3 cells transfected with polyI:C (Smad3 gene inactivation, gRNA#2)

description: anti-IRF3 ChIP-seq, BT549, Smad3 gRNA#2, polyI:C-transfected

value: Smad3 gRNA #2


title: IRF3 binding region in BT549 cells transfected with polyI:C (control gRNA)

description: anti-IRF3 ChIP-seq, BT549, control gRNA, polyI:C-transfected

value: control gRNA


title: Smad3 binding region in BT549-caSmad3 cells transfected with polyI:C

description: anti-Smad3 ChIP-seq, BT549, caSmad3 cells, polyI:C-transfected

data_processing:
Reference files of the human reference sequence assembly (UCSC hg38) were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html)
ChIP-seq reads were trimmed down to 50 bp and were aligned using Bowtie2 (version 2.2.2.6) (Langmead et al., 2009) with the command “-q --local”.
Smad3 or IRF3 binding regions were identified using MACS2 software (Model based analysis of ChIP-seq) (version 2.1.0.20151222) (Zhang et al, 2008) with the command "callpeak --bdg --nomodel --extsize 100 --keep-dup auto" and a q-value threshold of 0.05 (two sample analysis using GSM2795975 mapped to hg 38 as an input DNA).
bdg files were sorted using sort command  (sort -k1,1 -k2,2n).
bdg to wig conversion was performed  using bedClip, bedGraphToBigWig, bigWigToWig (ENCODE programs).
Genome_build: hg38
Supplementary_files_format_and_content: BED and WIG files were generated using MACS2 (version 2.1.0) and ENCODE programs as described above.

extract_protocol:
ChIP-seq of BT549 cells were performed using 10 μg of anti-Smad3 antibody (Isogaya et al, Cell Res 2011) or anti-IRF3 antibody (#655704, Biolegend, San Diego, CA, USA, lot number unavailable) as described previously (Koinuma D et al, Mol cell biol, 2009).
The libraries were constructed as described (Murai et al, Cell Discov, 2015), using IonXpress Plus Fragment Library Kit (Thermo Fisher Scientific). Adaptor-ligated samples were amplified by 15 cycles of PCR and purified by E-Gel SizeSelect (Thermo Fisher Scientific).

treatment_protocol: BT549 cells were infected with lentiviral vectors to stably express HA or caSmad3. Cells were transfected with polyI:C and treated with 1ng/ml of TGF-beta for 1.5h or left untreated.

tag: stable expression

value: caSmad3 (constitutively active Smad3)


title: Smad3 binding region in BT549-HA cells transfected with polyI:C

description: anti-Smad3 ChIP-seq, BT549, control cells, polyI:C-transfected, TGF-b treated

value: HA (control)

value: TGF-beta, 1ng/ml, 1.5 h


title: 20JV_Experiment3

city: San Diego

first: Michael

last: McHeyzer-Williams

address: 10550 N Torrey Pines Rd

institute: Scripps Research Institute

description: ~500 amplified mRNA targets

data_processing:
Bcl2fastq (Illumina) was used to demultiplex sequencing libraries using plate barcodes and assort reads by well barcodes prior to sequence alignment using Bowtie2 (v2.2.9) to a custom genome consisting of the amplicon regions for the specifically targeted genes used in the experiment based on the murine genome GRCm38.p6, version R97 (Ensembl). HTseq was used for read and UMI reduced tabulation.
Quality control excluded cells that contained over 2000 UMIs and fewer than 1000 reads, 60 UMI counts, and 25 unique genes detected. A secondary quality control filter included T cells that contained expressed Cd3e, Cd3d, or Cd3g. A total of 1924 T cells from 5 experiments were analyzed.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Processed data files consist of a cell x gene matrix of raw UMI counts with metadata headers

source_name: LN

extract_protocol:
Single cells were index sorted into 384 well plates containing 1uL of reverse transcription (RT) master mix using a FACS Aria III with FACS Diva software (BD Biosciences). The RT master mix consisted of: 0.2μL SuperScript IV 5x buffer (Invitrogen), 0.03μL SuperScript IV taq (Invitrogen), 0.03 DTT 0.1M (Invitrogen), 0.03μL RNaseOUT (Invitrogen), 0.012μL dNTPs (Invitrogen), 0.19μL RNase Free H2O and 0.5μL of oligoDT primer [1μM stock] (custom made, IDT) per well. A unique oligoDT primer that contains a 6 basepair well barcode and a 10 54 basepair unique molecular identifier was added to each well. Reverse transcription was performed at 42C for 50 minutes followed by heat inactivation at 80C for 10 minutes.
cDNA libraries were amplified using a custom targeted strategy the exact detailsf of which are described by Andrew G. Shuparski et. al. Single cell qtSEQ: cell-indexed quantitative and targeted RNA sequencing for sorted rare lymphocyte subpopulations STAR Protocols 2021

tag: treatment

value: Immunization analysis at naive, D7, D14, D28


title: 20JZ_Experiment4

description: ~500 amplified mRNA targets


title: 20JO_Experiment2

description: ~500 amplified mRNA targets


title: IRF3 binding region in BT549-caSmad3 cells transfected with polyI:C

description: anti-IRF3 ChIP-seq, BT549, caSmad3 cells, polyI:C-transfected


title: 1KOe14

description: 2 μg


title: 170kb Enhancers + SynHoxA assemblon in WT mESCs, 96h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
A8_WT_compE_RnHoxA_96hRA/SAG_rep2
featurecounts_WTlines_synHoxAWTaligned.txt
H5L3MBGXC_n01_mb255

data_processing:
Basecall conversion to fastq files was performed using Picard
Alignment: Fastq files were aligned to the genome (mm10_synHoxA or mm10_synHoxA_delHoxA custom genomes) using HISAT2, using options: -p 20 -q --rna-strandness F.
Computing Abundance: Mapped reads were assigned to annotated genes using the featureCount function in Rsubread, using options -s 2.
Differential gene expression analysis: Read counts were normalized using the ‘rlog’ or regularized log transformation in DESeq2 and used as inputs for the Principal Component Analysis (PCA). The log2 fold change (FC) and adjusted p-value in gene expression levels between 24h, 48h, and 96h vs. 0h was estimated using DESeq2 and plotted using ggplot. Normalized counts from DESeq2 were used to generate transgene/endogenous ratio plots, with the counts from endogenous locus being reduced by half to normalize the copy number between HoxA clusters. RNAseq track visualization was performed using combine tracks tool in IGV on bigwigs generated with deeptools bamCoverage and subsequent editing in Adobe Illustrator.
Genome_build: mm10_synHoxA or mm10_synHoxA_delHoxA custom genomes
Supplementary_files_format_and_content: Tab Separated Text File: Unnormalized Read Counts at annotated genes

molecule: polyA RNA

source_name: ES-derived embryoid bodies with variant synthetic Hox clusters

growth_protocol: mESCs were cultured on plastic tissue culture plates coated with 0.1% gelatin (EMD Millipore ES-006-B) at 37°C and 5% CO2 in ‘80/20’ medium comprising 80% 2i medium and 20% mESC medium. mESCs were grown at 37°C and 8% CO2 before differentiation experiments.  2i medium was made from a 1:1 mix of Advanced DMEM/F12 (Gibco 12634010) and Neurobasal-A (Gibco 10888022), containing 1X N-2 supplement (Gibco 17502048), 1X B-27 supplement (Gibco 17504044), 2mM Glutamax (Gibco 35050061), 0.1mM Beta-Mercaptoethanol (Gibco 31350010), 103 units/mL LIF (Millipore, ESG1107), 1 μM MEK1/2 inhibitor (Stemgent, PD0325901), and 3 μM GSK3 inhibitor (R&D Systems, CHIR99021). mESC medium was made from Knockout DMEM (Gibco 10829018), containing 15% Fetal Bovine Serum (Gemini), 0.1 mM Beta-Mercaptoethanol (Gibco 31350010), 1X MEM Non Essential Amino Acids (Gibco 11140050), Glutamax (Gibco 35050061), 1X Nucleosides (Millipore ES-008-D) and LIF (Millipore ESG1107).

extract_protocol:
Cells were collected at 0h or 24h, 48h, or 96h after RA/SAG treatment. RNA was extracted with the TRIzol LS Reagent (Life Technologies) followed by purification with the RNAeasy mini kit (Qiagen). RNA integrity was checked with the Agilent High Sensitivity RNA Screentape (Agilent, 5067-5579).
500 ng of RNA was used to prepare libraries and spiked-in with ERCC Exfold Spike-in mixes (Thermo Fisher 4456739). The TruSeq Stranded mRNA Library Preparation kit (Illumina 20020594) was used to prepare RNA-seq libraries. Library size was checked on the High Sensitivity DNA ScreenTape (Agilent 5067-5584). The KAPA library amplification kit was used to quantify libraries on the Bio-Rad CFX96 or the Roche Lightcycler 480 before pooling libraries. Libraries were sequenced on the Illumina NextSeq 500 using V2.5 chemistry (75 cycles, single-end 75 bp) or on the Illumina NovaSeq 6000 using the SP Reagent Kit (100 cycles, single-end 100bp) at the Genomics Core Facility at NYU.

