title: BXD45-ATAC-ESC

data_processing:
Bulk RNA reads were aligned to transcriptome (mm10 or modified to include known D2 SNPs, R78-REL1505) using bowtie v.1.0.0. ChIP and ATAC reads were aligned to genome using hisat2 v.2.0.5.
Allele specific gene counts were performed using EMASE. For ChIP and ATAC, peaks were called using MACS v.1.4.2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt files representing ensembl gene id along with normalized read counts for each sample. tab-delimited txt files representing the position of identified ChIP peaks in mm10 coordinates along with normalized read counts. Expression libraries for single cell RNAseq gene-cell: matrices are provided in the format produced by CellRanger. MULTI-seq Libraries for single cell RNAseq: barcode-cell matrices are provided in CSV format. The columns in the matrix Byers_EB_lipidhash_deMULTIplex_matrix.csv.gz represent individual embryoid body samples identified by unique lipid-modified oligos.

extract_protocol:
A single cell suspension of ESCs and EpiLCs were harvested at a concentration of 1 million cells/mL; 1 million cells were lysed and RNA extracted using RNeasy (Qiagen) RNA extraction kit; 100,000 cells were used for transposition reaction. For ChIP, 10 million cells were harvested and nuclei isolated using hypotonic lysis. Chromatin was fragmented using Covaris followed by dialysis and immunoprecipitation against protein targets was performed. For single cell RNAseq, single cell suspension was achieved for EB cultures and 500,000 cells for each individual sample was labeled with unique Multiseq LMO barcode. Labelled samples were pooled at 3,000 cells per sample and 40,000 cells were loaded onto a single lane of a 10X Chromium microfluidic chip. Cells were lysed in droplets using 10X Chromium instrument and reverse transcription was performed in droplet and library construction performed according to 10X Chromium v3 chemistry.
Libraries were constructed using the KAPA mRNA HyperPrep Kit for ESC and EpiLC bulk RNA samples. Modified Illumina Nextera adapters were used to construct ATAC libraries. ChIP-seq librariers were constructed using KAPA HyperPrep Kit. Single cell RNA-seq library preparation was performed using 10X Chromium v3.


title: CDX2_ChIP in CDX2 KO colonic epithelium

status: Public on Oct 05 2021

type: SRA

city: Shanghai

first: Wei

last: Gu

state: Shanghai

address: 51 Rijing Road

department: Beigene Institute

country: China

institute: Beigene

description: CDX2_ChIP (Negative Control)

library_source: genomic

data_processing:
All reads were trimmed with trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and subjected to quality control with FastQC before and after adapter trimming.
Bowtie2 (Langmead and Salzberg, 2012) was used to align the two independent ChIP-Seq analyses to the mouse (mm10) genome with default parameters.
Aligned ChIP-Seq data in SAM format were transformed to BAM files and non-uniquely mapped reads were filtered-out.
Duplicate alignments were then marked and removed using Sambamba.
The merge function in samtools was used to merge the BAM files of different replicates and filter out non-uniquely mapped reads.
Deeptools bamCoverage (duplicate reads ignored, RPKM normalized) was used to generate bigWig files from BAM files.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Bigwig files for visualization of TFs genomic binding peaks.

molecule: genomic DNA

organism: Mus musculus

source_name: Intestine epithelium

extract_protocol:
50 µl of pelleted cross-linked cells were resuspended in 350 µl sarkosyl lysis buffer (0.25% sarkosyl, 1 mM DTT and protease inhibitor in RIPA buffer) and sonicated at 15% amplification by a tip sonicator (Qsonica, Q125) to obtain 200bp to 800bp chromatin fragments. Diluted lysates were incubated with TFs antibodies at 4°C overnight and were additionally incubated with 30 µl protein A/G magnetic beads. ChIPed DNA was purified with a MinElute purification kit.
Libraries were prepared using the ThruPLEX DNA-Seq Kit
Exactly followed the protocol from Takara bio, R400428 or R400427 (Same protocol with R400428, different index system). All final libraries were size selected (200-800 bp) by AMPure XP beads (Beckman, A63880) and loaded for sequencing.

treatment_protocol: Epithilal tissues were collected by the EDTA method 30 days after tamoxifen injection and cross-linked with 2mM DSG and 1% formaldehye.

tag: genotyping

tag: intestine part

value: Colon


title: ASZ_RasV12_TGFbR1-kd_rep1

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

country: USA

institute: Stanford University

data_processing:
bowtie used for alignment.
duplicate fragments were removed using samtools
macs2 used for peak calling
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: ASZ_ RasV12_TGFbR1-kd/Dox-4OHT

growth_protocol: ASZ001 cells were cultured in 154CF medium (Life Technologies) supplemented with 2% chelated FBS and 0.05 mM CaCl2.

extract_protocol:
ATAC-seq cell lysis and transposition with Tn5 was carried out based on published protocol by Buenrostro et. al (Nature Methods, 2013) with minor modifications for on-plate transposition. Briefly, 50,000 ASZ001 cells were plated per replicate in a 48-well plate, then serum starved for 24 hours. Wells were washed with cold PBS and lysed using 0.1% NP40 in resuspension buffer for 10 minutes at 25°C. Wells were washed again, then 100 µl of transposition mixture was added per well and incubated for 37°C for 30 min, shaking at 1000 RPM using a thermoshaker. DNA was purified using the Qiagen MinElute columns per manufacturer's instructions.
Libraries were generated using custom Nextera PCR primers and PCR conditions from published protocol by Buenrostro et. al (Nature Methods, 2013).

tag: treatment

value: 6 days Dox/4OHT

tag: genotype

tag: cell line


title: WT_Day6

library_source: transcriptomic

data_processing:
Adapter and low quality bases trimming (Q<20) using Trim Galore! with default parameters
Paired end alignment using STAR with defaut parameters
Generation of counts relative to genes using featureCounts with defaut paramets (unstranded mode)
Generation of normalized read counts and differential expression genes with normal shrinkage mode by DEseq2 package in Rstudio
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized gene counts table (Counts of Day 30 were processed from GSE167284 )

molecule: total RNA

growth_protocol: All mouse experiments were conducted under the IACUC protocol 03-132 at Dana-Farber Cancer Institute

extract_protocol:
RNA was extracted with TRIZOL Plus RNA purification kit (Thermo Fisher Scientific)
NEBNext® Ultra™ RNA Library Prep Kit for Illumina, following manufacturer's protocol.
Library construction performed by Novogene.co.  Non-directional eukaryotic mRNA library

treatment_protocol: Mice were injected once with Tamoxifen at 1mg per 20g body weight. Epithelial tissues from the proximal colon were collected by three subsequent incubations as follows: 10mM EDTA in DMEM medium (Corning) while rotating at 30rpm, vigorous shaking and centrifugation of supernatant at 400g for 2min. Three combined supernatants were directly lysed in TRIZOL. As control samples served both Sat2-cKO mice (non-injected, Day0) and injected littermate wild type mice (Satb2 f/f)

tag: time point

value: WT


title: WT Ileum Organoid rep 1

data_processing:
Adapter and low quality bases trimming (Q<20) using Trim Galore! with default parameters
Paired end alignment using STAR with defaut parameters
Generation of counts relative to genes using featureCounts with defaut paramets (unstranded mode)
Generation of normalized read counts and differential expression genes with normal shrinkage mode by DEseq2 package in Rstudio
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized gene counts table

source_name: 3D cultured mouse Organoids

growth_protocol: Crypts were collected from mice intestine by EDTA method and embedded in materigel with large intestine culture medium. After one passage, organoids were differentiated and collected for RNA extraction. Genotypes include Vil-CreER;Satb2f/f and Satb2f/f control mice, after 30 days of tamoxifen injection.

extract_protocol:
Qiagen Mini RNA extract kit
NEBNext® Ultra™ RNA Library Prep Kit for Illumina, following manufacturer's protocol.
Library construction performed by Novogene.co.  Non-directional eukaryotic mRNA library

treatment_protocol: Materigel was removed by Cell recovery solution, pellet organoids were resuspended in RLT lysis buffer (Qigen Kit)

value: Wild Type

value: Ileum


title: WT_Day2


title: ASZ_TGFbR1-kd_rep1

source_name: ASZ_ RasV12_TGFbR1-kd

value: 6 days DMSO


title: CDX2_ChIP in wild type colonic epithelium rep 2


title: BXD81-ATAC-ESC

city: Bar Harbor

first: Christopher

last: Baker

state: ME

address: 600 Main St

institute: The Jackson Laboratory

source_name: embryonic stem cell

growth_protocol: Mouse embryonic stem cells were derived and maintained in naive conditions following protocol from Czechanski et al. 2014 (Nature Protocols). Culture conditions to transition ESCs to EpiLCs followed Buecker et al. 2014 (Cell Stem Cell). Spontaneous differentiation of ESCs to EBs was achieved by first transitioning through EpiLC state for 48 hours followed by seeding cells on AggreWell400 Plates (STEMCELL Technologies) in EB medium ensuring 750 cells/EB. Aggregates were allowed to form for 48 hours and then filtered to remove unincorporated cells. Collected EBs were then plated on 100mm Corning Ultra-low attachment culture dishes and continued growth with rotation on BellyButton rotator for another 48 hours.

tag: cell type

value: naive esc

tag: mouse strain

value: bxd


title: CDX2_ChIP in SATB2 KO colonic epithelium rep 1


title: BXD66-ATAC-ESC


title: KO_Day6_rep2


title: KO_Day6_rep1


title: ASZ_TGFbR1-kd_rep2


title: BXD87-ATAC-ESC


title: CDX2_ChIP in wild type colonic epithelium rep 1


title: ASZ_RasV12_rep2

source_name: ASZ_ RasV12_NS/Dox-4OHT


title: BXD125-ATAC-ESC


title: KO_Day4_rep2


title: KO_Day4_rep1


title: BXD90-ATAC-ESC


title: ASZ_RasV12_rep1


title: BXD74-ATAC-ESC


title: ASZ_control_rep2

source_name: ASZ_ RasV12_NS

value: control


title: SATB2_ChIP in SATB2 KO colonic epithelium

description: SATB2_ChIP (Negative Control)


title: SATB2_ChIP in wild type colonic epithelium rep 2


title: HNF4A_ChIP in wild type colonic epithelium rep 1


title: BXD84-ATAC-ESC


title: KO_Day2_rep2


title: ASZ_control_rep1


title: SATB2_ChIP in wild type colonic epithelium rep 1


title: DAC203-ATAC-ESC-rep3


title: KO_Day1_rep2


title: Fos_dox_24h_UO126_10uM_rep2

data_processing:
Tophat used for alignment.
Homer is used to calculate raw counts and FPKM values.
deseq2 is used for differential analysis.
Genome_build: mm9
Supplementary_files_format_and_content: RNAseq_inhibitor_tx_counts.txt: Tab-delimited text file includes raw count values for each sample.

source_name: ASZ001 murine BCC cell line

extract_protocol:
RNA samples were obtained from adherent cells using RNeasy kit from QIAGEN according to manufacturer's instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Upon dox induction for 24h, cells are either treated with afatinib (5uM) or UO126 (10uM) or DMSO control for 6h.

value: c-Fos

value: Dox + UO126


title: KO_Day2_rep1


title: set4 deletion mutant hypoxic Rep 3

city: Baltimore

first: Erin

middle: M

last: Green

state: MD

address: 1000 Hilltop Cir, Bs 325

department: Biological Sciences

institute: UMBC

description: Jethmalani et al_processed data_gene counts_logFC.xlsx

data_processing:
Data quality visualized using FastQC
Adaptor removal and read trimming performed with Trimmomatic v.0.36
Read mapping performed with STAR aligner v.2.5.2b
Gene hit counts calculated using featureCounts from Subread package v.1.5.2
Log fold-change values calculated using DESeq2
Genome_build: ENSEMBL reference genome
Supplementary_files_format_and_content: excel file with log fold change values calculated from DESeq2 and gene counts for three replicates of each sample

organism: Saccharomyces cerevisiae

source_name: whole cell lysate

growth_protocol: YPD medium, 30 degrees C, mid log phase growth under aerobic conditions; for hypoixa, cells were grown for 18 hours to mid log phase using BD GasPak anaerobe pouches

extract_protocol:
total RNA isolation from yeast with rRNA depletion using Illumina ribo zero kit
standard Illumina library preparation using stranded TruSeq library preparation kit

tag: strain

tag: condition

value: hypoxic


title: set4 deletion mutant hypoxic Rep 2


title: D55-ATAC-ESC-rep1


title: D29-ATAC-ESC-rep2


title: KO_Day1_rep1


title: KO_Day0_rep2


title: set4 deletion mutant hypoxic Rep 1


title: Fos_dox_24h_UO126_10uM_rep1


title: Fos_dox_24h_DMSO_rep2

value: Dox + DMSO


title: Fos_dox_24h_DMSO_rep1


title: B44-ATAC-ESC-rep3


title: KO_Day0_rep1


title: B51-ATAC-ESC-rep2


title: B41-ATAC-ESC-rep1


title: Wildtype hypoxic Rep 2

value: wildtype


title: SATB2_KO_Day7_Rep2

extract_protocol:
RNA was extracted with TRIZOL Plus RNA purification kit (Thermo Fisher Scientific) and on-column DNAse digestion (Qiagen).
NEBNext® Ultra™ RNA Library Prep Kit for Illumina, following manufacturer's protocol.
Library construction performed by Novogene.co.  Non-directional eukaryotic mRNA library

treatment_protocol: Mice were injected with Tamoxifen at 1mg per 20g body weight for four consecutive days. Epithelial tissues from the proximal colon were collected by three subsequent incubations as follows: 10mM EDTA in DMEM medium (Corning) while rotating at 30rpm, vigorous shaking and centrifugation of supernatant at 400g for 2min. Three combined supernatants were directly lysed in TRIZOL

value: Proximal Colon


title: DAC203-RNA-ESC-rep3


title: Fos_dox_24h_afatinib_5uM_rep1

value: Dox + afatinib


title: Fos_dox_24h_afatinib_5uM_rep2


title: Wildtype hypoxic Rep 1


title: empty_dox_24h_rep2

value: Dox


title: set4 deletion mutant aerobic Rep 2

value: aerobic


title: EED_SATB2_KO_Day7_Rep3

value: EED and SATB2cKO


title: set4 deletion mutant aerobic Rep 3


title: D55-RNA-ESC-rep1


title: EED_SATB2_KO_Day7_Rep2


title: set4 deletion mutant aerobic Rep 1


title: empty_dox_24h_rep1


title: ASZ_cFOS_rnaseq_rep2

data_processing:
Tophat used for alignment.
Homer is used to calculate raw counts and RPKM values.
deseq2 is used for differential analysis.
Genome_build: mm9
Supplementary_files_format_and_content: ASZ_FOS_countFile.txt: Tab-delimited text file includes raw count values for each sample.

value: c-FOS


title: SATB2_KO_Day7_Rep1


title: Wildtype aerobic Rep 3


title: EED_KO_Day7_Rep3

value: EEDcKO


title: B44-RNA-ESC-rep3


title: Wildtype hypoxic Rep 3


title: B51-RNA-ESC-rep2


title: EED_SATB2_KO_Day7_Rep1

value: EED  and SATB2cKO


title: EED_KO_Day7_Rep2


title: B41-RNA-ESC-rep1


title: Wildtype aerobic Rep 1


title: ASZ_ctrl_rep2


title: ASZ_ctrl_rep1


title: BXD99-RNA-ESC


title: EED_KO_Day7_Rep1


title: Wildtype aerobic Rep 2


title: ASZ_TGFbR1kd_RasV12_rep2

data_processing:
Tophat used for alignment.
Homer is used to calculate raw counts and RPKM values.
deseq2 is used for differential analysis.
Genome_build: mm9
Supplementary_files_format_and_content: ASZRas_TGFBR_RNAseq_counts.txt: Tab-delimited text file includes RPKM values for each sample.


title: ASZ_cFOS_rnaseq_rep1


title: Fos_dox_UO126_rep2

data_processing:
bowtie2 used for alignment.
duplicate fragments were removed using samtools
macs2 used for peak calling
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: ASZ

treatment_protocol: ASZ cells with dox-inducible c-FOS construct were treated with doxycycline in serum-free medium for 24h. Cells were then treated with either 5µM of afatinib, 10µM of UO126 or DMSO for 6h. ASZ cells with an empty construct were treated with doxycycline in serum-free medium for 24h as the control. Following the inhibition assay, cells were harvested for ATAC-seq.

value: ASZ

value: dox and UO126


title: D29-RNA-ESC-rep2

value: naive esc


title: ASZ_TGFbR1kd_RasV12_rep1


title: Fos_dox_UO126_rep1


title: BXD161-RNA-ESC

value: bxd


title: ASZ_NS_RasV12_rep2


title: hot1-4 shot2 Heat rep3

city: Amherst

first: Minsoo

last: Kim

state: MA

address: 240 Thatcher Rd. N340B

department: BMB

institute: University of Massachusetts Amherst

description: rRNA-depleted RNA

data_processing:
Illumina RTA2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using HiSat2 v2.0.5 with parameters -q --dta
The number of reads for each gene were counted using HTseq v0.10.0 with htseq-count -m intersection-nonempty --stranded reverse
The numbers of read counts for each sample were merged into one file.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files containing read counts for each gene. Merged count matrix table with raw read counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: hot1-4 and hot1-4 shot2 seedlings were grown on half-strength MS agar plates containing 0.5% sucrose and 0.8% phytoagar until stage 1.02.

extract_protocol:
whole plant seedlings were harvested and flash-frozen on liquid nitrogen. Total RNA was extracted using a RNeasy Plant Mini kit (Qiagen, 74904). All samples were treated with DNase I using a RNase-Free DNase Set (Qiagen 79254) and quantified. 7 µg total RNA was used for rRNA depletion with RiboMinus (Invitrogen, A10838-08) according to the manufacturer’s instructions.
100 ng of rRNA-depleted RNA was used for library preparation using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7420S) according to the manufacturer’s protocol.

treatment_protocol: Seedling on the agar plates were treated with or without heat stress at 38 °C for 3h in darkness followed by 22 °C for 1h in light.

tag: cultivar

tag: developmental stage

value: hot1-4 shot2

value: Heat stress 38°C/3h, 22°C/1h


title: Fos_dox_DMSO_rep2

value: dox and DMSO


title: ASZ_NS_RasV12_rep1


title: hot1-4 shot2 Heat rep2

description: rRNA-depleted RNA


title: Fos_dox_DMSO_rep1


title: BXD154-RNA-ESC


title: ASZ_TGFbR1kd_rep2

value: DMSO


title: Fos_dox_afatinib_rep2

value: dox and afatinib


title: BXD125-RNA-ESC


title: hot1-4 Heat rep3

description: rRNA-depleted RNA


title: ASZ_TGFbR1kd_rep1


title: Fos_dox_afatinib_rep1


title: Model-SC

type: RNA

city: Beijing

first: Wu

last: Dan

address: Dongzhimennei south steet 16

institute: Institute of Chinese Materia Medica，China Academy of Chinese Medical Sciences

description: Gene expression data from spinal cord in CCI rat

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Gene expression profiling analyses were performed using R (http://www.rproject.org/, version 3.1.1) with Bioconductor packages (http://www.bioconductor.org/). Raw intensities were normalized using Robust multi-array average (RMA method). Significant DEGs of the sham vs. CCI groups were identified using the criteria of a |log2fold change (FC)|>1.0 and P value <0.05.

label: biotin

organism: Rattus norvegicus

source_name: Rattusc spinal cord on postoperative day 10

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Adult male Sprague-Dawley rats (180-200 g)  were housed with a fixed light/dark cycle (12/12 h), a room temperature of 21–22 ℃, and ad libitum access to food and water. CCI rat model was established as previously described. Briefly, the left common sciatic nerve in each rat was exposed at the mid-thigh level. The area proximal to the sciatic nerve’s trifurcation was freed of adhering tissue, and four ligatures were tied loosely around it with approximately 1 mm between each ligature. The sciatic nerve was exposed but not ligated in sham group animals.

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

treatment_protocol: SC tissues (L4-L6) collected from the rats in the Sham and CCI groups on postoperative day 10 were immersed in TRIzol(Invitrogen, CA, USA) , and immediately frozen in liquid nitrogen for the whole-genome microarray detection

tag: tissue

value: Lumbar spinal cord(L4-L6)  of adult male Sprague-Dawley rat


title: BXD124-RNA-ESC


title: BXD75-RNA-ESC


title: empty_rep2


title: hot1-4 Heat rep2

description: rRNA-depleted RNA


title: ASZ_NS_rep2

value: control


title: ASZ_NS_rep1


title: hot1-4 Heat rep1

description: rRNA-depleted RNA


title: empty_rep1


title: BXD95-RNA-ESC


title: hot1-4 shot2 RT rep3

description: rRNA-depleted RNA

value: Room temperature


title: BXD87-RNA-ESC


title: hot1-4 shot2 Heat rep1

description: rRNA-depleted RNA


title: hot1-4 shot2 RT rep2

description: rRNA-depleted RNA


title: BXD90-RNA-ESC


title: BXD86-RNA-ESC


title: hot1-4 shot2 RT rep1

description: rRNA-depleted RNA


title: B51-RNA-EpiLC-rep1

description:
epilc_counts.norm.tsv.gz
RNA10

source_name: epiblast-like stem cell

value: esc transitioned to formative EpiLC


title: B41-RNA-EpiLC-rep3

description:
epilc_counts.norm.tsv.gz
RNA12


title: B44-RNA-EpiLC-rep2

description:
epilc_counts.norm.tsv.gz
RNA11


title: hot1-4 RT rep3

description: rRNA-depleted RNA


title: MI_B14

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

description:
htseq_gene_count_mat.txt.gz
rsem_gene_count_mat.txt.gz
rsem_trans_count_mat.txt.gz

data_processing:
Illumina HSC 1.6.0/RTA 3.4.4 software used for sequencing and basecalling.
Trim Galore (v0.6.4) to trim adapters from reads and remove low quality bases in the data, with arguments length >= 25, stringency = 3 and quality = 25
STAR (v2.7.6a) to map the trimmed reads against the mouse reference genome (mm10) and its corresponding GENCODE gene annotation (VM20).
HTSeq (v0.12.4) to count the reads aligned to each gene for gene-level expression quantification.
In parallel, RSEM (v1.3.1) to align and calculate the expression at both the gene level and the transcript level.
Genome_build: mm10
Supplementary_files_format_and_content: txt: gene-level read counts by HTSeq
Supplementary_files_format_and_content: txt: gene-level expected read counts by RSEM
Supplementary_files_format_and_content: txt: isoform-level expected read counts by RSEM

source_name: Oocyte

extract_protocol:
After washed three times with 0.1% BSA/PBS, each oocyte was then transferred into 0.2 mL PCR tubes containing 2 μl lysis buffer.
Transcriptome libraries were prepared following the Smart-seq2 protocol. Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions.