treatment_protocol: Trypsinized (Gibco) mESCs were plated in AK medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), 7% KnockOut SR (vol/vol) (Gibco), 2 mM L-glutamine, 0.1 mM ß-mercaptoethanol and penicillin–streptomycin (Gibco)) to induce formation of embryoid bodies (EBs), at 37°C, 5% CO2. 3.5x105 cells were plated in 100 mm suspension plates (Corning) for RNA-seq experiments, while 3.5x106 cells were plated in 245 mm x 245 mm square plates (Corning) for ChIP-seq experiments. After 2 days (0h timepoint), the EBs were split 1:2 and plated in fresh AK medium supplemented with 1 μM all-trans retinoic acid (RA) and 0.5 μM smoothened agonist (SAG) (Millipore 566660). For CHIR differentiation, in place of RA/SAG, CHIR99021 was added at 3 µM concentration

value: 96h of RA+SAG differentiation

value: Embryoid Bodies


title: IRF3 binding region in BT549-HA cells transfected with polyI:C

description: anti-IRF3 ChIP-seq, BT549, control cells, polyI:C-transfected


title: 170kb Enhancers + SynHoxA assemblon in WT mESCs, 0h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
A8_WT_compE_RnHoxA_t=0_rep2
featurecounts_WTlines_synHoxAWTaligned.txt
H5L3MBGXC_n01_mb251

value: 0h of RA+SAG differentiation


title: 170kb Enhancers + SynHoxA assemblon in WT mESCs, 96h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
A8_WT_compE_RnHoxA_96hRA/SAG_rep1
featurecounts_WTlines_synHoxAWTaligned.txt
H5L3MBGXC_n01_mb249


title: 134kb SynHoxA assemblon in WT mESCs, 24h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
A5_WT_RnHoxA_24hRA/SAG_rep2
featurecounts_WTlines_synHoxAWTaligned.txt
H5L3MBGXC_n01_mb252

value: 134kb SynHoxA assemblon in WT mESCs

value: 24h of RA+SAG differentiation


title: 134kb SynHoxA assemblon in WT mESCs, 0h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
A5_WT_RnHoxA_t=0_rep2
featurecounts_WTlines_synHoxAWTaligned.txt
H5L3MBGXC_n01_mb250


title: 134kb SynHoxA assemblon in WT mESCs, 48h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
A5_WT_RnHoxA_48hRA/SAG_rep1
featurecounts_WTlines_synHoxAWTaligned.txt
HCWTLBGXF_n01_mb359

value: 48h of RA+SAG differentiation


title: 134kb SynHoxA assemblon in WT mESCs, 48h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
A5_WT_RnHoxA_48hRA/SAG_rep2
featurecounts_WTlines_synHoxAWTaligned.txt
HCWTLBGXF_n01_mb360


title: 134kb SynHoxA assemblon in WT mESCs, 24h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
A5_WT_RnHoxA_24hRA/SAG_rep1
featurecounts_WTlines_synHoxAWTaligned.txt
H5L3MBGXC_n01_mb246


title: 134kb SynHoxA assemblon in WT mESCs, 96h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
A5_WT_RnHoxA_96hRA/SAG_rep2
featurecounts_WTlines_synHoxAWTaligned.txt
H5L3MBGXC_n01_mb254


title: 134kb SynHoxA assemblon in WT mESCs, 96h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
A5_WT_RnHoxA_96hRA/SAG_rep1
featurecounts_WTlines_synHoxAWTaligned.txt
H5L3MBGXC_n01_mb248


title: 170kb Enhancers + SynHoxA assemblon in WT mESCs, 0h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
A8_WT_compE_RnHoxA_t=0_rep1
featurecounts_WTlines_synHoxAWTaligned.txt
H5L3MBGXC_n01_mb245


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 2, H3K27Ac ChIP

data_processing:
Basecall conversion to fastq files was performed using Picard
Alignment: Fastq files were aligned to the mm10_synHoxA_delHoxA custom genome using Bowtie 2, using options -p 20. Samtools was used to create sorted bam files for inputs into the bamCoverage tool from deeptools to create bigWig files, using options: --binSize 1 --scaleFactor 0.001 --normalizeUsingRPKM --ignoreForNormalization chrX -p max --extendReads 100.
Sliding windows: To generate sliding window plots of ChIP-seq signal, bedtools makewindows was used to generate bins of 3kb sliding 300 bp. Bedtools coverage was then used to compute the mean coverage in each bin from the sorted bam files. Coverage was normalized across samples using RPKM that was calculated as: reads-per-bin/(number of mapped reads (in millions) * bin length (kb)). Mean value and standard deviation of replicates was then plotted using Python matplotlib.
Genome_build: mm10_synHoxA_delHoxA custom genome

extract_protocol:
Cells were collected at 0h or 24h, 48h, or 96h after RA/SAG treatment. Cells were crosslinked at room temperature in 1 mM DSG (ProteoChem) for 15 min, followed by the addition of 1% FA (vol/vol) for 15 min. The reaction was quenched with Glycine and cells were washed with 1 × PBS. Samples were divided into ~25-30x106 cell aliquots, pelleted by centrifugation at 275 g, and frozen at -80°C. Cell aliquots were thawed on ice and lysis was performed in 5 mL of 50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% glycerol (vol/vol), 0.5% Igepal (vol/vol), 0.25% Triton X-100 (vol/vol) with 1 × protease inhibitors (Roche, 11697498001) for 10 min at 4°C. Cells were pelleted by centrifugation for 5 min at 1200 g, resuspended in 5 mL of 10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0 with 1 × protease inhibitors, and incubated for 10 min at 4°C on a rotating platform. Cells were centrifuged for 5 min at 1200 g and resuspended in 2 mL of Sonication Buffer (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 1% Triton X-100 (vol/vol), 0.1% sodium deoxycholate (wt/vol), 0.1% SDS (vol/vol) with 1 × protease inhibitors). For sonication, each sample was split in two Bioruptor tubes with added sonication beads. Sonication was performed using the Bioruptor Pico (Diagenode) for 18 cycles of 30 sec on and 30 sec off to sheer DNA into an average size of approximately 200bp. Immunoprecipitation was performed for 16h at 4°C on a rotating platform by incubating with Dynabeads protein-G (Thermo Fisher Scientific) conjugated with antibodies. For histone modifications, half of each original cell aliquot was incubated with Dynabeads protein-G conjugated with 5 µg of rabbit polyclonal to Histone H3K27me3 (Active motif 39155) or rabbit polyclonal to Histone H3 (acetyl K27) (Abcam ab4729) antibodies. For CTCF, the entire cell aliquot was incubated with Dynabeads protein-G conjugated with 5 µl of rabbit polyclonal to CTCF (EMD 07-729) antibody. After the immunoprecipitation, washes were performed with the following ice-cold buffers: sonication buffer, sonication buffer with 500 mM NaCl, LiCl wash buffer (20 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5% Igepal (vol/vol), 0.5% sodium deoxycholate (wt/vol)), and TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8). Elution was performed in elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS (vol/vol)) by incubating for 45 min at 65°C with occasional flicking of the tube. Samples were incubating for 16h at 65°C to perform reversal of crosslinks. 200 μL of TE and RNase A (Sigma) at a final concentration of 0.2 mg/mL was added to digest RNA by and incubating for 2h at 37°C. Proteins were digested by adding Proteinase K (Invitrogen) at a final concentration of 0.2 mg/mL, supplemented with CaCl2, at 55°C for 30 min. DNA was purified with phenol:chloroform:isoamyl alcohol (25:24:1; vol/vol) (Invitrogen) followed by an ethanol precipitation. DNA pellets were resuspended in 70 μL of water.
lllumina DNA sequencing libraries were prepared with approximately one third of the ChIP sample (24 μL) or a 1:100 dilution of the input sample in water. Library preparation was performed by end repair, A-tailing and ligating Illumina-compatible Bioo Scientific multiplexed adapters. Agencourt AmpureXP beads (Beckman Coulter) were used to remove unligated adapters. PCR amplification was performed with Phusion polymerase (New England Biolabs) and TruSeq primers (Sigma). Libraries were gel purified (Qiagen) between 250 and 550bp in size. Libraries were quantified before pooling using the KAPA library amplification kit on the Roche Lightcycler 480 or the Bio-Rad CFX96. The libraries were sequenced on Illumina NextSeq 500 using V2.5 chemistry (75 cycles, single-end 75bp) or on Illumina NovaSeq 6000 using the SP Reagent Kit (100 cycles, single-end 100bp) at the Genomics Core Facility at NYU.

treatment_protocol: Trypsinized (Gibco) mESCs were plated in AK medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), 7% KnockOut SR (vol/vol) (Gibco), 2 mM L-glutamine, 0.1 mM ß-mercaptoethanol and penicillin–streptomycin (Gibco)) to induce formation of embryoid bodies (EBs), at 37°C, 5% CO2. 3.5x105 cells were plated in 100 mm suspension plates (Corning) for RNA-seq experiments, while 3.5x106 cells were plated in 245 mm x 245 mm square plates (Corning) for ChIP-seq experiments. After 2 days (0h timepoint), the EBs were split 1:2 and plated in fresh AK medium supplemented with 1 μM all-trans retinoic acid (RA) and 0.5 μM smoothened agonist (SAG) (Millipore 566660).

value: 130kb RARE{delta} SynHoxA assemblon in HoxA -/- mESCs

tag: chip target

tag: chip antibody

value: abcam, #ab4729


title: 134kb SynHoxA assemblon in WT mESCs, 0h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
A5_WT_RnHoxA_t=0_rep1
featurecounts_WTlines_synHoxAWTaligned.txt
H5L3MBGXC_n01_mb244


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 1, H3K27Ac ChIP


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 2, H3K27Ac ChIP


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 1, H3K27Ac ChIP


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 2, H3K27Ac ChIP

value: 48h of RA differentiation


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 1, H3K27Ac ChIP


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 2, H3K27Ac ChIP

description: C1_A-/-_compE_RnHoxA_24hRA/SAG_rep2_H3K27Ac


title: Smad3 binding region in BT549-HA cells

description: anti-Smad3 ChIP-seq, BT549, control cells, TGF-b treated

value: mock transfected


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 1, H3K27Ac ChIP

description: C1_A-/-_compE_RnHoxA_24hRA/SAG_rep1_H3K27Ac


title: 20IQ_Experiment1

description: ~500 amplified mRNA targets


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 2, H3K27Ac ChIP

description: C1_A-/-_compE_RnHoxA_t=0_2D_EBs_H3K27Ac_rep2


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 1, H3K27Ac ChIP


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 1, H3K27me3 ChIP

description: C1_A-/-_compE_RnHoxA_48hRA_rep1_H3K27me3

value: activemotif, #39155


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 2, H3K27me3 ChIP

description: C1_A-/-_compE_RnHoxA_t=0_2D_EBs_H3K27me3_rep2


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 1, H3K27me3 ChIP

description: C1_A-/-_compE_RnHoxA_24hRA/SAG_rep1_H3K27me3


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 2, H3K27me3 ChIP

description: C1_A-/-_compE_RnHoxA_24hRA/SAG_rep2_H3K27me3


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 1, H3K27me3 ChIP

description: C1_A-/-_compE_RnHoxA_t=0_2D_EBs_H3K27me3_rep1


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 2, CTCF ChIP

value: CTCF


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 2, H3K27me3 ChIP

description: C1_A-/-_compE_RnHoxA_48hRA_rep2_H3K27me3


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 1, CTCF ChIP


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 2, CTCF ChIP

description: C1_A-/-_compE_RnHoxA_t=0_2D_EBs_CTCF_rep2


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 1, H3K27Ac ChIP


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 2, H3K27Ac ChIP


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 2, H3K27Ac ChIP


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 1, CTCF ChIP

description: C1_A-/-_compE_RnHoxA_t=0_2D_EBs_CTCF_rep1


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 1, H3K27me3 ChIP


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 1, H3K27Ac ChIP


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 2, H3K27me3 ChIP


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 2, H3K27me3 ChIP

description: B10_A-/-_RnHoxA_t=0_2D_EBs_H3K27me3_rep2


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 2, H3K27me3 ChIP


title: LIVER WT13

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

data_processing:
Indexed sequences were sorted by Illumina BaseSpace FASTQ generation | version: 1.0.0
Reads were mapped to the GRCm38.88 reference genome using STAR | version 2.4 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.2 with parameters -bh -F 3840 -q 255
Read counts over annotated genes gencode.vM15.annotation.gtf were obtained using featureCount (subreads | version: 1.4.6) with parameters -p -T 10
Genome_build: tab-delimited text files include gene counts for each sample