value: MI

tag: sample id

tag: batch

value: B

value: Oocyte


title: MI_B13


title: DAC203-RNA-EpiLC-rep3

description:
epilc_counts.norm.tsv.gz
RNA9


title: MI_B12


title: BXD98-RNA-ESC


title: D55-RNA-EpiLC-rep2

description:
epilc_counts.norm.tsv.gz
RNA8


title: Sham-SC


title: BXD84-RNA-ESC


title: BXD83-RNA-ESC


title: hot1-4 RT rep2

description: rRNA-depleted RNA


title: MI_B11


title: D29-RNA-EpiLC-rep1

description:
epilc_counts.norm.tsv.gz
RNA7


title: BXD81-RNA-ESC


title: MI_B15


title: MI_B9


title: KO Colon rep 4

description: Intestinal_epithelial_normalized_counts.txt

extract_protocol:
Qiagen Mini RNA extract kit
The library was constructed with NEBNext® Ultra™ RNA Library Prep Kit for Illumina, following manufacturer's protocol.
Library construction strategy was non-directional eukaryotic mRNA library  Sequencing strategy was Pair-end 150 (PE150)

treatment_protocol: Epithilal tissues collected by EDTA method 30 days after Tamoxifen injection.  Genotypes include Vil-CreER;Satb2f/f and Satb2f/f control mice

value: Satb2 Knock out

value: Colon


title: BXD74-RNA-ESC


title: KO Cecum rep 4

value: Cecum


title: hot1-4 RT rep1

description: rRNA-depleted RNA


title: NLS-GFP:dam_L4_rep-2_Exp-2

city: London

first: Dimitris

last: Katsanos

address: Sir Alexander Fleming building, Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description: amplicons of GATC-6mA-methylated genomic DNA fragments

data_processing:
Library strategy: DamID-seq
Sequencing data were fully processed using the automated pipeline defined by the perl script damidseq_pipeline v1.4.5 (Marshall and Brand, 2015) (available at https://github.com/owenjm/damidseq_pipeline). The pipeline  was used calling Bowtie 2 v2.3.4 (Langmead and Salzberg, 2012) for alignment to C. elegans bowtie indices from genome assembly WBcel235 (available from illumina® iGenomes page), Samtools v1.9 (Li et al., 2009) for alignment manipulations and generation of BAM files. Using a GATC fragment file with the coordinates of all GATC fragments across the C. elegans genome in gff format, built from a WBcel235 FASTA file (available at https://www.ensembl.org/Caenorhabditis_elegans/Info/Index) using the gatc.track.marker.pl script (available at https://github.com/owenjm/damidseq_pipeline), the pipeline calculated genome-wide log2(TF:dam/NLS-GFP:dam) signal enrichment scores per GATC fragment of the genome as gff files from pairs of BAM files from TF:dam and NLS-GFP:dam samples.
Using damidseq_pipeline v1.4.5 all pairwise calculations of log2(TF:dam/NLS-GFP:dam) scores between pairs of TF:dam and NLS-GFP:dam samples replicates from the same experiment  and developmental stage were performed producing 4 independet gff signal files for each TF at each stage.
The 4 gff signal files were averaged arithmetically per GATC fragment of the genome to genarate the single averaged signla gff file each TF at each developmental stage.
Statistically significant enrichment peaks with an FDR<0.05 were identified from the averaged profiles using the the perl script find_peaks (available at https://github.com/owenjm/find_peaks) which generated peak interval gff files
Genome_build: WBcel235
Supplementary_files_format_and_content: GFF interval files representing coordinates of GATC fragments of the genome with a log2(TF:dam/NLS-GFP:dam) score each
*averaged.gatc.chr.gff = averaged log2 signal across replicates per GATC fragment
*peaks.gff = scored peak files

organism: Caenorhabditis elegans

source_name: Epidermis

growth_protocol: For each replicate of each strain used for TaDa nine 55 mm NGM plates seeded with dam-/dcm- bacterial lawns and fully populated by gravid adults were used for large-scale egg preparation with isolated embryos seeded in new dam-/dcm- plates that were incubated at 20 °C. Half of the resulting synchronised populations were collected in a 15 ml centrifuge tube after 24 hours at the L2 stage and the other half after 48 hours at the L4 stage. All collected populations pellets (~100 μl) underwent extensive washing with 10 ml M9 at least 5 times.

extract_protocol:
gDNA for each sample was extracted by lysing animal pellets with Cell Lysis Solution (QIAGEN) containing Proteinase K. RNA was removed by treating with RNase A  and DNA was isolated after treatment with Protein precipitation solution (QIAGEN) by percipitating in isopropanol and washing with 70% ethanol. gDNA was redissolved in water. For isolation and amplification of the GATC methylated gDNA fragments the protocol followed was an adapted version of the one presented in (Marshall et al., 2016)
Amplicon sonication and library preparation was outsourced to GENEWIZ which used illumina protocols for sequencing on the Illumina HiSeq 2x150 platform

value: Epidermis - wrt-2 expression domain

tag: biological replicate

value: Replicate 2

tag: experiment number

tag: sequenced molecule

value: DNA amplicons


title: BXD85-RNA-ESC

value: naive esc

value: bxd


title: nhr-25:dam_L4_rep-2_Exp-2


title: MI_B8


title: KO Ileum rep 4

value: Ileum


title: BXD73-RNA-ESC


title: nhr-25:dam_L2_rep-2_Exp-2


title: MI_B7


title: NLS-GFP:dam_L2_rep-2_Exp-2


title: KO Jejunum rep 4

value: Jejunum


title: BXD71-RNA-ESC


title: MI_B6


title: nhr-25:dam_L4_rep-1_Exp-2

value: Replicate 1


title: KO Colon rep 3


title: BXD68-RNA-ESC


title: MI_B5


title: MI_B10


title: MI_B4


title: NLS-GFP:dam_L2_rep-1_Exp-2


title: nhr-25:dam_L2_rep-1_Exp-2


title: KO Ileum rep 3


title: KO Jejunum rep 3


title: MI_B3


title: BXD66-RNA-ESC


title: BXD67-RNA-ESC


title: MI_B2


title: KO Colon rep 2


title: MI_B1


title: KO Cecum rep 2


title: BXD64-RNA-ESC


title: BXD69-RNA-ESC


title: NLS-GFP:dam_L4_rep-2_Exp-1


title: lin-22:dam_L4_rep-2_Exp-1


title: NLS-GFP:dam_L2_rep-2_Exp-1


title: NLS-GFP:dam_L4_rep-1_Exp-2


title: KO Ileum rep 2


title: KO Cecum rep 3


title: BXD62-RNA-ESC


title: KO Jejunum rep 2


title: lin-22:dam_L2_rep-2_Exp-1


title: BXD63-RNA-ESC


title: GV_B9

value: GV


title: NLS-GFP:dam_L4_rep-1_Exp-1


title: KO Colon rep 1


title: GV_B8


title: GV_B7


title: lin-22:dam_L4_rep-1_Exp-1


title: BXD55-RNA-ESC


title: GV_B6


title: NLS-GFP:dam_L2_rep-1_Exp-1


title: BXD49-RNA-ESC


title: GV_B10


title: BXD48-RNA-ESC


title: GV_B5


title: KO Cecum rep 1


title: GV_B4


title: KO Jejunum rep 1


title: BXD45-RNA-ESC


title: BXD44-RNA-ESC


title: GV_B3


title: BXD61-RNA-ESC


title: WT Cecum rep 3

value: wild type


title: WT Colon rep 3


title: BXD43-RNA-ESC


title: WT Ileum rep 3


title: GV_B2


title: GV_B1


title: KO Ileum rep 1


title: X167-CA1

last: Ge

state: State...

address: 5 Dong Dan San Tiao, Dongcheng District

department: Department of Immunology

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

data_processing:
Basecalls performed using bcl2fastq software
raw data fastqc
sequencing data filtering and statistics using fastp software
clean data fastqc
Genome_build: Homo_sapiens.GRCh38

organism: Homo sapiens

source_name: hippocampus

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit from frozen hippocampus (Cat#74106, QIAGEN)following  the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA,US).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AD


title: WT Jejunum rep 3


title: MII_A5

value: MII

value: A


title: WT Colon rep 2


title: lin-22:dam_L2_rep-1_Exp-1


title: MII_A6

value: Oocyte


title: X150-CA1


title: WT Cecum rep 2


title: MII_A4


title: WT Ileum rep 2


title: X119-CA1


title: X142-CA1


title: WT Colon rep 1


title: MII_A2


title: MII_A1


title: X161-CA1


title: X157-CA1

value: Health


title: WT Jejunum rep 2


title: WT Cecum rep 1


title: MII_A3


title: sample37: Peritonium tissue (Normal)

city: Singapore

first: Kie Kyon

last: Huang

state: Select State/Province

address: 8 College Road

country: Singapore

institute: Duke-NUS Graduate Medical School

description: *** Raw files were not submitted due to patient privacy concerns ***

data_processing:
Cellranger v3.0 was used to align FASTQ sequencing reads to the hg38 reference transcriptome, generating single cell feature counts for each sample
Using Seruat version 3.0, each sample was considered for genes/features shared by 3 or more cells, and cells showing 500 or more features and less than 6000 features. Cells with mitochondrial RNA percentages of >20 were filtered out
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell for each sample

molecule: polyA RNA

source_name: peritoneum

extract_protocol:
Single cell were  dissociated from gastric tissue sample using tumor dissociation kit from Miltenyi Biotec
10x Genomics Single Cell 5′ Library kit

value: Peritonium tissue (Normal)


title: GV_A5


title: X166-CA1


title: X164-CA1


title: GV_A6


title: GV_A4


title: Bodenlos_mutant_rep2

city: Wageningen

first: Dolf

last: Weijers

address: Stippeneng 4

department: Biochemistry

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 Fluidics Station using the protocolFS450_0002, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the GeneChip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'affy' (v1.44).

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: All seeds were sterilized in 25% bleach/75% ethanol solution for 10 minutes and were afterwards washed twice with 70% ethanol and once with 100% ethanol. Dried seed were plated on half-strength Murashige and Skoog (MS) medium and the appropriate antibiotic (in concentration: 50 mg/l kanamycin or 15 mg/l phosphinothricin) for selection of transgenic seeds. After 24hours incubation at 4°C, the plants were grown under long-day conditions at 22°C in a growth room.

extract_protocol: Total RNA was isolated using Trizol-Chloroform extraction followed by clean-up using the RNeasy Plant Mini kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Ovules were collected from ~60 siliques using vacuum extraction. Siliques were stuck to double-sided tape and sliced open using a needle. Open siliques were submerged in 1x PhosphateBuffered Saline (PBS) buffer and ovules were collected using a vacuum pump through 50 µm filters. Collected ovules were then transferred to Isolation buffer (1x First Strand Buffer (FSB; Invitrogen), 1mM Dithiotreitol (DTT), 4% RNAseLater, MQ), and volume was reduced to ~20 µL. Embryo isolation was performed according to (Raissig, 2013) with the following adaptations. A Zeiss Confocor 1 inverted microscope (Carl Zeiss Microscopy GmbH, Jena, Germany) together with an Eppendorf Transferman 4r micromanipulator (Eppendorf AG) and VacuTip II microcapillaries (Eppendorf) were used to isolate about 40-50 washed embryos in 50 μl isolation buffer.

tag: ecotype background

value: Columbia (Col-0)

tag: genotype/variation

value: Bodenlos (IAA12) mutant

value: 8-cell embryos


title: KO Colon rep 2 (ATAC-seq)

data_processing:
Alignment BAM files for the ATAC-seq were generated with the mm10 reference genome using nf-core pipelines
Narrow peaks were called using standard MACS2.
ATAC-seq peak files had regions of less than 1kb from TSS removed using bedtool.
Biological replicates were concatenated and sorted, and peaks merged within a maximum distance of 500 bp.
Six optimum clusters were determined for k-means clustering using the elbow method. The top 3 clusters were not unique across samples and, therefore, merged into one, according to signal pattern similarity. Cluster 6 was excluded due to very low non-distinct signal.
The three resulting clusters were then annotated in R 3.6.0 using the annotatePeak function from the ChIPseeker package using known mm10 genes.
Genome_build: mm10 reference genome
Supplementary_files_format_and_content: called peaks .bed files

source_name: Intestine epithelium

extract_protocol:
Nuclei were exacted in ATAC-Resuspension Buffer (RSB, 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) with 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. DNA was fragmented by Netera Tn5 Transposase (Illumina)
NEBNext 2x MasterMix to pre-Amplify for 5 cycles and determined the required number of additional cycles by qPCR amplification. The final libraries were size selected (200bp to 800bp, including index) with AMpure beads
Sequencing strategy was on Illumina HiSeq-2000 Pair-end 150 (PE150)

treatment_protocol: 50K intestinal epithelial cells were purified by FACS . Genotypes include Vil-CreER;Satb2f/f and Satb2f/f control mice

tag: genotype

value: Satb2 Knockout

value: Colon


title: Col-0_wildtype_rep3


title: Bodenlos_mutant_rep1


title: X158-CA1


title: Luminal#5

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

description:
Sample 83
AllSamplesNormReadCount_raw_191004xlsx.xlsx

data_processing:
Quality control: QC was carried out by MIT BMC/BCC in house pipeline including sequencing error rate estimation, sequencing reads complexity estimation, fastqc report, and sample contamination estimation. Hierarchical clustering and heatmap creation were carried out by TIBCO Spotfire 7.11.1.0.12 basing on log2(fpkm+1) values of the expressed coding genes to observe sample relationship and to detect outliers.
For HMLE/HMLER, raw sequence reads were collapsed by sequence identity and UMI (Unique Molecular Identifier) and aligned to the human genome (UCSC hg19 build) using TopHat v. 2.0.4. Genic read counts were quantified using the End Sequence Analysis Toolkit (ESAT v1). Count normalization and differential analyses were conducted using the DESeq package (R/Bioconductor) and genes with q-value < 0.05 and absolute fold change greater than 2 were tagged as differentially expressed. Row-normalized heatmaps for differentially expressed genes were created using Heatplus (R/Bioconductor).
For breast tumors, reads were mapped to the human genome (USCS hg19 build) using TopHat v. 2.1.0 and transcript abundance was determined using HTSeqCount v. 0.9.1. Molecular subtyping, PAM50 and Claudin-low, was performed using the Genefu v.2.20.0 R package (http://www.pmgenomics.ca/bhklab/software/genefu).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Excel format matrix of normalized gene expression abundance. Each gene is a row, and each sample is a column.

source_name: Tumor

growth_protocol: HMLE and HMLER cells were grown to high confluence and serum starved.

extract_protocol:
For gene expression analysis in HMLE and HMLER cells, total RNA was extracted from cells using the Qiagen RNeasy kit according to the manufacturer's instructions. For gene expression analysis in breast tumors, total RNA was extracted from frozen sections of breast tumor samples using the Nucleospin RNA set for Nucleozol kit according to the manufacturer’s protocol (Macherey-Nagel).
For HMLE and HMLER extracts, 25 ng for each of the two biological replicates per condition was used to generate libraries for whole-transcriptome analysis following High Throughput 3’ Digital Gene Expression library preparation. For breast tumor extracts, libraries were prepared using a modified version of the Takara SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian kit.

treatment_protocol: DMSO or Ciliobrevin A were added to the serum starvation medium.

value: Breast tumor

tag: tumor type

value: Luminal


title: X159-CA1


title: BXD65-RNA-ESC

data_processing:
Bulk RNA reads were aligned to transcriptome (mm10 or modified to include known D2 SNPs, R78-REL1505) using bowtie v.1.0.0. ChIP and ATAC reads were aligned to genome using hisat2 v.2.0.5.
Allele specific gene counts were performed using EMASE. For ChIP and ATAC, peaks were called using MACS v.1.4.2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt files representing ensembl gene id along with normalized read counts for each sample. tab-delimited txt files representing the position of identified ChIP peaks in mm10 coordinates along with normalized read counts. Expression libraries for single cell RNAseq gene-cell: matrices are provided in the format produced by CellRanger. MULTI-seq Libraries for single cell RNAseq: barcode-cell matrices are provided in CSV format. The columns in the matrix Byers_EB_lipidhash_deMULTIplex_matrix.csv.gz represent individual embryoid body samples identified by unique lipid-modified oligos.

extract_protocol:
A single cell suspension of ESCs and EpiLCs were harvested at a concentration of 1 million cells/mL; 1 million cells were lysed and RNA extracted using RNeasy (Qiagen) RNA extraction kit; 100,000 cells were used for transposition reaction. For ChIP, 10 million cells were harvested and nuclei isolated using hypotonic lysis. Chromatin was fragmented using Covaris followed by dialysis and immunoprecipitation against protein targets was performed. For single cell RNAseq, single cell suspension was achieved for EB cultures and 500,000 cells for each individual sample was labeled with unique Multiseq LMO barcode. Labelled samples were pooled at 3,000 cells per sample and 40,000 cells were loaded onto a single lane of a 10X Chromium microfluidic chip. Cells were lysed in droplets using 10X Chromium instrument and reverse transcription was performed in droplet and library construction performed according to 10X Chromium v3 chemistry.
Libraries were constructed using the KAPA mRNA HyperPrep Kit for ESC and EpiLC bulk RNA samples. Modified Illumina Nextera adapters were used to construct ATAC libraries. ChIP-seq librariers were constructed using KAPA HyperPrep Kit. Single cell RNA-seq library preparation was performed using 10X Chromium v3.

value: naive esc

value: bxd


title: KO Colon rep 1 (ATAC-seq)


title: GV_A3

value: GV


title: Col-0_wildtype_rep4

value: wild type


title: Col-0_wildtype_rep1


title: GV_A1


title: WT Colon rep 2 (ATAC-seq)


title: Luminal#3

description:
Sample 81
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: WT Colon rep 1 (ATAC-seq)


title: IgG Control for WT Ileum

description: IgG

data_processing:
Reads (H3K4me1 and H3K27ac) were trimmed with trim_galore.
Paired-end reads were then mapped to the mm10 genome using Bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Only uniquely mapped reads were retained with samtools
Peaks were called from macs2 with pooled reads and with both replicate samples by merge broad and narrow peak files.
only peaks ±2 Kb outside TSSs were permitted, using ‘distal peaks’ as enhancer peaks
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Bigwig files for visualization of enhancer peaks

extract_protocol:
10x5 cells were attached to Concanavalin A conjugated magnetic beads, permeabilized, and incubated with histone enhancer maker antibodies at RT for 20 mins. pAG-MNase (1:1000) was added in digitonin buffer to bind with the antibodies. Finally, targeted chromatins were digested and released into the supernatant. DNA was purified with a MinElute purification kit.
Libraries were prepared using the ThruPLEX DNA-Seq Kit
Exactly followed the protocol from Takara bio (R400665). All final libraries were size selected (200-800 bp) by AMPure XP beads (Beckman, A63880) and loaded for sequencing.

treatment_protocol: EDTA stripped epithelium were dissociated into single cells with TrypLE. Dead cells were removed using a Dead Cell Removal Kit (Miltenyi Biotec).

tag: genotyping

value: Wild Type

tag: intestine part

value: Ileum


title: Luminal#4

description:
Sample 82
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: IgG Control for SATB2KO Colon

description: IgG


title: Luminal#1

description:
Sample 79
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: WT Jejunum rep 1

data_processing:
Adapter and low quality bases trimming (Q<20) using Trim Galore! with default parameters
Paired end alignment using STAR with defaut parameters
Generation of counts relative to genes using featureCounts with defaut paramets (unstranded mode)
Generation of normalized read counts and differential expression genes with normal shrinkage mode by DEseq2 package in Rstudio
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized gene counts table

value: Jejunum


title: Luminal#2

description:
Sample 80
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: WT Ileum rep 2 (ATAC-seq)


title: WT Ileum rep 1


title: IgG Control for WT Colon

description: IgG


title: TNBC#62

description:
Sample 78
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: TNBC


title: WT Ileum rep 1 (ATAC-seq)


title: Col-0_wildtype_rep2


title: H3K4Me1 in WT Ileum rep2


title: TNBC#61

description:
Sample 77
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: GV_A2

value: A

tag: cell type

value: Oocyte


title: TNBC#60

description:
Sample 76
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: TNBC#59

description:
Sample 75
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: H3K4Me1 in WT Ileum rep1


title: H3K4Me1 in SATB2KO Colon rep1


title: H3K4Me1 in SATB2KO Colon rep2


title: TNBC#58

description:
Sample 74
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: Bodenlos_mutant_rep3

value: Columbia (Col-0)


title: HB1.33.13

city: Chapel Hill

first: Xiaohua

last: Gao

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC

data_processing: RNA counts generated by nCounter were normalized using remove unwanted variation (RUV) and missing data was imputed using the R package impute.

source_name: Non–Muscle-Invasive Bladder Cancer

extract_protocol: All specimens from UNC and MSK were archival FFPE NMIBC tissue samples procured by transurethral resection of bladder tumor (TURBT) from treatment-naïve, newly diagnosed patients and were reviewed by a genitourinary pathologist (S.E. Wobker, H.A. Al-Ahmadie) to confirm grade, stage, and urothelial histology.

tag: study

value: MSK

value: Bladder Cancer

tag: hede

value: Luminal CIS-like (H2)

tag: mda

tag: lund

tag: immune

value: high

tag: Sex

value: M

tag: Stage

value: Ta

tag: grade

value: High

tag: cis

value: Yes

tag: recurrence

value: Recurrence

tag: bcg

value: BCG


title: HB1.33.15

tag: tissue

value: Luminal (H1)

value: Low

value: No

value: MMC


title: TNBC#57

description:
Sample 73
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

value: TNBC


title: H3K4Me1 in WT Colon rep1

value: Wild Type

value: Colon


title: H3K27Ac in WT Ileum rep2

value: Ileum


title: H3K27Ac in SATB2KO Colon rep2


title: TNBC#54

description:
Sample 70
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: H3K27Ac in WT Ileum rep1


title: TNBC#53

description:
Sample 69
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: HB1.33.10

value: MSK

value: Bladder Cancer

value: Luminal CIS-like (H2)


title: HB1.33.08

value: Luminal

value: Infiltrated

value: high

value: M


title: HB1.33.12

value: GenomicUnstable

value: High

value: Yes

value: BCG


title: TNBC#56

description:
Sample 72
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: TNBC#55

description:
Sample 71
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: HB1.33.09

value: No

value: Observation


title: HB1.33.07

value: F

value: Ta

value: Recurrence


title: H3K4Me1 in WT Colon rep2

value: Wild Type

value: Colon


title: H3K27Ac in WT Colon rep1


title: TNBC#52

description:
Sample 68
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

value: TNBC


title: TNBC#50

description:
Sample 66
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: H3K27Ac in SATB2KO Colon rep1


title: TNBC#51

description:
Sample 67
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: H3K27Ac in WT Colon rep2


title: HB1.33.02

value: MSK

value: Bladder Cancer

value: Luminal (H1)

value: Luminal

value: UrobasalA

value: low


title: HB1.31.12

value: Infiltrated

value: Low

value: MMC


title: HB1.31.11

value: high

value: M

value: No

value: BCG


title: KO Colon re-RNA-Seq rep 2

data_processing:
Adapter and low quality bases trimming (Q<20) using Trim Galore! with default parameters
Paired end alignment using STAR with defaut parameters
Generation of counts relative to genes using featureCounts with defaut paramets (unstranded mode)
Generation of normalized read counts and differential expression genes with normal shrinkage mode by DEseq2 package in Rstudio
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized gene counts table and RPKM table

extract_protocol:
Qiagen Mini RNA extract kit
NEBNext® Ultra™ RNA Library Prep Kit for Illumina, following manufacturer's protocol.
Library construction performed by Novogene.co.  Non-directional eukaryotic mRNA library

treatment_protocol: Epithilal tissues collected by EDTA method 30 days after Tamoxifen injection.