source_name: liver

extract_protocol:
liver tissues (~30mg) was collected from mice and immediately preserved in RNAlater and RNA was extracted using RNEasy Extraction Kit (Qiagen)
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit(NEB#E7490/NEB#E7760)

value: 8-12 weeks old

value: WT


title: LIVER WT12


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 1, H3K27me3 ChIP

description: B10_A-/-_RnHoxA_t=0_2D_EBs_H3K27me3_rep1


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 1, H3K27me3 ChIP


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 1, CTCF ChIP


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 2, CTCF ChIP


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 1, CTCF ChIP


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 2, CTCF ChIP


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 1, H3K27Ac ChIP


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 2, H3K27Ac ChIP


title: LIVER WT07


title: LIVER WT08


title: LIVER HC286


title: LIVER HC288


title: LIVER HC281


title: LIVER HC260


title: ILEUM WT08

data_processing:
Indexed sequences were sorted by Illumina BaseSpace FASTQ generation | version: 1.0.0
Reads were mapped to the GRCm38.88 reference genome using STAR | version 2.4 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.2 with parameters -bh -F 3840 -q 255
Read counts over annotated genes gencode.vM15.annotation.gtf were obtained using featureCount (subreads | version: 1.4.6) with parameters -p -T 10
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample

source_name: ileum

extract_protocol:
Ileal tissues (~30mg) was collected from mice and immediately preserved in RNAlater and RNA was extracted using RNEasy Extraction Kit (Qiagen)
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit(NEB#E7490/NEB#E7760)


title: ILEUM WT13


title: ILEUM WT12


title: ILEUM HC288


title: ILEUM WT11


title: ILEUM WT07


title: ILEUM HC262


title: LIVER HC262


title: ILEUM HC286


title: ILEUM HC260


title: LIVER WT11


title: ILEUM HC281


title: 416B_CTCF_ChIP-seq Rep2

city: Oxford

first: Dominic

last: Owens

address: John Radcliffe Hospital

department: MRC WIMM

country: United Kingdom

institute: University of Oxford

description:
CTCF ChIP-seq
416B_Ctcf_merge_0.02_peaks.bed

data_processing:
Illumina NextSeq/MiSeq base calling
Tiled-C processed as in Oudelaar et al 2020
RNA-seq processed with STAR and featurecounts
Bisulfite seq processed as in Jeziorska et al 2017
ATAC-seq processed with bowtie2, deeptools, and MACS2
Genome_build: mm9
Supplementary_files_format_and_content: Tiled-C_iced_2kb_matrix
Bisulfite-seq_%_methylated_CpG_bedGraph
ATAC-seq_peaks
Poly-A-minus_RNA-seq_featureCounts
ChIP-seq_peaks
ChIP-seq_bigwig
RNA-seq bigwig

growth_protocol: Undiff: Feeder-free LIF conditioned mESC growth medium. Flk1, CD41: Defined serum-free protocol + BMP4 + Activin-A + SCF + VEGF. 416B: Fischer's medium + 20% horse serum.

extract_protocol:
Tiled-C: (Oudelaar et al 2020). Poly-A-minus RNA-seq: Qiazol + miRNeasy Mini kit, RiboMinus Eukaryote System v2, NEBNext Ultra directional library prep kit + poly A selection module (NEB). ATAC-seq: (Buenrostro et al., 2013). CTCF ChIP-seq: Millipore ChIP agarose kit. Bisulfite-seq: (Jeziorska et al 2017)
Tiled-C/RNA-seq/ChIP-seq/Bisulfite-seq: NEBNext Ultra II. ATAC-seq: Tn5 and custom PCR primers (Buenrostro et al., 2013)

value: Hematopoietic progenitor cell line

tag: passages

tag: cell sex

value: F

value: Wild type

tag: differentiation

value: Hematopoietic (cell line)

value: Millipore 07-729


title: 416B_CTCF_ChIP-seq Rep1

tag: cell type

tag: strain

tag: genotype


title: ATAC-seq_Wild-type_Flk1_bioRep2_techRep1

description:
ATAC-seq
ATAC-seq_peaks_Wild-type_Flk1.bed

value: Embryonic stem cells

value: M

value: Mesoderm (day 4)


title: ATAC-seq_Wild-type_Flk1_bioRep2_techRep2


title: ATAC-seq_Wild-type_Flk1_bioRep1_techRep2


title: ATAC-seq_Wild-type_Flk1_bioRep1_techRep1


title: CTCF-ChIP-seq_P2-CTCF-KO_Undiff_E9.1_seqRun2

description:
CTCF ChIP-seq
CTCF-ChIP-seq_P2-CTCF-KO_Undiff_E9.1.bw

value: Undifferentiated (day 0)


title: CTCF-ChIP-seq_P2-CTCF-KO_Undiff_E9.1_seqRun1


title: ATAC-seq_Wild-type_CD41_bioRep1_techRep2

description:
ATAC-seq
ATAC-seq_peaks_Wild-type_CD41.bed

value: Hematopoeitic (day 7)


title: ATAC-seq_Wild-type_CD41_bioRep1_techRep1


title: CTCF-ChIP-seq_P2-CTCF-KO_Undiff_D2.1_seqRun2

description:
CTCF ChIP-seq
CTCF-ChIP-seq_P2-CTCF-KO_Undiff_D2.1.bw


title: CTCF-ChIP-seq_P2-CTCF-KO_Undiff_D2.1_seqRun1


title: CTCF-ChIP-seq_P2-CTCF-KO_Undiff_D10.1_seqRun1

description:
CTCF ChIP-seq
CTCF-ChIP-seq_P2-CTCF-KO_Undiff_D10.1.bw


title: CTCF-ChIP-seq_P1-CTCF-KO_Undiff_E9.1_seqRun1

description:
CTCF ChIP-seq
CTCF-ChIP-seq_P1-CTCF-KO_Undiff_E9.1.bw


title: CTCF-ChIP-seq_P1-CTCF-KO_Undiff_E9.1_seqRun2


title: CTCF-ChIP-seq_P1-CTCF-KO_Undiff_E7.2_seqRun2

description:
CTCF ChIP-seq
CTCF-ChIP-seq_P1-CTCF-KO_Undiff_E7.2.bw


title: CTCF-ChIP-seq_P1-CTCF-KO_Undiff_E7.1_seqRun2

description:
CTCF ChIP-seq
CTCF-ChIP-seq_P1-CTCF-KO_Undiff_E7.1.bw


title: CTCF-ChIP-seq_P1-CTCF-KO_Undiff_E7.1_seqRun1


title: Input-ChIP-seq_P2-CTCF-KO_Undiff_D2.1_seqRun2

description:
Input ChIP-seq
Input-ChIP-seq_P2-CTCF-KO_Undiff_D2.1.bw


title: Input-ChIP-seq_P1-CTCF-KO_Undiff_E9.1_seqRun2

description:
Input ChIP-seq
Input-ChIP-seq_P1-CTCF-KO_Undiff_E9.1.bw


title: Input-ChIP-seq_P1-CTCF-KO_Undiff_E9.1_seqRun1


title: Input-ChIP-seq_P2-CTCF-KO_Undiff_E9.1_seqRun2

description:
Input ChIP-seq
Input-ChIP-seq_P2-CTCF-KO_Undiff_E9.1.bw


title: Input-ChIP-seq_P1-CTCF-KO_Undiff_E7.2_seqRun1

description:
Input ChIP-seq
Input-ChIP-seq_P1-CTCF-KO_Undiff_E7.2.bw


title: Input-ChIP-seq_P2-CTCF-KO_Undiff_D2.1_seqRun1


title: Input-ChIP-seq_P2-CTCF-KO_Undiff_E9.1_seqRun1


title: Input-ChIP-seq_P1-CTCF-KO_Undiff_E7.2_seqRun2


title: Input-ChIP-seq_P1-CTCF-KO_Undiff_E7.1_seqRun1

description:
Input ChIP-seq
Input-ChIP-seq_P1-CTCF-KO_Undiff_E7.1.bw


title: Input-ChIP-seq_P1-CTCF-KO_Undiff_E7.1_seqRun2


title: RNA-seq-A-minus_Wild-type_CD41_bioRep_B9.3

description:
polyA-minus-RNA-seq
s2_features_counts_mm9_Owens.txt


title: RNA-seq-A-minus_Wild-type_CD41_bioRep_C8.1


title: RNA-seq-A-minus_Wild-type_CD41_bioRep_B9.3-2


title: CTCF-ChIP-seq_P2-CTCF-KO_Undiff_D10.1_seqRun2


title: RNA-seq-A-minus_Wild-type_Flk1_bioRep_C6.1


title: RNA-seq-A-minus_Wild-type_Flk1_bioRep_B9.3


title: RNA-seq-A-minus_Wild-type_Undiff_bioRep_E14_techRep1


title: CTCF-ChIP-seq_P1-CTCF-KO_Undiff_E7.2_seqRun1


title: RNA-seq-A-minus_P2-CTCF-KO_CD41_bioRep_E9.1


title: RNA-seq-A-minus_Wild-type_CD41_bioRep_C6.1


title: RNA-seq-A-minus_P2-CTCF-KO_CD41_bioRep_D2.1-2


title: RNA-seq-A-minus_P2-CTCF-KO_CD41_bioRep_D10.1


title: RNA-seq-A-minus_Wild-type_Flk1_bioRep_C8.1


title: RNA-seq-A-minus_P2-CTCF-KO_CD41_bioRep_D2.1


title: Input-ChIP-seq_P2-CTCF-KO_Undiff_D10.1_seqRun1

description:
Input ChIP-seq
Input-ChIP-seq_P2-CTCF-KO_Undiff_D10.1.bw


title: RNA-seq-A-minus_P2-CTCF-KO_Flk1_bioRep_E9.1


title: Input-ChIP-seq_P2-CTCF-KO_Undiff_D10.1_seqRun2


title: RNA-seq-A-minus_P2-CTCF-KO_CD41_bioRep_D10.1-2


title: RNA-seq-A-minus_P2-CTCF-KO_Flk1_bioRep_D10.1


title: RNA-seq-A-minus_Wild-type_Undiff_bioRep_E14_techRep2


title: RNA-seq-A-minus_Wild-type_416B_bioRep2_Lane2

description:
polyA-minus-RNA-seq
416B_RNA_Aminus_bs30_RPKM.bw


title: RNA-seq-A-minus_P1-CTCF-KO_Flk1_bioRep_E7.1


title: RNA-seq-A-minus_Wild-type_416B_bioRep2_Lane1


title: RNA-seq-A-minus_P1-CTCF-KO_Flk1_bioRep_E9.1


title: RNA-seq-A-minus_Wild-type_416B_bioRep2_Lane3


title: RNA-seq-A-minus_P1-CTCF-KO_CD41_bioRep_E7.1


title: RNA-seq-A-minus_P1-CTCF-KO_CD41_bioRep_E7.2


title: RNA-seq-A-minus_Wild-type_416B_bioRep1_Lane3


title: RNA-seq-A-minus_Wild-type_416B_bioRep1_Lane2


title: RNA-seq-A-minus_Wild-type_416B_bioRep1_Lane1


title: RNA-seq-A-minus_Wild-type_416B_bioRep2_Lane4


title: RNA-seq-A-minus_Wild-type_416B_bioRep1_Lane4


title: Tiled-C_Wild-type_CD41_bioRep_C6.1-2_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_CD41_C6.1-2_iced.matrix

data_processing:
Library strategy: Tiled-C
Illumina NextSeq/MiSeq base calling
Tiled-C processed as in Oudelaar et al 2020
RNA-seq processed with STAR and featurecounts
Bisulfite seq processed as in Jeziorska et al 2017
ATAC-seq processed with bowtie2, deeptools, and MACS2
Genome_build: mm9
Supplementary_files_format_and_content: Tiled-C_iced_2kb_matrix
Bisulfite-seq_%_methylated_CpG_bedGraph
ATAC-seq_peaks
Poly-A-minus_RNA-seq_featureCounts
ChIP-seq_peaks
ChIP-seq_bigwig
RNA-seq bigwig


title: Tiled-C_Wild-type_CD41_bioRep_B9.3_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_CD41_B9.3_iced.matrix


title: Tiled-C_Wild-type_CD41_bioRep_C8.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_CD41_C8.1_iced.matrix


title: Tiled-C_Wild-type_Flk1_bioRep_C6.1-2_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_Flk1_C6.1-2_iced.matrix


title: Tiled-C_Wild-type_Flk1_bioRep_C6.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_Flk1_C6.1_iced.matrix


title: Tiled-C_Wild-type_CD41_bioRep_C6.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_CD41_C6.1_iced.matrix


title: Tiled-C_Wild-type_Flk1_bioRep_B9.3_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_Flk1_B9.3_iced.matrix


title: Tiled-C_Wild-type_Undiff_bioRep_B9.3_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_Undiff_B9.3_iced.matrix


title: Tiled-C_Wild-type_Flk1_bioRep_C8.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_Flk1_C8.1_iced.matrix


title: Tiled-C_P2-CTCF-KO_CD41_bioRep_D2.1-2_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_CD41_D2.1-2_iced.matrix


title: Tiled-C_Wild-type_Undiff_bioRep_C8.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_Undiff_C8.1_iced.matrix


title: Tiled-C_Wild-type_Undiff_bioRep_C6.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_Undiff_C6.1_iced.matrix


title: RNA-seq-A-minus_P1-CTCF-KO_CD41_bioRep_E9.1


title: Tiled-C_P2-CTCF-KO_CD41_bioRep_D2.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_CD41_D2.1_iced.matrix


title: RNA-seq-A-minus_P1-CTCF-KO_Flk1_bioRep_E7.2


title: RNA-seq-A-minus_P2-CTCF-KO_Flk1_bioRep_D2.1


title: Tiled-C_P2-CTCF-KO_CD41_bioRep_D10.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_CD41_D10.1_iced.matrix


title: Tiled-C_P2-CTCF-KO_CD41_bioRep_E9.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_CD41_E9.1_iced.matrix


title: Tiled-C_P2-CTCF-KO_Flk1_bioRep_D2.1-2_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_Flk1_D2.1-2_iced.matrix


title: Tiled-C_P2-CTCF-KO_Flk1_bioRep_E9.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_Flk1_E9.1_iced.matrix


title: Egg9

city: Uppsala

first: Eva

last: Sundberg

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

data_processing:
reads quality was checked with FastQC
Reads were filtered through fastp and bbduk to remove low quality sequences, adapters, runs of polyA, polyT, and sequences matching rRNA
Filtered reads were pseudoaligned to P. patens cDNA sequences version 3.3 (https://peatmoss.online.uni‑marburg.de/downloads/Annotations/P.patens_v3.3/P.patens_v3.3_cDNA.fasta) and quantified per gene using kallisto
Genome_build: V3.3
Supplementary_files_format_and_content: Matrix table with raw gene counts for all genes from samples generated in the present study plus those of additional vegetative samples generated by Perroud et al. 2018. The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data. Plant J. 95: 168-182.  Raw data for these re-analyzed samples are available at: https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=PhypatAtlaPlate2

organism: Physcomitrium patens

source_name: Egg cells stage 9

growth_protocol: Subcultivation was done by growing protonemal tissue on solid MM plates (Landberg et al., 2020) at 25°C in continuous white light in a Percival Scientific CU-41L4 growth chamber (Perry, IA, USA) with F25T8/TL741 fluorescent tubes (Philips, Somerset, NJ, USA), at 35 μmol m2 s1. The plates were then moved to gametangia-inducing conditions, 15°C and 8 h of light (30 μmol m-2 s-1) per day in a Sanyo MLR-350 light chamber. For egg cell transcriptomics, gametophores with gametangia were harvested after 19 and 25 days under these conditions and in order to expose the reproductive organs, leaves were detached under a dissecting microscope (Leica MZ16).

extract_protocol:
RNA was extracted using the Picopure RNA extraction kit from Arcturus (Thermo Fisher Scientific, Waltham, USA) and amplified with SMARTer Ultra Low Input RNA kit for Sequencing v3 (Clontech Laboratories, Mountain View, USA) using polyT primers, and following the manufacturer’s protocol applying 16 amplification cycles
Libraries were created with the ThruPLEX® DNA-seq Kit (Rubicon Genomics, Ann Arbor, USA)

treatment_protocol: Single cells were dissected using a SL μCut instrument (MMI, Glattbrugg, Switzerland).

value: Gransden

tag: tissue

value: egg

tag: biological replicate

tag: tissue extraction

value: single cell laser-assisted microdissection (LAM)


title: Tiled-C_P2-CTCF-KO_Flk1_bioRep_D10.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_Flk1_D10.1_iced.matrix

tag: cell line


title: Egg8

source_name: Egg cells stage 8


title: Tiled-C_P2-CTCF-KO_Flk1_bioRep_D2.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_Flk1_D2.1_iced.matrix


title: Tiled-C_P2-CTCF-KO_Undiff_bioRep_D2.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_Undiff_D2.1_iced.matrix


title: Tiled-C_P2-CTCF-KO_Undiff_bioRep_E9.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_Undiff_E9.1_iced.matrix


title: Shoot apex

source_name: Gametophore shoot apex

value: Gametophore shoot apex

value: laser-assisted microdissection (LAM)


title: Cavity wall

source_name: Archegonium cavity wall

value: Archegonium cavity wall


title: Tiled-C_P1-CTCF-KO_CD41_bioRep_E7.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_CD41_E7.1_iced.matrix


title: Tiled-C_P1-CTCF-KO_CD41_bioRep_E7.1-2_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_CD41_E7.1-2_iced.matrix


title: Tiled-C_P2-CTCF-KO_Undiff_bioRep_D10.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_Undiff_D10.1_iced.matrix


title: Tiled-C_P1-CTCF-KO_Flk1_bioRep_E7.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_Flk1_E7.1_iced.matrix


title: Tiled-C_P1-CTCF-KO_CD41_bioRep_E7.2_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_CD41_E7.2_iced.matrix


title: Unwounded Skin

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

description: UnwoundedSkin

data_processing:
We created a custom pig transcriptome generated using the Sus scrofa genome (Ensemble, v11.1) in accordance with 10X protocols for non-model organisms, and we have made it publicly available with instructions to implement as part of a modified 10X Cell Ranger pipeline. Briefly, the swine reference genome (Sus scrofa 11.1, release 98) was obtained from the Ensembl web server (https://uswest.ensembl.org/Sus_scrofa/Info/Index). Fasta files for individual chromosomes were merged using batch concatenation in cshell. GTF annotations were filtered using the Cell Ranger (10X Genomics) “mkgtf” function.
These GTF and FASTQ files were then assembled using the Cell Ranger “mkref” command with default parameterization. All read fragments were aligned to this transcriptome using standard base-matching thresholds, followed by cell-level demultiplexing and UMI batch correction, allowing us to generate single-cell mRNA count matrices for each pig sample.
The custom pig transcriptome has been made publicly available at https://tinyurl.com/Gurtner-PigCustomTranscriptome.
Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 200 unique transcripts profiled, less than 10,000 total transcripts, and less than 10% of their transcriptome of mitochondrial origin.
Unique molecular identifiers (UMIs) from each cell barcode were retained for all downstream analysis.
Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1).
Highly variable genes were identified, and cells were scaled by regression to the fraction of mitochondrial transcripts. Aggregated data was then evaluated using uniform manifold approximation and projection (UMAP) analysis.
Genome_build: Custom pig transcriptome publicly available at https://tinyurl.com/Gurtner-PigCustomTranscriptome.
Supplementary_files_format_and_content: Barcodes.tsv, features.tsv, matrix.mtx files.