value: Satb2 Knock out


title: HB1.31.10

value: Luminal CIS-like (H2)

value: Basal

value: medium

value: F

value: High


title: KO Colon re-RNA-Seq rep 3

value: Colon


title: TNBC#48

description:
Sample 64
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

value: TNBC


title: HB1.31.08

value: MSK

value: Bladder Cancer

value: Luminal (H1)

value: GenomicUnstable

value: low

value: Ta

value: Observation


title: HB1.33.04

value: SCC-Like

value: No

value: Recurrence

value: BCG


title: TNBC#47

description:
Sample 63
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: TNBC#46

description:
Sample 62
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: TNBC#45

description:
Sample 61
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: KO Colon re-RNA-Seq rep 1

value: Satb2 Knock out


title: WT Colon re-RNA-Seq rep 3

value: Wild Type


title: WT Colon re-RNA-Seq rep 2


title: HB1.31.07

value: Early Basal-like (H3)

value: high

value: M

value: High

value: Yes


title: HB1.31.04

value: MSK

value: Bladder Cancer


title: HB1.33.01

value: Luminal CIS-like (H2)

value: medium


title: WT Colon re-RNA-Seq rep 1

value: Colon


title: TNBC#44

description:
Sample 60
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

value: TNBC


title: HB1.31.06

value: Luminal

value: UrobasalB

value: F

value: Ta

value: No


title: HB1.31.02

value: Luminal (H1)

value: Low

value: MMC


title: TNBC#49

description:
Sample 65
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: WT Ileum re-RNA-Seq rep 1

value: Wild Type

value: Ileum


title: TNBC#43

description:
Sample 59
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: WT Ileum re-RNA-Seq rep 3


title: WT Ileum re-RNA-Seq rep 2


title: TNBC#41

description:
Sample 57
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: TNBC#42

description:
Sample 58
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: HB1.11.24

value: UNC

value: Basal

value: GenomicUnstable

value: High


title: HB1.31.01

value: MSK

value: Bladder Cancer

value: Luminal CIS-like (H2)

value: SCC-Like

value: high

value: M

value: BCG


title: Mouse_Cas9_SATB2KO_3

source_name: 3D cultured mouse colonic organoids

growth_protocol: Mouse colonic organoids were cultured at P2. Lentivirus, contain control, Foxd2 or Satb2 sgRNA along with Cas9, infected organoids and selected with puromycin.

treatment_protocol: Mouse organoid were differentiated for 4 days. Materigel was removed by Cell recovery solution, pellet organoids were resuspended in RLT lysis buffer (Qigen Kit)

value: Satb2 sgRNA

value: Colonic Organoid


title: HB1.11.21

value: UrobasalB

value: low

value: No


title: HB1.11.23

value: UrobasalA

value: F


title: Mouse_Cas9_SATB2KO_2


title: HB1.11.22

value: UNC

value: Early Basal-like (H3)

value: Ta

value: Low

value: Yes


title: TNBC#39

description:
Sample 55
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

value: TNBC


title: TNBC#38

description:
Sample 54
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: Mouse_Cas9_FOXD2KO_3

value: Foxd2 sgRNA


title: Mouse_Cas9_SATB2KO_1


title: HB1.11.15

value: Bladder Cancer

value: high

value: M

value: High


title: TNBC#37

description:
Sample 53
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: HB1.11.14

value: Luminal CIS-like (H2)

value: GenomicUnstable


title: TNBC#36

description:
Sample 52
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: Mouse_Cas9_Ctrl_3

value: Ctrl sgRNA

value: Colonic Organoid


title: Mouse_Cas9_FOXD2KO_1


title: TNBC#35

description:
Sample 51
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: TNBC#40

description:
Sample 56
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: Mouse_Cas9_Ctrl_2


title: HB1.09.12

value: Basal

value: Infiltrated

value: No


title: HB1.09.10

value: UNC

value: Early Basal-like (H3)

value: SCC-Like


title: HB1.09.11


title: Human_colonic_organoid_H275

data_processing:
Adapter and low quality bases trimming (Q<20) using Trim Galore! with default parameters
Paired end alignment using STAR with defaut parameters
Generation of counts relative to genes using featureCounts with defaut paramets (unstranded mode)
Generation of normalized read counts and differential expression genes with normal shrinkage mode by DEseq2 package in Rstudio
Genome_build: Grch38
Supplementary_files_format_and_content: Normalized gene counts table

source_name: 3D cultured human organoids

growth_protocol: High wnt condition culture medium in materigel

treatment_protocol: Materigel was removed by Cell recovery solution, pellet organoids were resuspended in RLT lysis buffer (Qiagen Kit)

tag: cluture condition

value: High Wnt Medium

value: Colonic


title: TNBC#32

description:
Sample 48
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

tag: tumor type

value: TNBC


title: Human_colonic_organoid_H273


title: TNBC#33

description:
Sample 49
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: GFP_Postive_mouse_3

extract_protocol:
Qiagen Micro RNA extract kit
SmartSeq V4 kit along with Nextera XT kit, following manufacturer's protocol.
Library construction performed by Novogene.co.  Non-directional eukaryotic mRNA library

treatment_protocol: EDTA stripped epithelium were dissociated into single cells with TrypLE. Single cell suspensions were loaded in a SONY MA900 sortor for collection of both GFP+ and GFP- cells.

tag: genotyping

value: GFP Postive

value: Ileum


title: TNBC#34

description:
Sample 50
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: HB1.09.08

value: Bladder Cancer

value: Luminal (H1)

value: Luminal

value: low

value: M

value: Ta

value: Low

value: Yes


title: HB1.09.07

value: UNC

value: high

value: High

value: No


title: Human_colonic_organoid_H254

value: High Wnt Medium

tag: intestine part

value: Colonic


title: GFP_Postive_mouse_2


title: HB1.09.06

value: Early Basal-like (H3)

value: Basal

value: Infiltrated


title: TNBC#30

description:
Sample 46
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

value: TNBC


title: Human_colonic_organoid_H176


title: GFP_Postive_mouse_1

value: GFP Postive

value: Ileum


title: HB1.09.05

value: Bladder Cancer

value: Luminal (H1)

value: Luminal

value: UrobasalA

value: low

value: M


title: Mouse_Cas9_FOXD2KO_2

value: Foxd2 sgRNA

value: Colonic Organoid


title: Mouse_Cas9_Ctrl_1

value: Ctrl sgRNA


title: TNBC#31

description:
Sample 47
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: TNBC#29

description:
Sample 45
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: HB1.09.03

value: UNC

value: GenomicUnstable

value: Ta

value: Low

value: Yes


title: TNBC#28

description:
Sample 44
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

value: TNBC


title: Human_duodenal_organoid_H407

value: High Wnt Medium

value: Duodenal


title: GFP_Negative_mouse_3

value: GFP Negative

value: Ileum


title: GFP_Negative_mouse_2


title: TNBC#27

description:
Sample 43
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: GFP_Negative_mouse_1


title: HB1.09.01

value: Bladder Cancer

value: Early Basal-like (H3)

value: SCC-Like

value: high

value: High

value: No


title: Human_duodenal_organoid_H357


title: HB1.05.03

value: UNC

value: Luminal (H1)

value: Basal

value: UrobasalA

value: medium

value: M


title: TNBC#26

description:
Sample 42
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

value: TNBC


title: HB.13.08

value: UrobasalB

value: F


title: HB1.05.02

value: GenomicUnstable

value: Ta

value: Low

value: Yes


title: Human_duodenal_organoid_H424

value: High Wnt Medium

value: Duodenal


title: Human_89_Cas9_SATB2KO

source_name: 3D cultured human colonic organoids

growth_protocol: Human colonic organoids cultured from 5 different donors were knock out the SATB2 gene by CRISPR method. Organoids were differentiated for 3 days before collecting RNA.

value: SATB2 Knock out

value: Ascending Colon


title: BD-LMO-EB-10

molecule: other

source_name: pooled embryoid body samples

tag: cell type

value: spontaneously formed EBs from esc

tag: mouse strain

value: mixture of B6 and D2


title: Human_88_Cas9_SATB2KO


title: TNBC#23

description:
Sample 39
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: BXD161-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC146

value: esc transitioned to formative EpiLC

value: bxd


title: TNBC#24

description:
Sample 40
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: Human_87_Cas9_SATB2KO


title: BD-scRNA-EB-10


title: BXD154-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC145


title: HB.13.05

tag: study

value: UNC

value: Bladder Cancer

tag: hede

value: Luminal (H1)

value: Basal

value: medium

value: M


title: TNBC#22

description:
Sample 38
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

value: TNBC


title: Human_83_Cas9_SATB2KO


title: TNBC#25

description:
Sample 41
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: Human_duodenal_organoid_H389


title: BXD98 -ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC143


title: HB.13.03

value: Early Basal-like (H3)

tag: mda

tag: lund

value: GenomicUnstable

value: high

value: F

value: High

value: No


title: HB.13.04

value: UrobasalA

tag: immune

tag: Sex


title: HB.13.06

value: Luminal CIS-like (H2)

value: Luminal

tag: Stage

tag: grade


title: BXD95-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC142

value: esc transitioned to formative EpiLC

value: bxd


title: Human_80_Cas9_SATB2KO

value: SATB2 Knock out

value: Ascending Colon


title: Human_89_Cas9_Ctrl

value: Control


title: HB.13.01

value: UNC

value: Bladder Cancer

value: Basal

value: SCC-Like

value: M

tag: cis

tag: recurrence


title: BXD90-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC141


title: ELK3.118.21

value: MSK

tag: tissue

value: Early Basal-like (H3)

value: high

value: Recurrence

tag: bcg

value: BCG


title: Human_88_Cas9_Ctrl


title: BXD85-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC140


title: ELK3.118.20

value: Luminal CIS-like (H2)

value: UrobasalB

value: low

value: Ta

value: High

value: No

value: Observation


title: Human_87_Cas9_Ctrl

value: Control

value: Ascending Colon


title: Human_83_Cas9_Ctlr


title: BXD84-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC139

value: esc transitioned to formative EpiLC

value: bxd


title: TNBC#21

description:
Sample 37
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

tag: tumor type

value: TNBC


title: BXD68-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC137


title: BXD75-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC138


title: TNBC#16

description:
Sample 32
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: TNBC#15

description:
Sample 31
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: TNBC#17

description:
Sample 33
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: TNBC#18

description:
Sample 34
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: TNBC#20

description:
Sample 36
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: ELK3.118.17

value: MSK

value: Bladder Cancer

value: medium

value: M


title: BXD66-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC136


title: TNBC#14

description:
Sample 30
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: ELK3.118.16

value: Luminal (H1)

value: Basal

value: F

value: Recurrence


title: BXD65-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC135


title: C15_Severe_COVID_72hour_Dex_Treated_Male

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

description: Cells Recovered: 4,455 cells; Mean reads per cell: 58,700

data_processing:
All raw FASTQs reads were aligned to GRCh38 human reference using the STAR algorithm and quantified through the 10X Genomics cellranger v3.0.0 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat R toolkit for quality control and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low quality cells (<300 genes/cell and <20 cells/gene) were excluded from the overall experiment. Gene expression was log normalized to a scale factor of 10,000. To begin unsupervised clustering of cells, a selection of highly variable genes was obtained and used to calculate up to 50 principle components. Significance of principle components was determined using JackStraw analysis and by creating a PCElbowPlot. PCs 1 to 25 were used to run and plot a tSNE plot for all cells.
Genome_build: Homo_sapiens : GRCh38
Supplementary_files_format_and_content: Filtered feature - barcode HDF5 file output from CellRanger pipeline

source_name: 50% of total blood cells were mixed with 50% of enriched lymphocytes

extract_protocol:
Blood samples were treated with RBC lysis. 50% of total blood cells were mixed with 50% of enriched lymphycytes (STEM Cell Kit).
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v3.1 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 12 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using the NovaSeq S2 chip at a read depth of 32,000 reads/cell on an average of 4000 cells/sample.