organism: Sus scrofa

source_name: Unwounded Skin Cells

growth_protocol: Pigs were given full thickness wounds and treated with split thickness skin grafts (STSGs). STSG were either untreated or treated with FAKI (focal adhesion kinase inhibitor) hydrogel. After either 7 or 90 days, STSG samples were explanted, and porcine unwounded skin was also collected.

extract_protocol:
Tissue was enzymatically digested, cells were collected and washed. These cellular suspensions were then submitted for droplet-based microfluidic single-cell RNA sequencing (scRNA-seq) at the Stanford Functional Genomics Facility (SFGF) using the 10x Chromium Single Cell platform (Single Cell 3’ v3, 10x Genomics, USA).
cDNA was fragmented followed by end repair and A-tailing at 65°C for 30min. cDNA were double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20°C for 15min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA libraries were sequenced on a HiSeq 4000 Illumina platform aiming for 50,000 reads per cell.

treatment_protocol: Either untreated or treated with FAKI hydrogels (dressings changed every other day).

value: Skin

value: Freshly isolated and submitted

tag: condition

value: Unwounded


title: STSG Day 90

source_name: Pig Cells from STSG, Day 90

value: STSG

tag: time point

value: Day 90


title: Tiled-C_P1-CTCF-KO_Flk1_bioRep_E7.1-2_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_Flk1_E7.1-2_iced.matrix


title: Tiled-C_P1-CTCF-KO_Flk1_bioRep_E9.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_Flk1_E9.1_iced.matrix


title: STSG+FAKI Day 7

source_name: Pig Cells from STSG treated with FAKI Hydrogel, Day 7

value: FAK inhibitor

value: Day 7


title: Tiled-C_P1-CTCF-KO_Flk1_bioRep_E7.2_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_Flk1_E7.2_iced.matrix

value: Embryonic stem cells

value: M


title: STSG Day 7

source_name: Pig Cells from STSG, Day 7


title: Tiled-C_P1-CTCF-KO_Undiff_bioRep_E9.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_Undiff_E9.1_iced.matrix

value: Undifferentiated (day 0)


title: Tiled-C_P1-CTCF-KO_Undiff_bioRep_E7.2_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_Undiff_E7.2_iced.matrix


title: Tiled-C_Wild-type_CD41_bioRep_C6.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_CD41_C6.1_iced.matrix

value: Wild type

value: Hematopoeitic (day 7)


title: 170kb Enhancers + SynHoxA assemblon in WT mESCs, 96h of 3µM Chir differentiation, replicate 2, RNA-Seq

description:
Chir_312_D6r2
featurecounts_ChirDifferentiation_synHoxAWTaligned.txt
H55WYDRXY_n01_dpr314

value: 96h of 3µM Chir differentiation

value: Embryoid Bodies


title: Tiled-C_Wild-type_CD41_bioRep_C6.1-2_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_CD41_C6.1-2_iced.matrix


title: Tiled-C_P1-CTCF-KO_CD41_bioRep_E9.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_CD41_E9.1_iced.matrix


title: Hippocampus_72 hours_Tibial fracture rep1

type: RNA

city: Yuzhong district

first: wei

last: ran

state: chongqing

address: No.1 Youyi Road

department: anesthesiology

institute: The First Affiliated Hospital of Chongqing Medical University

description: Gene expression after 72hr in mouse hippocampus

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 1 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

source_name: Hippocampus_72 hours_rep1

label_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Mice were feed with standard rodent chow in laboratory with  temperature 25℃, humidity 55% and 12-hour light/dark cycles.

extract_protocol: According to the manufacturer's instructions, Total RNA was extracted from both groups using Trizol reagent (Invitrogen, Carlsbad, CA, USA).The concentrations of the RNA samples were determined by OD260 using a NanoDrop ND-1000 instrument. The integrity of RNA were assessed by electrophoresis on a denaturing agarose gel.

treatment_protocol: Animal modle of POD was established by Intramedullary nail fixation of tibial fracture on left hind leg was performed under isoflurane anesthesia and butorphenol subcutaneous Analgesia,while the mice in control group only accept the same anesthesia and analgesia, all surgeries were completed within 15 minutes.

value: Hippocampus tissue

tag: Sex

value: Male

tag: group

value: tibial fracture

tag: age


title: Hippocampus_72 hours_Control rep1

value: control


title: Hippocampus_72 hours_Tibial fracture rep2

source_name: Hippocampus_72 hours_rep2


title: 170kb Enhancers + SynHoxA assemblon in WT mESCs, 0h of 3µM Chir differentiation, replicate 2, RNA-Seq

description:
Chir_312_D2r2
featurecounts_ChirDifferentiation_synHoxAWTaligned.txt
H55WYDRXY_n01_dpr311

tag: treatment

value: 0h of 3µM Chir differentiation


title: 134kb SynHoxA assemblon in WT mESCs, 96h of 3µM Chir differentiation, replicate 2, RNA-Seq

description:
Chir_305_D6r2
featurecounts_ChirDifferentiation_synHoxAWTaligned.txt
H55WYDRXY_n01_dpr313

value: 134kb SynHoxA assemblon in WT mESCs


title: 134kb SynHoxA assemblon in WT mESCs, 0h of 3µM Chir differentiation, replicate 2, RNA-Seq

description:
Chir_305_D2r2
featurecounts_ChirDifferentiation_synHoxAWTaligned.txt
H55WYDRXY_n01_dpr310


title: Tiled-C_Wild-type_CD41_bioRep_C8.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_CD41_C8.1_iced.matrix


title: STSG+FAKI Day 90

source_name: Pig Cells from STSG treated with FAKI Hydrogel, Day 90

value: Skin

value: Freshly isolated and submitted

value: STSG


title: 134kb SynHoxA assemblon in WT mESCs, 96h of 3µM Chir differentiation, replicate 1, RNA-Seq

description:
Chir_305_D6r1
featurecounts_ChirDifferentiation_synHoxAWTaligned.txt
H55WYDRXY_n01_dpr307


title: Hippocampus_72 hours_Control rep2


title: Hippocampus_72 hours_Control rep3

source_name: Hippocampus_72 hours_rep3


title: Hippocampus_72 hours_Tibial fracture rep3


title: 170kb Enhancers + SynHoxA assemblon in WT mESCs, 96h of 3µM Chir differentiation, replicate 1, RNA-Seq

description:
Chir_312_D6r1
featurecounts_ChirDifferentiation_synHoxAWTaligned.txt
H55WYDRXY_n01_dpr308


title: Tiled-C_Wild-type_Flk1_bioRep_C6.1-2_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_Flk1_C6.1-2_iced.matrix

value: Mesoderm (day 4)


title: 170kb Enhancers + SynHoxA assemblon in WT mESCs, 0h of 3µM Chir differentiation, replicate 1, RNA-Seq

description:
Chir_312_D2r1
featurecounts_ChirDifferentiation_synHoxAWTaligned.txt
H55WYDRXY_n01_dpr305


title: Tiled-C_Wild-type_Flk1_bioRep_C6.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_Flk1_C6.1_iced.matrix

value: Embryonic stem cells


title: Tiled-C_Wild-type_Flk1_bioRep_B9.3_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_Flk1_B9.3_iced.matrix

value: M


title: 134kb SynHoxA assemblon in WT mESCs, 0h of 3µM Chir differentiation, replicate 1, RNA-Seq

description:
Chir_305_D2r1
featurecounts_ChirDifferentiation_synHoxAWTaligned.txt
H55WYDRXY_n01_dpr304


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
C1_A-/-_compE_RnHoxA_96hRA/SAG_rep2
featurecounts_delHoxAlines_synHoxAdelHoxAaligned.txt
featurecounts_delHoxAlines_synHoxAWTaligned.txt
HVHT2DRXX_l02_n01_mb394

value: 96h of RA+SAG differentiation


title: Tiled-C_Wild-type_Flk1_bioRep_C8.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_Flk1_C8.1_iced.matrix

value: Wild type


title: Tiled-C_P1-CTCF-KO_Undiff_bioRep_E7.1_seqRun2

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_Undiff_E7.1_iced.matrix

value: Undifferentiated (day 0)


title: Tiled-C_Wild-type_Undiff_bioRep_B9.3_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_Undiff_B9.3_iced.matrix


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
C1_A-/-_compE_RnHoxA_96hRA/SAG_rep1
featurecounts_delHoxAlines_synHoxAdelHoxAaligned.txt
featurecounts_delHoxAlines_synHoxAWTaligned.txt
HVHT2DRXX_l02_n01_mb393


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
C1_A-/-_compE_RnHoxA_48hRA/SAG_rep2
featurecounts_delHoxAlines_synHoxAdelHoxAaligned.txt
featurecounts_delHoxAlines_synHoxAWTaligned.txt
HVHT2DRXX_l01_n01_mb390

value: 48h of RA+SAG differentiation


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
C1_A-/-_compE_RnHoxA_48hRA/SAG_rep1
featurecounts_delHoxAlines_synHoxAdelHoxAaligned.txt
featurecounts_delHoxAlines_synHoxAWTaligned.txt
HVHT2DRXX_l01_n01_mb389

value: Embryoid Bodies


title: Tiled-C_Wild-type_Undiff_bioRep_C6.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_Undiff_C6.1_iced.matrix


title: Tiled-C_Wild-type_CD41_bioRep_B9.3_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_CD41_B9.3_iced.matrix

value: Hematopoeitic (day 7)


title: Tiled-C_Wild-type_Undiff_bioRep_C8.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_Wild-type_Undiff_C8.1_iced.matrix


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
C1_A-/-_compE_RnHoxA_24hRA/SAG_rep2
featurecounts_delHoxAlines_synHoxAdelHoxAaligned.txt
featurecounts_delHoxAlines_synHoxAWTaligned.txt
HVHT2DRXX_l01_n01_mb386

value: 24h of RA+SAG differentiation


title: Tiled-C_P2-CTCF-KO_CD41_bioRep_D2.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_CD41_D2.1_iced.matrix


title: Tiled-C_P2-CTCF-KO_CD41_bioRep_E9.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_CD41_E9.1_iced.matrix


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
C1_A-/-_compE_RnHoxA_t=0_rep1
featurecounts_delHoxAlines_synHoxAdelHoxAaligned.txt
featurecounts_delHoxAlines_synHoxAWTaligned.txt
HVHT2DRXX_l01_n01_mb381

value: 0h of RA+SAG differentiation


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
B10_A-/-_RnHoxA_96hRA/SAG_rep2
featurecounts_delHoxAlines_synHoxAdelHoxAaligned.txt
featurecounts_delHoxAlines_synHoxAWTaligned.txt
HVHT2DRXX_l02_n01_mb392


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
C1_A-/-_compE_RnHoxA_t=0_rep2
featurecounts_delHoxAlines_synHoxAdelHoxAaligned.txt
featurecounts_delHoxAlines_synHoxAWTaligned.txt
HVHT2DRXX_l01_n01_mb382


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
C1_A-/-_compE_RnHoxA_24hRA/SAG_rep1
featurecounts_delHoxAlines_synHoxAdelHoxAaligned.txt
featurecounts_delHoxAlines_synHoxAWTaligned.txt
HVHT2DRXX_l01_n01_mb385


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
B10_A-/-_RnHoxA_48hRA/SAG_rep1
featurecounts_delHoxAlines_synHoxAdelHoxAaligned.txt
featurecounts_delHoxAlines_synHoxAWTaligned.txt
HVHT2DRXX_l01_n01_mb387


title: Tiled-C_P2-CTCF-KO_Flk1_bioRep_D2.1-2_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_Flk1_D2.1-2_iced.matrix


title: Tiled-C_P2-CTCF-KO_CD41_bioRep_D10.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_CD41_D10.1_iced.matrix


title: Tiled-C_P2-CTCF-KO_Flk1_bioRep_D2.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_Flk1_D2.1_iced.matrix


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
B10_A-/-_RnHoxA_48hRA/SAG_rep2
featurecounts_delHoxAlines_synHoxAdelHoxAaligned.txt
featurecounts_delHoxAlines_synHoxAWTaligned.txt
HVHT2DRXX_l01_n01_mb388


title: Tiled-C_P2-CTCF-KO_Flk1_bioRep_E9.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_Flk1_E9.1_iced.matrix


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
B10_A-/-_RnHoxA_24hRA/SAG_rep2
featurecounts_delHoxAlines_synHoxAdelHoxAaligned.txt
featurecounts_delHoxAlines_synHoxAWTaligned.txt
HVHT2DRXX_l01_n01_mb384


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
B10_A-/-_RnHoxA_96hRA/SAG_rep1
featurecounts_delHoxAlines_synHoxAdelHoxAaligned.txt
featurecounts_delHoxAlines_synHoxAWTaligned.txt
HVHT2DRXX_l02_n01_mb391


title: Tiled-C_P2-CTCF-KO_Flk1_bioRep_D10.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_Flk1_D10.1_iced.matrix


title: Tiled-C_P2-CTCF-KO_Undiff_bioRep_D10.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_Undiff_D10.1_iced.matrix


title: Tiled-C_P2-CTCF-KO_Undiff_bioRep_E9.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_Undiff_E9.1_iced.matrix


title: Tiled-C_P2-CTCF-KO_Undiff_bioRep_D2.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_Undiff_D2.1_iced.matrix


title: Tiled-C_P1-CTCF-KO_CD41_bioRep_E7.1-2_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_CD41_E7.1-2_iced.matrix


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
B10_A-/-_RnHoxA_24hRA/SAG_rep1
featurecounts_delHoxAlines_synHoxAdelHoxAaligned.txt
featurecounts_delHoxAlines_synHoxAWTaligned.txt
HVHT2DRXX_l01_n01_mb383


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
B10_A-/-_RnHoxA_t=0_rep2
featurecounts_delHoxAlines_synHoxAdelHoxAaligned.txt
featurecounts_delHoxAlines_synHoxAWTaligned.txt
HVHT2DRXX_l01_n01_mb380


title: Tiled-C_P1-CTCF-KO_CD41_bioRep_E7.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_CD41_E7.1_iced.matrix


title: RNA-seq in dsir2_rep2

city: Chuncheon-si, Gangwon-do

first: soojin

last: yeom

address: 1 Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

description: RNA-seq sample of dsir2

data_processing:
The Illumina Hiseq generates raw images utilizing HCS(HiSeq Control Software v2.2) for system control
Base calling through an integrated primary analysis software called RTA(Real Time Analysis. v1.18)
The BCL(base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq(v1.8.4)
Adapters are not trimmed away from the reads.
Genome_build: sacCer3

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: S. cerevisiae strains were grown in YPD media (1% yeast extracts, 2% peptone, 2% glucose) at 30˚C. Overnigh cultured cells were diluted to OD600 of 0.1 into fresh 10ml YPD and grown at 30˚C until OD600 of 1.0.

extract_protocol:
Total RNA was extracted using NucleoSpin® RNA (MN, MN740955) according to the protocol of the manufacturer. For sequencing, mRNA was captured using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).
A strand-specific sequencing library was synthesized using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (NEB, E7420) according to the instruction manual.


title: RNA-seq in FM391 (WT)_rep2

description: RNA-seq sample of FM391


title: RNA-seq in dsir2_rep1

description: RNA-seq sample of dsir2


title: Tiled-C_P2-CTCF-KO_CD41_bioRep_D2.1-2_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P2-CTCF-KO_CD41_D2.1-2_iced.matrix


title: Tiled-C_P1-CTCF-KO_CD41_bioRep_E9.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_CD41_E9.1_iced.matrix


title: 166kb Enhancers + RARE∆ assemblon in WT mESCs, 96h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
394_D6r3
featurecounts_WTlines_synHoxAWTaligned.txt
H55WYDRXY_n01_dpr302

value: 166kb Enhancers + RARE{delta} assemblon in WT mESCs


title: control genomic data in HaCaT cells

description: control genomic DNA data

source_name: A human epidermal keratinocyte cell line

tag: ChIP

value: control genome

tag: stimulation

value: TGF-beta, 1 ng/ml, 1.5h

value: HaCaT


title: 166kb Enhancers + RARE∆ assemblon in WT mESCs, 96h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
394_D6r1
featurecounts_WTlines_synHoxAWTaligned.txt
H55WYDRXY_n01_dpr294

source_name: ES-derived embryoid bodies with variant synthetic Hox clusters


title: Tiled-C_P1-CTCF-KO_Flk1_bioRep_E7.1-2_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_Flk1_E7.1-2_iced.matrix

tag: passages

tag: cell sex


title: Tiled-C_P1-CTCF-KO_Flk1_bioRep_E9.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_Flk1_E9.1_iced.matrix

tag: cell type

tag: differentiation


title: Tiled-C_P1-CTCF-KO_Flk1_bioRep_E7.2_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_Flk1_E7.2_iced.matrix

tag: strain

tag: genotype


title: 166kb Enhancers + RARE∆ assemblon in WT mESCs, 48h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
394_D4r3
featurecounts_WTlines_synHoxAWTaligned.txt
H55WYDRXY_n01_dpr301


title: Tiled-C_P1-CTCF-KO_Undiff_bioRep_E7.2_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_Undiff_E7.2_iced.matrix


title: Tiled-C_P1-CTCF-KO_Undiff_bioRep_E9.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_Undiff_E9.1_iced.matrix


title: Tiled-C_P1-CTCF-KO_Undiff_bioRep_E7.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_Undiff_E7.1_iced.matrix


title: 166kb Enhancers + RARE∆ assemblon in WT mESCs, 48h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
394_D4r1
featurecounts_WTlines_synHoxAWTaligned.txt
H55WYDRXY_n01_dpr293


title: GK3R85-GDS2: DSS_Colon_GFP_2

city: Vari

first: Vasiliki

last: Koliaraki

state: Attiki

address: 34 Fleming street

country: Greece

institute: BSRC "Alexander Fleming"

description:
GK3R85-GDS2
processed data file: metaseqr_all_out_TDS_vs_GDS.txt
processed data file: metaseqr_all_out_UDS_vs_GDS.txt
processed data file: metaseqr_all_out_G_vs_GDS.txt

data_processing:
The RNA-Seq FASTQ files obtained after Ion Proton sequencing were mapped using TopHat2 [Kim2013], with default settings and using additional transcript annotation data for the mm10 genome from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). According to the Ion Proton manufacturers recommendation, the reads which remained unmapped were submitted to a second round of mapping using Bowtie2 [Langmead2012] against the mm10 genome with the --very-sensitive switch turned on and merged with the initial mappings.
The raw bam files were summarized to read counts table using the Bioconductor package GenomicRanges
The gene counts table was normalized for inherent systematic or experimental biases using the Bioconductor package DESeq after removing genes that had zero counts over all the RNA-Seq samples.
The resulting gene counts table was subjected to differential expression analysis using the Bioconductor package DESeq
All the above were performed through the Bioconductor package metaseqr
Differential expression analysis files were subjected to additional filtering by removing the genes that had less than three natural normalized counts in more than four samples.
Genome_build: mm10
Supplementary_files_format_and_content: txt (tab separated) files containing all the results from metaseqr analysis including expression per replicate, fold change compared to control and p-values.