value: peripheral blood with enriched lymphocytes

tag: clinical group

value: Severe COVID-ARDS

tag: dexamethasone status

tag: collection time

value: 72 hours

tag: time between dexamethasone administration to t1 blood draw

value: 55 hours

tag: library preparation

value: 10X Genomics Single Cell RNAseq v3.1

value: male


title: G5_Healthy_Cnt_Female

description: Cells Recovered: 2,959 cells; Mean reads per cell: 79,804

value: Healthy Control


title: C13_Severe_COVID_72hour_Dex_Treated

description: Cells Recovered: 2,589 cells; Mean reads per cell: 112,373

value: 216 hours


title: TNBC#19

description:
Sample 35
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

value: TNBC


title: TNBC#13

description:
Sample 29
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: ELK3.118.15

tag: study

value: MSK

value: Bladder Cancer

tag: hede

value: UrobasalA

value: Ta

value: Low

value: No

value: MMC


title: ELK3.118.14

value: Luminal CIS-like (H2)

tag: mda

value: Luminal

tag: lund

value: SCC-Like

value: medium

value: M

value: High

value: BCG


title: BXD62-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC134

tag: cell type

value: esc transitioned to formative EpiLC

tag: mouse strain

value: bxd


title: TNBC#12

description:
Sample 28
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

value: TNBC


title: Human_80_Cas9_Ctrl

tag: genotyping

value: Control

tag: intestine part

value: Ascending Colon


title: ELK3.118.11

value: MSK

value: Bladder Cancer

value: Luminal (H1)

tag: immune

value: low

tag: Sex

tag: Stage

value: Ta

tag: grade

tag: cis

tag: recurrence

value: Recurrence


title: B7_Severe_Bacterial_ARDS_ICU_72h_Male

description: Cells Recovered: 6,175 cells; Mean reads per cell: 39,018

tag: tissue

value: peripheral blood with enriched lymphocytes

tag: clinical group

value: Severe non-COVID ICU

tag: dexamethasone status

tag: collection time

value: 72 hours

value: 10X Genomics Single Cell RNAseq v3.1

value: male


title: ELK3.118.19

tag: study

tag: hede

value: Luminal CIS-like (H2)

value: Basal

value: UrobasalA

value: medium

value: M

value: High

value: No

tag: bcg

value: BCG


title: BXD55-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC133

tag: cell type

value: esc transitioned to formative EpiLC

value: bxd


title: TNBC#11

description:
Sample 27
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

tag: tumor type

value: TNBC


title: G4_Healthy_Cnt_Male

description: Cells Recovered: 2,819 cells; Mean reads per cell: 103,404

value: peripheral blood with enriched lymphocytes

value: Healthy Control

tag: library preparation


title: BXD49-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC132

tag: mouse strain


title: G3_Healthy_Cnt_Male

description: Cells Recovered: 3,552 cells; Mean reads per cell: 93,863


title: TNBC#9

description:
Sample 25
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: BXD45-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC131


title: ELK3.118.10

value: MSK

value: Bladder Cancer

value: Early Basal-like (H3)

tag: mda

tag: lund

value: SCC-Like

tag: immune

value: low

value: Recurrence


title: G2_Healthy_Cnt_Male

description: Cells Recovered: 4,675 cells; Mean reads per cell: 55,024

value: 10X Genomics Single Cell RNAseq v3.1


title: ELK3.118.09

value: Luminal CIS-like (H2)

value: UrobasalA

tag: Sex

value: M

tag: Stage

value: Ta

tag: grade


title: BXD44-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC130

value: esc transitioned to formative EpiLC


title: ELK3.118.07

tag: tissue

value: high

value: F

value: High

tag: cis

value: No

tag: recurrence

value: BCG


title: BXD125-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC120

value: bxd


title: BXD124-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC119


title: G1_Healthy_Cnt_Female

description: Cells Recovered: 6,499 cells; Mean reads per cell: 49,337

value: peripheral blood with enriched lymphocytes

tag: clinical group

value: Healthy Control

tag: dexamethasone status

tag: collection time


title: ELK3.118.08

tag: study

value: MSK

value: Bladder Cancer

tag: hede

value: Early Basal-like (H3)

tag: bcg


title: TNBC#6

description:
Sample 22
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

tag: tumor type

value: TNBC


title: TNBC#8

description:
Sample 24
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: TNBC#7

description:
Sample 23
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: ELK3.118.06

value: Luminal CIS-like (H2)

value: GenomicUnstable

value: medium


title: ELK3.118.05

value: Luminal (H1)

value: M

value: Ta

value: Yes


title: TNBC#5

description:
Sample 21
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: BXD87-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC117

tag: cell type

value: esc transitioned to formative EpiLC

tag: mouse strain


title: TNBC#10

description:
Sample 26
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: TNBC#4

description:
Sample 20
AllSamplesNormReadCount_raw_191004xlsx.xlsx


title: BXD99-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC118


title: ELK3.118.04

tag: mda

value: Basal

tag: lund

value: SCC-Like

value: High

value: No

value: BCG


title: ELK3.118.03

value: MSK

value: Bladder Cancer

value: UrobasalA

tag: immune

value: low

tag: Sex

value: Recurrence


title: BXD81-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC115

value: bxd


title: C11_Severe_COVID_72hour_Dex_Treated_Male

description: Cells Recovered: 3,145 cells; Mean reads per cell: 60,398

value: peripheral blood with enriched lymphocytes

value: Severe COVID-ARDS

value: 72 hours

tag: time between dexamethasone administration to t1 blood draw

value: 23 hours

tag: library preparation

value: 10X Genomics Single Cell RNAseq v3.1

value: male


title: C9_Severe_COVID_72hour_No_Dex_Female

description: Cells Recovered: 3,297 cells; Mean reads per cell: 79,784

tag: tissue

value: female


title: TNBC#2

description:
Sample 18
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

value: TNBC


title: ELK3.118.02

value: Luminal (H1)

value: Basal

value: SCC-Like

value: medium

value: M

tag: Stage

value: Ta

tag: grade

value: Low

tag: cis

value: No

tag: recurrence

value: MMC


title: E4_Severe_Bacterial_ARDS_ICU_7day_Female

description: Cells Recovered: 5,363 cells; Mean reads per cell: 44,524

value: peripheral blood with enriched lymphocytes

tag: clinical group

value: COVID Recovered

tag: dexamethasone status

tag: collection time


title: BXD86-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC116

value: esc transitioned to formative EpiLC

value: bxd


title: C10_Severe_COVID_72hour_Dex_Treated_Male

description: Cells Recovered: 1,587 cells; Mean reads per cell: 108,535

value: Severe COVID-ARDS

value: 72 hours

value: 39 hours

value: 10X Genomics Single Cell RNAseq v3.1

value: male


title: C12_Severe_COVID_72hour_Dex_Treated_Female

description: Cells Recovered: 5,659 cells; Mean reads per cell: 37,371

value: 13 hours

value: female


title: E3_Severe_Bacterial_ARDS_ICU_7day_Male

description: Cells Recovered: 6,353 cells; Mean reads per cell: 33,960


title: BXD74-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC113


title: C7_Severe_COVID_72hour_No_Dex_Male

description: Cells Recovered: 3,697 cells; Mean reads per cell: 61,564


title: BXD73-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC112


title: ELK3.117.17

tag: study

value: MSK

value: Bladder Cancer

tag: hede

value: Early Basal-like (H3)

value: medium

value: High

tag: bcg

value: BCG


title: C8_Severe_COVID_72hour_No_Dex_Female

description: Cells Recovered: 4,576 cells; Mean reads per cell: 67,846

value: peripheral blood with enriched lymphocytes


title: HMLE+SNL+CilA#2

description:
Sample 16
ALL_samples_formatted_gene_quart_0_NORM_table_170725.xls

source_name: HMLE

tag: cell line

value: HMLE

tag: cell type

value: Mammary gland epithelial cells

tag: e-m status

value: M-like

tag: treatment

value: Ciliobrevin A


title: HMLE+SNL+DMSO#2

description:
Sample 15
ALL_samples_formatted_gene_quart_0_NORM_table_170725.xls

value: DMSO


title: C6_Severe_COVID_72hour_No_Dex_Male

description: Cells Recovered: 3,059 cells; Mean reads per cell: 70,752

value: Severe COVID-ARDS

value: 72 hours

tag: Sex


title: TNBC#1

description:
Sample 17
AllSamplesNormReadCount_raw_191004xlsx.xlsx

value: Breast tumor

tag: tumor type

value: TNBC


title: BXD71-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC111

value: esc transitioned to formative EpiLC

tag: mouse strain

value: bxd


title: TNBC#3

description:
Sample 19
AllSamplesNormReadCount_raw_191004xlsx.xlsx

tag: tissue


title: HMLE+SNL+CilA#1

description:
Sample 14
ALL_samples_formatted_gene_quart_0_NORM_table_170725.xls


title: BXD69-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC110


title: ELK3.118.01

value: MSK

value: Bladder Cancer

value: Luminal CIS-like (H2)

tag: mda

value: Basal

tag: lund

value: UrobasalA

tag: immune

value: F

tag: Stage

value: Ta

tag: grade

value: No

value: Cystectomy


title: BXD83-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC97


title: ELK3.117.13

value: GenomicUnstable

value: low

value: M

value: High

tag: cis

tag: recurrence

value: Recurrence

value: BCG


title: C5_Severe_COVID_72hour_No_Dex_Male

description: Cells Recovered: 4,722 cells; Mean reads per cell: 51,303

value: peripheral blood with enriched lymphocytes

tag: clinical group

value: Severe COVID-ARDS

tag: dexamethasone status

tag: collection time

value: 72 hours

tag: library preparation

value: 10X Genomics Single Cell RNAseq v3.1

value: male


title: HMLE+SNL+DMSO#1

description:
Sample 13
ALL_samples_formatted_gene_quart_0_NORM_table_170725.xls

tag: cell line

value: HMLE

tag: cell type

value: Mammary gland epithelial cells

tag: e-m status

value: M-like

value: DMSO


title: C4_Severe_COVID_72hour_No_Dex_Male

description: Cells Recovered: 8,077 cells; Mean reads per cell: 50,283

tag: Sex


title: ELK3.117.11

tag: study

value: MSK

value: Bladder Cancer

tag: hede

value: Luminal (H1)

value: Luminal

value: Ta

value: No

tag: bcg


title: BXD67-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC95

value: esc transitioned to formative EpiLC

tag: mouse strain

value: bxd


title: ELK3.117.12

tag: tissue

tag: mda

tag: lund

value: UrobasalA

tag: immune

value: medium

value: M

value: Low

value: Recurrence

value: Observation


title: HMLER+shEcad+CilA#2

description:
Sample 12
ALL_samples_formatted_gene_quart_0_NORM_table_170725.xls

source_name: HMLER

value: HMLER

value: Mammary gland epithelial cells

tag: treatment

value: Ciliobrevin A


title: C3_Severe_COVID_72hour_No_Dex_Female

description: Cells Recovered: 8,320 cells; Mean reads per cell: 51,691

value: peripheral blood with enriched lymphocytes

tag: clinical group

value: Severe COVID-ARDS

value: 72 hours

value: 10X Genomics Single Cell RNAseq v3.1

value: female


title: HMLER+shEcad+DMSO#2

description:
Sample 11
ALL_samples_formatted_gene_quart_0_NORM_table_170725.xls

value: M-like

value: DMSO


title: C2_Severe_COVID_72hour_No_Dex_Male - Excluded from analysis

description:
Cells Recovered: 6,455 cells; Mean reads per cell: 59,924
Reason for exclusion from analysis: the patient did not have ARDS and suffered from a stroke.

tag: dexamethasone status

value: male


title: BXD64-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC92

value: esc transitioned to formative EpiLC

value: bxd


title: ELK3.117.16

value: MSK

value: Bladder Cancer

value: Luminal (H1)

value: Basal

value: GenomicUnstable

value: low

value: F

tag: Stage

value: Ta

tag: grade

value: High

tag: cis

value: No

tag: recurrence

value: BCG


title: ELK3.117.10

value: medium

value: M

value: Recurrence


title: C1_Severe_COVID_72hour_No_Dex_Male

description: Cells Recovered: 1,709 cells; Mean reads per cell: 133,895

value: peripheral blood with enriched lymphocytes

value: Severe COVID-ARDS

tag: collection time

value: 72 hours

tag: library preparation

value: 10X Genomics Single Cell RNAseq v3.1

value: male


title: HMLER+shEcad+CilA#1

description:
Sample 10
ALL_samples_formatted_gene_quart_0_NORM_table_170725.xls

tag: cell line

value: HMLER

tag: cell type

value: Mammary gland epithelial cells

tag: e-m status

value: M-like

value: Ciliobrevin A


title: BXD61-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC90

value: esc transitioned to formative EpiLC

tag: mouse strain

value: bxd


title: ELK3.117.08

tag: study

value: MSK

tag: tissue

value: Bladder Cancer

tag: hede

value: Luminal CIS-like (H2)

value: Luminal

value: UrobasalA

value: high

tag: Sex

value: Ta

value: High

tag: bcg


title: BXD63-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC91


title: B5_Severe_Bacterial_ARDS_72h_Male

description: Cells Recovered: 3,538 cells; Mean reads per cell: 76,928

value: peripheral blood with enriched lymphocytes

tag: clinical group

value: Severe non-COVID ICU

value: 72 hours

value: Male


title: HMLER+shEcad+DMSO#1

description:
Sample 9
ALL_samples_formatted_gene_quart_0_NORM_table_170725.xls

value: HMLER

value: Mammary gland epithelial cells

tag: treatment

value: DMSO


title: BXD48-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC89

value: esc transitioned to formative EpiLC


title: BXD43-ATAC-EpiLC

description:
epiatac_normcounts.tsv.gz
ATAC88

value: bxd


title: HMLE+SNL#2

description:
Sample 8
ALL_samples_formatted_gene_quart_0_NORM_table_170725.xls

value: HMLE

value: M-like

value: Untreated


title: ELK3.117.05

value: MSK

value: Bladder Cancer

value: Luminal CIS-like (H2)

tag: mda

value: Basal

tag: lund

value: GenomicUnstable

tag: immune

value: low

value: F

tag: Stage

value: No

value: Recurrence

value: BCG


title: B4_Severe_Bacterial_ARDS_ICU_72h_Female

description: Cells Recovered: 4,028 cells; Mean reads per cell: 56,986

value: peripheral blood with enriched lymphocytes

value: Severe non-COVID ICU

tag: dexamethasone status

tag: collection time

value: 72 hours

value: 10X Genomics Single Cell RNAseq v3.1

value: female


title: HMLE+CTL#2

description:
Sample 7
ALL_samples_formatted_gene_quart_0_NORM_table_170725.xls

tag: cell line

value: HMLE

value: Mammary gland epithelial cells

value: E-lke


title: ELK3.117.04

value: MSK

value: Bladder Cancer

value: Early Basal-like (H3)

value: high

value: Ta

tag: grade

value: High

tag: cis

value: Yes

tag: recurrence


title: A12_Severe_COVID_7day_Dex_Treated_Female

description: Cells Recovered: 4,258 cells; Mean reads per cell: 57,708

value: Severe COVID-ARDS

value: 7 days

tag: library preparation


title: ELK3.117.09

tag: study

tag: tissue

value: Basal

value: SCC-Like

value: M

value: BCG


title: DAC203-ATAC-EpiLC-rep3

description:
epiatac_normcounts.tsv.gz
ATAC78

tag: cell type

value: esc transitioned to formative EpiLC

tag: mouse strain


title: D55-ATAC-EpiLC-rep2

description:
epiatac_normcounts.tsv.gz
ATAC77


title: A10_Severe_COVID_7day_Dex_Treated_Male

description: Cells Recovered: 3,028 cells; Mean reads per cell: 91,807

value: peripheral blood with enriched lymphocytes

tag: clinical group

value: 10X Genomics Single Cell RNAseq v3.1

tag: Sex

value: male


title: ELK3.117.02

value: MSK

tag: hede

value: Luminal (H1)

tag: mda

value: low

value: No

value: Recurrence

tag: bcg

value: Observation


title: D29-ATAC-EpiLC-rep1

description:
epiatac_normcounts.tsv.gz
ATAC76


title: A6_Severe_COVID_7day_No_Dex_Male

description: Cells Recovered: 5,403 cells; Mean reads per cell: 99,729


title: HMLE+CTL#1

description:
Sample 5
ALL_samples_formatted_gene_quart_0_NORM_table_170725.xls

value: HMLE

value: Mammary gland epithelial cells

tag: e-m status

value: E-lke

tag: treatment

value: Untreated


title: B44-ATAC-EpiLC-rep2

description:
epiatac_normcounts.tsv.gz
ATAC74


title: ELK3.117.07

value: Bladder Cancer

value: Early Basal-like (H3)

tag: lund

tag: immune

value: high

tag: Stage

value: High

value: Yes


title: ELK3.117.01

value: Basal

value: GenomicUnstable

value: M

tag: grade

tag: cis

value: BCG


title: HMLER+shCTL#2

description:
Sample 3
ALL_samples_formatted_gene_quart_0_NORM_table_170725.xls

tag: cell line

value: HMLER


title: ELK3.115.06

tag: study

value: UNC

value: Luminal CIS-like (H2)

value: Infiltrated

value: Ta

value: No

tag: recurrence


title: B51-ATAC-EpiLC-rep3

description:
epiatac_normcounts.tsv.gz
ATAC75

tag: cell type

value: esc transitioned to formative EpiLC


title: ELK3.115.04

tag: tissue


title: A8_Severe_COVID_7day_No_Dex_Female

description: Cells Recovered: 4,004 cells; Mean reads per cell: 72,646

value: peripheral blood with enriched lymphocytes

tag: clinical group

value: Severe COVID-ARDS

tag: dexamethasone status

tag: collection time

value: 7 days

tag: library preparation

value: 10X Genomics Single Cell RNAseq v3.1

value: female


title: HMLER+shEcad#1

description:
Sample 2
ALL_samples_formatted_gene_quart_0_NORM_table_170725.xls

value: Mammary gland epithelial cells

value: M-like

value: Untreated


title: ELK3.115.05

value: Bladder Cancer

tag: hede

tag: mda

value: high

tag: Sex

value: M

value: High

tag: bcg


title: ELK3.115.01

value: UNC

value: Early Basal-like (H3)

value: Basal

tag: lund

value: GenomicUnstable

tag: immune

value: F

value: Low


title: A3_Severe_COVID_7day_No_Dex_Female

description: Cells Recovered: 3,223 cells; Mean reads per cell: 85,119

value: peripheral blood with enriched lymphocytes

value: Severe COVID-ARDS


title: znfA_HA_ctrl_2

status: Public on Oct 04 2021

city: Ribeirao Preto

first: Gustavo

middle: Henrique

last: Goldman

state: Sao Paulo

address: Avenida do Cafe

country: Brazil

institute: Sao Paulo University

description: ZnfA:3xHA control (untreated)

data_processing:
Raw data was aligned to A. fumigatus reference genome using Bowtie2 v2.3.5 tool. Initial 8bp of reads were clipped during mapping step using argument "bowtie2  --trim5 8 --local  "
Normalized the reads depth to 1 million mapped reads using "macs2 bdgopt " command from MACS2 v2.1.1
Converted bedGraph files to bigWig files using UCSC Kent Utils v369 tool "bedGraphToBigWig"
Genome_build: Aspergillus fumigatus Af293 reference genome from AspGD. Version s03-m05-r06
Supplementary_files_format_and_content: bigwig files were generated using UCSC Kent Utils v369; Scores represent normalized read depth to 1 million reads

organism: Aspergillus fumigatus

source_name: cultured colonies

growth_protocol: 1.108 conidia of CEA17, ∆znfA or znfA::HA strains were grown into 100 ml of liquid minimal media for 16 h at 37oC under shaking conditions

extract_protocol:
15mg of dry mycelia were lysed in 800 μl of FA lysis buffer for 3 min using a Bullet Blender (Next Advance), resuspended in 500 μl of FA lysis buffer and sonicated using the Qsonica Q800R at 100% amplitude with 10 seconds ON and 15 seconds OFF cycles for a total sonication time of 30 minutes. Approximately 2µg of the chromatin recovered immuno-precipitated using 2 ng of anti-RNA polymerase II (RNA-PolII) subunit antibody (clone 3E8, Millipore) or anti-HA (HA) antibody (F7, Santa Cruz Biotecnology) for 1.5 h, followed by incubation with ∼15 μl of packed Protein A Sepharose matrix (GE Healthcare) for another 1.5 h at room temperature. The Protein A beads were washed with increasing ionic strength solutions to remove the unspecific bindings. The DNA was eluted and de-crosslinked at 65 °C overnight.
Library preparation was carried out using NEBNext® Ultra II Library Prep kit (Illumina, cat. no. E7645L) according to manufacturer’s protocol.

treatment_protocol: 2 µg/ml of caspofungin was added or not (controls) for one hour.The DNA was crosslinked by adding 3 ml of formaldehyde 37% to the culture media with gentle rocking for 20 min at room temperature. To stop the reaction, glycine was added to a final concentration of 1M and incubated for additional 10 min. Mycelia were filtered using miracloth, washed twice with cold water, frozen with liquid nitrogen and dried.