source_name: Intestinal Mesenchymal Cells

extract_protocol:
Intestinal mesenchymal cells were isolated as previously described (Koliaraki et al., 2015) and total RNA was extracted using RNAeasy Mini kit (QIAGEN), according to the manufacturer's instructions.
The quantity and quality of RNA samples from sorted cells were analyzed using the bioanalyzer form Agilent in combination with the Agilent RNA 6000 Nano. RNA samples with RNA Integrity Number (RIN) > 7 were further used for library preparation using the 3’ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™) according to manufacturer’s instructions. The quantity and quality of libraries were assessed using the DNA High Sensitivity Kit in the bioanalyzer, according to the manufacturer’s instructions (Agilent Technologies). Libraries were subsequently pooled and templated using the Ion PI IC200 Chef Kit (ThermoFisher Scientific) on an Ion Proton Chef instrument or Ion OneTouch System. Sequencing was performed using the Ion PI™ Sequencing 200 V3 Kit and Ion Proton PI™ V2 chips (ThermoFisher Scientific) on an Ion Proton™ System, according to the manufacturer's instructions.

treatment_protocol: DSS-induced colitis was performed as previously described (Wirtz et al., 2017)

value: ColVI-cre, Rosa mTmG

tag: tissue

value: Colon

value: Intestinal Mesenchymal Cells

tag: cell isolation

value: Fresh isolation

tag: disease model

value: DSS-induced colitis


title: Tiled-C_P1-CTCF-KO_Flk1_bioRep_E7.1_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_Flk1_E7.1_iced.matrix

value: Embryonic stem cells

value: M

tag: cell line

value: Mesoderm (day 4)


title: 166kb Enhancers + RARE∆ assemblon in WT mESCs, 24h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
394_D3r3
featurecounts_WTlines_synHoxAWTaligned.txt
H55WYDRXY_n01_dpr300


title: I109 mock 24h

city: Houston

first: Noah

last: Shroyer

state: Texas

address: One Baylor Plaza, Room N710

department: Medicine Section of Gastroenterology and Hepatology

institute: Baylor College of Medicine

description:
Differentiated Ileum treated w/ Mock
Line - I109

data_processing:
Pseudosalignment was performed using Kallisto (https://pachterlab.github.io/kallisto/) and raw gene counts were output as tsv files
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited files with raw gene counts for every gene and every sample

source_name: Intestine

growth_protocol: Enteroids/colonoids were maintained CMGF+ and differentiated according to manuscript

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Enteroids on transwells were  treated with various infections or mocks for 6 or 24 hours

tag: segment

value: Ileum

tag: format

value: Transwell

tag: substrate

value: Collagen IV

tag: treatment time

value: 25 Hours


title: GK3R84-GDS1: DSS_Colon_GFP_1

description:
GK3R84-GDS1
processed data file: metaseqr_all_out_TDS_vs_GDS.txt
processed data file: metaseqr_all_out_UDS_vs_GDS.txt
processed data file: metaseqr_all_out_G_vs_GDS.txt


title: GK3R86-GDS3: DSS_Colon_GFP_3

description:
GK3R86-GDS3
processed data file: metaseqr_all_out_TDS_vs_GDS.txt
processed data file: metaseqr_all_out_UDS_vs_GDS.txt
processed data file: metaseqr_all_out_G_vs_GDS.txt


title: I103 mock 24h

description:
Differentiated Ileum treated w/ Mock
Line - I103

value: 24 Hours


title: GK3R83-TDS3: DSS_Colon_Tomato_3

description:
GK3R83-TDS3
processed data file: metaseqr_all_out_TDS_vs_GDS.txt
processed data file: metaseqr_all_out_UDS_vs_TDS.txt
processed data file: metaseqr_all_out_T_vs_TDS.txt


title: KR08_B

city: Aachen

first: Ivan

middle: Gesteira

last: Costa

state: Northrhine-Westphalia

address: Pauwelsstr. 19

department: Joint Research Center for Computational Biomedicine

country: Germany

institute: UKA RWTH Aachen

data_processing:
The Cell Ranger Software Suite (version 3.1.0) was used for processing sequencing information and single cell barcodes.
Seurat (version 3.2.2) was used to integrate the scRNA-seq data and predict cell labels.
Genome_build: GRCh38
Supplementary_files_format_and_content: barcodes: barcodes present in input data
Supplementary_files_format_and_content: matrix: a count matrix with Market Exchange Format (MEX). The first line contains the type code and the second line includes format and cell-ranger versions. Number of peaks, barcodes, and non-zero entries can be found in the third line. The rest of the lines represent nonzero entries with the first two numbers corresponding to peak and barcode indices and the last one corresponding to the number of cut sites.
Supplementary_files_format_and_content: genes: a bed file contains genes corresponding to row indices. For each gene, its gene ID and name are stored in the first and second column of the gene.tsv file, respectively.

source_name: V3.1 COVID-19 patient autopsy kidney tissue

extract_protocol: All protocols to generate scRNA-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here: https://support.10xgenomics.com/single-cell-gene-expression

treatment_protocol: Snap-frozen COVID-19 patient autopsy kidney tissue was obtained from the pathology department at Radboud UMC Nijmegen, the Netherlands. A small piece of kidney tissue (ca. 2x2x2 mm) was thawed in PBS and crushed using a glass douncer and tube (Duran Wheaton Kimble Life Sciences, Wertheim/Main, Germany). After passing the single cell suspension through a 70 µm cell strainer (Greiner), the suspension was centrifuged at 4ºC and 300xg for 5 min. Subsequently, the supernatant was discarded and the cell pellet was resuspended in Nuc101 cell lysis buffer supplemented with RNase and protease inhibitors (Recombinant RNase Inhibitor and Superase RNase Inhibitor, Thermo Fisher, and cOmplete Protease Inhibitor, Roche) incubated for one minute and centrifuged at 4ºC and 500xg for 5 min. After discarding the supernatant, the nuclei were carefully resuspended in PBS containing 1% (v/v) UltraPure BSA (Invitrogen Ambion, Thermo Fisher) and Protector RNase inhibitor (Sigma Aldrich), counted, and used in the usual single cell RNA sequencing workflow (10x Genomics, v3.1).

value: Kidney

tag: condition


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
B10_A-/-_RnHoxA_t=0_rep1
featurecounts_delHoxAlines_synHoxAdelHoxAaligned.txt
featurecounts_delHoxAlines_synHoxAWTaligned.txt
HVHT2DRXX_l01_n01_mb379

tag: treatment

value: 0h of RA+SAG differentiation

value: Embryoid Bodies


title: RNA-seq in FM391 (WT)_rep1

description: RNA-seq sample of FM391


title: GK3R82-TDS2: DSS_Colon_Tomato_2

description:
GK3R82-TDS2
processed data file: metaseqr_all_out_TDS_vs_GDS.txt
processed data file: metaseqr_all_out_UDS_vs_TDS.txt
processed data file: metaseqr_all_out_T_vs_TDS.txt


title: 166kb Enhancers + RARE∆ assemblon in WT mESCs, 0h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
394_D2r3
featurecounts_WTlines_synHoxAWTaligned.txt
H55WYDRXY_n01_dpr299

value: 166kb Enhancers + RARE{delta} assemblon in WT mESCs


title: Tiled-C_P1-CTCF-KO_CD41_bioRep_E7.2_seqRun1

description:
Tiled-C
Tiled-C_Iced_Matrix_P1-CTCF-KO_CD41_E7.2_iced.matrix

value: Hematopoeitic (day 7)


title: KR08_A

source_name: Targeted Sequencing (TAP-Seq) SARS-CoV2


title: GK3R81-TDS1: DSS_Colon_Tomato_1

description:
GK3R81-TDS1
processed data file: metaseqr_all_out_TDS_vs_GDS.txt
processed data file: metaseqr_all_out_UDS_vs_TDS.txt
processed data file: metaseqr_all_out_T_vs_TDS.txt

value: ColVI-cre, Rosa mTmG

value: Colon


title: GK3R79-UDS2: DSS_Colon_Unsorted_2

description:
GK3R79-UDS2
processed data file: metaseqr_all_out_UDS_vs_GDS.txt
processed data file: metaseqr_all_out_UDS_vs_TDS.txt

source_name: Intestinal Cells

value: Intestinal Cells

value: Fresh isolation


title: 130kb RARE∆ SynHoxA assemblon in WT mESCs, 96h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
pSP0328_WT_#C4_96hRA/SAG_rep2
featurecounts_WTlines_synHoxAWTaligned.txt
HKLHFDRXX_n01_mb318

value: 130kb RARE{delta} SynHoxA assemblon in WT mESCs

value: 96h of RA+SAG differentiation


title: 130kb RARE∆ SynHoxA assemblon in WT mESCs, 96h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
pSP0328_WT_#C4_96hRA/SAG_rep1
featurecounts_WTlines_synHoxAWTaligned.txt
HKLHFDRXX_n01_mb317


title: Bcl6f/f Cd4Cre mouse 3

city: West Haven

first: Ryan

middle: D

last: Chow

state: CT

address: 850 West Campus Drive

institute: Yale University

data_processing:
Library strategy: BCR-seq
UMI-barcoded paired-end sequencing reads were processed and analyzed with the Immcantation suite (Docker image v4.3.0). Read preprocessing was performed with the presto-abseq pipeline interface for pRESTO (v0.7.0) with default settings, using mouse constant region primers, isotype-specific internal constant region sequences, and template switch sequences provided by NEB. The preprocessed reads were aligned to the mouse germline V(D)J genes with the changeo-igblast pipeline interface for Change-O (v1.2.0) and IgBLAST (v1.17.1). Productive sequences aligning to immunoglobulin heavy chains were retained for further analysis. Each sequence was annotated with the corresponding germline V(D)J sequence, masking N/P and D-segment regions. Spectral clustering was performed using SCOPer (v1.2.0) to identify clonally-related sequences, based on the level of junction region homology and the mutation profiles in the V-J segments. Following clonal clustering, consensus germline sequences for each clone were reconstructed as above.
Downstream analysis was performed using Alakazam (v1.2.0) and SHazaM (v1.1.0).
Genome_build: GRCm38 mm10
Supplementary_files_format_and_content: Fully processed BCR repertoire data in AIRR tab-delimited format for each sample. Each row corresponds to one UMI-barcoded BCR sequence.

source_name: S-specific plasmablasts from mediastinal lymph node

extract_protocol:
RNA from spike-specific B cells was isolated using the RNeasy Plus Micro Kit (Qiagen) following manufacturer’s instructions.
BCR libraries were prepared using the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module (NEB, E6421) and NEBNext Immune Sequencing Kit (NEB, E6330), with additional reagents provided by NEB to integrate the two kits. 1-40 ng of high-quality RNA with RIN score ≥ 8 was used as input. Libraries were analyzed by Bioanalyzer High Sensitivity DNA assay, pooled in equal amounts with PhiX spike-in, and sequenced on an Illumina MiSeq using the V3 kit, with 325 bp for read 1 and 275 bp for read 2.

value: mediastinal lymph node, SARS-CoV-2 S-specific plasmablasts

tag: infection

value: SARS-CoV-2, 14 dpi

tag: background strain

value: Krt18-hACE2 Bcl6f/f Cd4Cre


title: Bcl6f/f Cd4Cre mouse 2


title: Bcl6f/f mouse 4

value: Krt18-hACE2 Bcl6f/f


title: Bcl6f/f Cd4Cre mouse 1


title: Bcl6f/f mouse 2


title: GK3R78-UDS1: DSS_Colon_Unsorted_1

description:
GK3R78-UDS1
processed data file: metaseqr_all_out_UDS_vs_GDS.txt
processed data file: metaseqr_all_out_UDS_vs_TDS.txt

value: DSS-induced colitis


title: Bisulfite-seq_Wild-type_In-vitro-methylated-control

description:
Bisulfite-seq
Bisulfite-seq_%methCpG_Wild-type_In-vitro-methylated-control.bedGraph

source_name: n/a (control DNA)

value: In-vitro-methylated-control

tag: passages

value: n/a (control DNA)

tag: cell sex

value: Wild type


title: Bcl6f/f mouse 3


title: Bisulfite-seq_Wild-type_416B

description:
Bisulfite-seq
Bisulfite-seq_%methCpG_Wild-type_416B.bedGraph

tag: cell type

value: Hematopoietic progenitor cell line

value: F

tag: differentiation

value: Hematopoietic (cell line)


title: 166kb Enhancers + RARE∆ assemblon in WT mESCs, 24h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
394_D3r1
featurecounts_WTlines_synHoxAWTaligned.txt
H55WYDRXY_n01_dpr292

tag: strain

value: 166kb Enhancers + RARE{delta} assemblon in WT mESCs

value: 24h of RA+SAG differentiation

value: Embryoid Bodies


title: Bisulfite-seq_Wild-type_E14

description:
Bisulfite-seq
Bisulfite-seq_%methCpG_Wild-type_E14.bedGraph

value: Embryonic stem cells

value: M

tag: genotype

value: Undifferentiated (day 0)


title: 130kb RARE∆ SynHoxA assemblon in WT mESCs, 48h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
pSP0328_WT_#C4_48hRA/SAG_rep1
featurecounts_WTlines_synHoxAWTaligned.txt
HKLHFDRXX_n01_mb313

value: 130kb RARE{delta} SynHoxA assemblon in WT mESCs

value: 48h of RA+SAG differentiation


title: 130kb RARE∆ SynHoxA assemblon in WT mESCs, 48h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
pSP0328_WT_#C4_48hRA/SAG_rep2
featurecounts_WTlines_synHoxAWTaligned.txt
HKLHFDRXX_n01_mb314


title: GK3R98-UI3: Wt_Small Intestine_Unsorted_3

description:
processed data file: metaseqr_all_out_UI_vs_GIH.txt
processed data file: metaseqr_all_out_UI_vs_GIL.txt
processed data file: metaseqr_all_out_UI_vs_TI.txt

data_processing:
The sample GK3R96-UI1 was excluded from analysis, because it did not match the quality control criteria.
The RNA-Seq FASTQ files obtained after Ion Proton sequencing were mapped using TopHat2 [Kim2013], with default settings and using additional transcript annotation data for the mm10 genome from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). According to the Ion Proton manufacturers recommendation, the reads which remained unmapped were submitted to a second round of mapping using Bowtie2 [Langmead2012] against the mm10 genome with the --very-sensitive switch turned on and merged with the initial mappings.
The raw bam files were summarized to read counts table using the Bioconductor package GenomicRanges.
The gene counts table was normalized for inherent systematic or experimental biases using the Bioconductor package DESeq after removing genes that had zero counts over all the RNA-Seq samples.
The resulting gene counts table was subjected to differential expression analysis using the Bioconductor package DESeq.
All the above were performed through the Bioconductor package metaseqr.
Differential expression analysis files were subjected to additional filtering by removing the genes that had less than three natural normalized read counts in more than four samples.
Genome_build: mm10
Supplementary_files_format_and_content: txt (tab separated) files containing all the results from metaseqr analysis including expression per replicate, fold change compared to control and p-values.

extract_protocol:
Intestinal mesenchymal cells were isolated as previously described (Koliaraki et al., 2015) and total RNA was extracted using RNAeasy Mini kit (QIAGEN), according to the manufacturer's instructions.
The quantity and quality of RNA samples from sorted cells were analyzed using the bioanalyzer form Agilent in combination with the Agilent RNA 6000 Nano. RNA samples with RNA Integrity Number (RIN) > 7 were further used for library preparation using the 3’ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™) according to manufacturer’s instructions. The quantity and quality of libraries were assessed using the DNA High Sensitivity Kit in the bioanalyzer, according to the manufacturer’s instructions (Agilent Technologies). Libraries were subsequently pooled and templated using the Ion PI IC200 Chef Kit (ThermoFisher Scientific) on an Ion Proton Chef instrument or Ion OneTouch System. Sequencing was performed using the Ion PI™ Sequencing 200 V3 Kit and Ion Proton PI™ V2 chips (ThermoFisher Scientific) on an Ion Proton™ System, according to the manufacturer's instructions.
3’ RNA-Seq (QuantSeq)

value: ColVI-cre, Rosa mTmG

tag: tissue

value: Small Intestine

value: Intestinal Cells

tag: cell isolation

value: Fresh isolation


title: Bcl6f/f Cd4Cre mouse 4

value: mediastinal lymph node, SARS-CoV-2 S-specific plasmablasts

value: SARS-CoV-2, 14 dpi

value: Krt18-hACE2 Bcl6f/f Cd4Cre


title: WT-Lambda

city: Guangzhou

first: Jinyong

last: Wang

state: GuangDong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health (GIBH)

data_processing:
Library strategy: BCR-seq
Raw data (fastq files) were generated using illumina bcl2fastq software.
The B cell receptor repertoires were aligned and assembled using software MiXCR(version 3.0.13)
The exported clonotypes were visualized in the form of chord diagram using VDJtools software(version 1.2.1)
Genome_build: mm10

source_name: B cells

growth_protocol: We identified that the coordinated expression of exogenous transcription factors efficiently guides PSC-derived hematopoietic progenitors (iHPC) preferentially towards B cell lineage commitment, which successfully regenerate B lymphopoiesis in B-cell deficient animals

extract_protocol:
Total RNA was extracted from the  iB cell using Trizol (Invitrogen). 5’ RACE was performed with SMARTer RACE cDNA Amplification Kit (Clontech). IgG /IgK/IgL NGS libraries were made by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB). Libraries were sequenced on the Illumina Miseq 2 × 300 platform.
5’ RACE was performed with SMARTer RACE cDNA Amplification Kit (Clontech). IgG /IgK/IgL NGS libraries were made by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB)

treatment_protocol: We performed BCR deep sequencing using the sorted naive follicular B cells from the spleen of one recipient at week 4 after iHPC transplantation and one C57BL/6 mouse as control.

value: B cells


title: GK3R97-UI2: Wt_Small Intestine_Unsorted_2

tag: disease model


title: GK3R96-UI1: Wt_Small Intestine_Unsorted_1


title: 130kb RARE∆ SynHoxA assemblon in WT mESCs, 24h of RA+SAG differentiation, replicate 2, RNA-Seq

city: Seattle

first: Sudarshan

last: Pinglay

institute: University of Washington

description:
pSP0328_WT_#C4_24hRA/SAG_rep2
featurecounts_WTlines_synHoxAWTaligned.txt
HKLHFDRXX_n01_mb310


title: WT-heavy


title: iB-Lambda


title: WT-Kappa


title: GK3R80-UDS3: DSS_Colon_Unsorted_3

description:
GK3R80-UDS3
processed data file: metaseqr_all_out_UDS_vs_GDS.txt
processed data file: metaseqr_all_out_UDS_vs_TDS.txt

value: Colon

value: DSS-induced colitis


title: iB-Kappa


title: 166kb Enhancers + RARE∆ assemblon in WT mESCs, 0h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
394_D2r1
featurecounts_WTlines_synHoxAWTaligned.txt
H55WYDRXY_n01_dpr291

value: 166kb Enhancers + RARE{delta} assemblon in WT mESCs

value: 0h of RA+SAG differentiation


title: GK3R95-TI3: Wt_Small Intestine_Tomato_3

description:
processed data file: metaseqr_all_out_TI_vs_GIH.txt
processed data file: metaseqr_all_out_TI_vs_GIL.txt
processed data file: metaseqr_all_out_UI_vs_TI.txt

value: Intestinal Mesenchymal Cells


title: Bcl6f/f mouse 1

value: Krt18-hACE2 Bcl6f/f


title: iB-heavy


title: 130kb RARE∆ SynHoxA assemblon in WT mESCs, 0h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
pSP0328_WT_#C4_t=0_rep1
featurecounts_WTlines_synHoxAWTaligned.txt
HKLHFDRXX_n01_mb305

value: Embryoid Bodies


title: GK3R94-TI2: Wt_Small Intestine_Tomato_2


title: 130kb RARE∆ SynHoxA assemblon in WT mESCs, 0h of RA+SAG differentiation, replicate 2, RNA-Seq

description:
pSP0328_WT_#C4_t=0_rep2
featurecounts_WTlines_synHoxAWTaligned.txt
HKLHFDRXX_n01_mb306

value: 130kb RARE{delta} SynHoxA assemblon in WT mESCs


title: GK3R93-TI1: Wt_Small Intestine_Tomato_1