tag: strain

value: ZnfA:3xHA [znfA::3xHA::pyrG, akuB (KU80)delta, MAT1-1]

tag: tagged protein

tag: chip antibody

value: anti-HA antibody (F7, Santa Cruz Biotecnology)

tag: treatment

value: untreated


title: ELK3.115.02

tag: study

value: SCC-Like

tag: Stage

tag: grade

tag: cis

value: No

tag: recurrence


title: HMLER+shCTL#1

description:
Sample 1
ALL_samples_formatted_gene_quart_0_NORM_table_170725.xls

tag: cell line

value: HMLER

tag: cell type

value: Mammary gland epithelial cells

tag: e-m status

value: E-lke

value: Untreated


title: HMLER+shEcad#2

description:
Sample 4
ALL_samples_formatted_gene_quart_0_NORM_table_170725.xls

value: M-like


title: B41-ATAC-EpiLC-rep1

description:
epiatac_normcounts.tsv.gz
ATAC73

value: esc transitioned to formative EpiLC

tag: mouse strain


title: HMLE+SNL#1

description:
Sample 6
ALL_samples_formatted_gene_quart_0_NORM_table_170725.xls

value: HMLE


title: A1_Severe_COVID_7day_No_Dex_Male

description: Cells Recovered: 7,768 cells; Mean reads per cell: 53,875

tag: tissue

tag: clinical group

tag: dexamethasone status

tag: collection time

value: 7 days

tag: library preparation

value: 10X Genomics Single Cell RNAseq v3.1

tag: Sex

value: male


title: A5_Severe_COVID_7day_No_Dex_Male

description: Cells Recovered: 6,192 cells; Mean reads per cell: 46,865

value: peripheral blood with enriched lymphocytes


title: CEA17_polII_ctrl_1

description: CEA17 control (untreated)

tag: strain

value: CEA17 [akuB (KU80)delta, MAT1-1]

tag: tagged protein

tag: chip antibody

value: anti-RNA polymerase II subunit antibodies (clone 3E8, Millipore)


title: del_znfA_polII_ctrl_1

description: ΔznfA control (untreated)

value: delta_znfA [delta_znfA::pyrG, akuB (KU80)delta, MAT1-1]

tag: treatment


title: znfA_HA_ctrl_1

description: ZnfA:3xHA control (untreated)

value: ZnfA:3xHA [znfA::3xHA::pyrG, akuB (KU80)delta, MAT1-1]

value: anti-HA antibody (F7, Santa Cruz Biotecnology)

value: untreated


title: CEA17_polII_ctrl_2

description: CEA17 control (untreated)


title: CEA17_polII_casp_1

description: CEA17 treated with caspofungin

value: caspofungin


title: znfA_HA_casp_1

description: ZnfA:3xHA treated with caspofungin


title: del_znfA_polII_casp_2

description: ΔznfA treated with caspofungin


title: znfA_HA_casp_2

description: ZnfA:3xHA treated with caspofungin


title: Control_2cell_3

city: Philadelphia

first: Natalie

middle: Alyce

last: Trigg

state: Pennsylvania

address: 421 Curie Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Raw sequence reads were filtered using BGI's SOAPnuke (v1.5.2) software with parameters -n 0.001 -I -q 0.4 -A 0.25 -Q 2 -G, to remove reads with adaptors and low quality reads.
Clean reads were mapped against Mus musculus genome (mm10) using HISAT2 (v2.0.4) with parameters --phred33 --sensitive--no-discordant --no-mixed -I 1 -X 1000
Diferentially expressed genes were detected with DEseq2 based on the negative binomial distribution
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files for RNA-seq contain geneID, FPKM and symbolID for each sample
Supplementary_files_format_and_content: excel files for embryo RNA-seq analysis contains symbol ID, geneID, FPKM values for group in triplicate, log2FC, Padj and Pvalue for all three comparisons of embryo groups

source_name: 2-cell embryo

extract_protocol:
Total RNA was extracted from purified mature cauda spermatozoa using a Direct-zol™ RNA MiniPrep Kit (Zymo Research Corporation, Irvine, CA, USA) according to manufacturer’s instructions. Total RNA was extracted from groups of 2-cell embryos using a Direct-zol RNA MicroPrep Kit (Zymo Research Corporation) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Ilumina protocols (sncRNA-seq) or Nugen trio kit RNA sample kit (RNA-seq).

treatment_protocol: Treatment involved the administration of 25mg/kg/bw/day of acrylamide or vehicle alone (PBS; control) for five conseuctive days via intraperitoneal injection. Sperm from acrylamide treated males was collected at two time points, either three (epididymal exposure, AAE) or twenty four (spermatocyte exposure, AAS) days following the final injection.

value: Swiss

value: control, PBS

value: 2-cell embryo

value: 2-cell embryo derived from IVF


title: CEA17_polII_casp_2

description: CEA17 treated with caspofungin


title: Control_2cell_1


title: AAS_2cell_3

value: acryamide, spermatocyte exposure


title: Control_2cell_2


title: AAS_2cell_1


title: AAS_2cell_2


title: del_znfA_polII_ctrl_2

description: ΔznfA control (untreated)


title: AAE_2cell_3

value: acrylamide, epididymal exposure


title: del_znfA_polII_casp_1

description: ΔznfA treated with caspofungin


title: endopleura, P147_1

first: Jie

last: Qiu

address: 100 Guilin Road

institute: Shanghai Normal Uiversity

description: replicate 1 for 147 DAP

data_processing:
The RNA-seq reads were aligned to J. regia v1.0 genome reference by Hisat2 v2.1.0.
StringTie v1.3.5 was adopted for quantification of expression.
Genome_build: J. regia v1.0 (available at http://www.xhhuanglab.cn/data/juglans.html or https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA002070)
Supplementary_files_format_and_content: endopleura_samples_FPKMs.txt

organism: Juglans regia

source_name: walnut endopleura

extract_protocol:
Total RNA was extracted using the universal total RNA kit (Tiangen, Beijing, China)
Libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Linzaoxiang

value: endopleura

tag: developmental stage

value: 147 days after pollination


title: endopleura, P147_3

description: replicate 3 for 147 DAP


title: endopleura, P147_2

description: replicate 2 for 147 DAP


title: endopleura, P119_3

description: replicate 3 for 119 DAP

value: 119 days after pollination


title: AAE_2cell_1


title: AAE_2cell_2


title: endopleura, P119_2

description: replicate 2 for 119 DAP


title: endopleura, P119_1

description: replicate 1 for 119 DAP


title: endopleura, P91_3

description: replicate 3 for 91 DAP

value: 91 days after pollination


title: D. sechellia HA 1

city: Middletown

first: Joseph

last: Coolon

state: CT

address: 52 Lawn Ave.

department: Biology

institute: Wesleyan University

data_processing:
FASTQC on each of the 6 raw fastq files
Bowtie2 alignment using the D. sechellia, D. simulans, and D. melanogaster reference genomes available at the time of analysis (Drosophila_sechellia.dsec_caf1.dna.toplevel.fa, Drosophila_simulans.ASM75419v3.dna.toplevel.fa, Drosophila_melanogaster.BDGP6.dna.toplevel.fa)
Cuffdiff for quantification and differential expression analysis using the D. sechellia, D. simulans, and D. melanogaster reference genomes available at the time of analysis (Drosophila_sechellia.dsec_caf1.dna.toplevel.fa, Drosophila_simulans.ASM75419v3.dna.toplevel.fa, Drosophila_melanogaster.BDGP6.dna.toplevel.fa) and gene files available at the time of analysis (Drosophila_sechellia.dsec_caf1.42.gff3, Drosophila_simulans.ASM75419v3.42.gff3, Drosophila_melanogaster.BDGP6.95.gff3) with geometric library normalization
Genome_build: Drosophila_sechellia.dsec_caf1.dna.toplevel.fa
Genome_build: Drosophila_simulans.ASM75419v3.dna.toplevel.fa
Genome_build: Drosophila_melanogaster.BDGP6.dna.toplevel.fa
Supplementary_files_format_and_content: Tab-delimited Cuffdiff output in text format

organism: Drosophila sechellia

source_name: Whole adults

growth_protocol: Flies were reared on cornmeal medium using a 16:8 light:dark cycle at 20 degrees Celsius

extract_protocol:
Total RNA was extracted from whole female adults using Promega SV Total RNA Isolation System
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Flies were exposed to 0.23% HA mixed into instant Drosophila food or control food for a period of 24 hours


title: endopleura, P91_1

description: replicate 1 for 91 DAP


title: endopleura, P63_3

description: replicate 3 for 63 DAP

value: 63 days after pollination


title: endopleura, P91_2

description: replicate 2 for 91 DAP


title: D. sechellia HA 2


title: endopleura, P63_2

description: replicate 2 for 63 DAP


title: D. sechellia Control 2


title: D. sechellia Control 1


title: endopleura, P35_2

description: replicate 2 for 35 DAP

value: 35 days after pollination


title: endopleura, P35_1

description: replicate 1 for 35 DAP


title: endopleura, P35_3

description: replicate 3 for 35 DAP


title: D. melanogaster  HA 1

description: Drum_et_al_2021_melanogaster_cuffdiff.txt

organism: Drosophila melanogaster


title: D. melanogaster  HA 2


title: D. melanogaster  HA 3


title: D. melanogaster  Control 3


title: D. sechellia Control 3


title: D. melanogaster Control 1


title: D. sechellia HA 3


title: endopleura, P63_1

description: replicate 1 for 63 DAP


title: SWHEL Irf4 Pool2

city: Davis

first: Monica

last: Britton

address: 451 Health Sciences Dr., Rm. 1300

department: Genome Center Service Cores

institute: University of California, Davis

data_processing:
10X Genomics Cell Ranger Software v. 3.1.0 was used to process fastq files to generate bam alignment files, and gene expression matrix files
Genome_build: mm10-3.0.0 (cellranger-refdata)
Supplementary_files_format_and_content: tab-separated text files (matrix output from CellRanger)

source_name: SWHEL Germinal Center B cell, day 10 after immunization

growth_protocol: SWHEL B cells were isolated from spleens of Irf4+/+ or Irf4+/- mice and the numbers of SWHEL B cells were quantified by flow cytometry based on Hen Egg Lysozyme (HEL) binding. Two mice were adoptively transferred with a 3:1 mixture of Irf4+/- to Irf4+/+ HEL-binding cells and injected intravenously with 2x108 sheep red blood cells conjugated to HEL2X protein in PBS. On day 10 of the response, CD45.1 expression was distinguished using CD45.1-biotin and TotalSeq-A0951 PE Streptavidin (Biolegend) and equivalent numbers of splenic CD45.1+CD45.2+ Irf4+/+ and CD45.2+ Irf4+/- FashiCD38lo HEL-specific donor B cells were bulk sorted into a single polypropylene 5mL tube containing PBS using an Astrios EQ high speed cell sorter. Viability was confirmed using a Countess prior to loading onto the 10X Genomics Chromium fluidic system using 10X Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3 for single cell RNA extraction and processing. Sequencing was performed on a NovaSeq instrument (Illumina).

extract_protocol:
10X Genomics Chromium fluidic system
10X Chromium Single Cell 3' GEM,

treatment_protocol: Mice were immunized with HEL-SRBC. Cells were collected by Fluoresence Activated Cell Sorting.

value: SWHEL HyHEL10 knock-in HEL+B220+FashiCD38lowCD45.1+CD45.2 and CD45.1- CD45.2+

tag: condition

value: Irf4+/+ and Irf4+/-


title: D. melanogaster  Control 2


title: SWHEL Irf4 Pool1

value: SWHEL HyHEL10 knock-in HEL+B220+FashiCD38lowCD45.1+ CD45.2+ and CD45.1- CD45.2+


title: sh15-LOX-2.2865-8

city: Nanchong

first: zhengmin

last: xu

address: Fujiang

department: Department of Pharmacy

institute: North Sichuan Medical College

data_processing:
Illumina sequencing workflow
Sequenced reads were mapped to GRCm38 whole genome using STAR v2.6.0 .
Transcripts Per Kilobase Million of library size (TPM) were calculated .
Genome_build: GRCm38
Supplementary_files_format_and_content: xlsx  files include TPM values for each Sample ...

growth_protocol: Ana-1-sh15-LOX-2 cells were generated by re-plating 6-well plate with complete RIPM 1640 medium

extract_protocol:
Ana-1-sh15-LOX-2 cells were harvested and transduced with shRNAs targeting either shAlox15b, fluorescence activated cell sorting of transduced cells were conducted 48h post-infection and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Control_3

city: Cincinnati

first: Brian

middle: Michael

last: Varisco

state: OH

address: 3333 Burnet Avenue, MLC 7006

department: Critical Care Medicine

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Novaseq 6000
STAR Alignment to mm10
DESeq2
ToppGene
Genome_build: mm10

source_name: Bulk Lung Tissue

extract_protocol: none provided by the submitter

value: lung

tag: age


title: TO_2


title: TO_3


title: TO_1


title: Control_2


title: sh15-LOX-2.1252-7

tag: cell type


title: sh15-LOX-2.1252-5


title: sh15-LOX-2.2865-10


title: TO_4


title: shRen-4

value: shRen


title: shRen-3


title: Control_4


title: Control_1


title: shRen-2


title: shRen-1