title: P1270RMC

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

data_processing:
Base calls were generated in real-time on the NovaSeq6000 instrument (RTA 3.1.5); (2) demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4); (3) sequence read and base quality are checked using the FASTX-toolkit (v0.0.13); (4) sequences are aligned to GRCh38 with reference transcriptome GENCODE release 29 using STAR (v2.6.1d
Briefly, 100bp paired-end reads were trimmed and aligned to the GENCODE reference transcriptome using STAR and reads were quantified using HT-Seq. Gene counts were generated for each sample and collated into a singular matrix for mixed-effects regression model in Dream.
Genome_build: GrCh38, GENCODE release 29
Supplementary_files_format_and_content: "Pheno.csv" contains sample metadata, "counts.csv" contains raw counts, "SummaryStats.csv" contains the number and percentages of reads mapped for each sample

source_name: Colon Organoid

growth_protocol: Normal 3D colon organoids included in the study were developed from biopsies of either distal or proximal colon using a modification of the method described by Sato et al. After isolation, colon crypts were embedded in Matrigel, and cell lines were established in growth media that included: advanced DMEM/F-12, 100U/ml penicillin, 100μg/ml streptomycin, 10mM Hepes, 1x N2, 1x B27, 2mM GlutaMAX, 1mM N-acetyl-cysteine, 10mM gastrin, 50% L-WRN conditioned media, 500nM A83-01, 10uM SB202190, 10mM nicotinamide, 50ng/ml EGF, 10μM Y27632. Colon organoids were grown and passaged as needed in 48-well culture plates.

extract_protocol:
For RNA isolation, media was gently removed and 300μl RNA lysis Solution RA1 + 6μl TCEP (Machery-Nagel; Cat No: 740902.50) was added to each well. The lysate was collected in a 1.5ml Eppendorf tube. Each tube was vortexed vigorously and placed on ice. Further steps were carried out according to manufacturer’s protocol of the Machel-Nagel RNA XS kit. RNA was checked for quality using the Agilent 4200 Tapestation. Samples with RIN > =8.5 were considered for library preparation and sequencing using the Illumina NovoSeq
Total RNA is normalized to 7.5ng/ul in a total volume of 50ul on the Perkin Elmer Janus Workstation (Perkin Elmer, Janus II).  Poly-A selection and cDNA synthesis are performed using the TruSeq Stranded mRNA kit as outlined by the manufacturer (Illumina, cat#RS-122-2103).  All steps are automated on the Perkin Elmer Sciclone NGSx Workstation to reduce batch to batch variability and to increase sample throughput.  Final RNASeq libraries are quantified using the Quant-it dsDNA High Sensitivity assay, and library insert size distribution is checked using a fragment analyzer (Advanced Analytical; kit ID DNF474).  Samples where adapter dimers constitute more than 4% of the electopherogram area are failed prior to sequencing.  Technical controls (K562,Thermo Fisher Scientific, cat# AM7832), are compared to expected results to ensure that batch to batch variability is minimized.  Successful libraries are normalized to 10nM for submission to sequencing.

treatment_protocol: MeIQx and PhIP were chosen to represent heterocyclic aromatic amines, BaP was chosen to represent polycyclic aromatic hydrocarbons, and NDEA was chosen to represent nitrosamines. Concentrations of each component in the carcinogen cocktail were: 5mM MelQx, 5mM PhIP, 1mM BaP, and 10mM NDEA. Three days prior to the initial exposure, organoids were passaged. One set of wells for each organoid line was exposed to the carcinogen cocktail, and a matching set of wells for each organoid line was exposed to a vehicle control (1.5mL DMSO and 2.52mL acetone per 10mL growth media).

value: Colon Organoid

value: F

value: Control

tag: pair

tag: age

value: R

tag: polyp

value: Yes


title: P1270RM

status: Public on Sep 22 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell type

tag: Sex

tag: treatment

value: Treated

tag: tissue


title: 4M K5VP16;Pparg Luminal Tumor Top rep2

city: New York

first: Cathy

last: Mendelsohn

state: NY

address: 1130 St. Nicholas Ave

department: Urology

institute: Columbia University

description:
DESeq2_kallisto_CT111_CT113_CT115_vs_CT126_CT128_CT132_CT140_CT143_counts_table_normalized
DESeq2_kallisto_CT111_CT113_CT115_vs_CT128_CT143_CT148_counts_table_normalized
DESeq2_kallisto_CT128_CT143_CT148_vs_CT129_CT144_CT149_counts_table_normalized

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0). We test for differentially expressed genes under various conditions using Sleuth, an R package designed to compute transcript and gene-level differential expression from kallisto abundance files.
Differential expression analysis was performed byreading kallisto counts files into R using the R packages tximport (v.1.10.1) and biomaRt (v.2.34.2),and running DESeq2 (v.1.18) to generate log fold change values and p-values between the twoexperimental groups. The heatmap and PCA plots were visualized after transforming the countsusing VST (variance stabilizing transformation)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-deliminated text files include TPM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Urothelium

extract_protocol:
5 month BBNK5VP16;Pparg and control bladders wereflash frozen sagitally in OCT and stored at-80°C. The specimen blocks were placed in the LeicaCM3050 cryostat chamber for 5-10min to temperature equilibrate. The tissue was sectioned at 5μm on Arcturus PEN Membrane glass slides (Applied Biosystems cat#LCM0522) and the slideswere immediately stored at-80°C. 1 hour prior to LCM, slides were removed from the-80°C andstained with Arcturus HistoGene Staining Solution (ThermoFisher Scientificcat#KIT0415)according to the manufacturer’s protocol. Tissue was then laser captured on a ZeissAxioObserver.Z1 inverted microscope into AdhesiveCap 200 opaque caps (Zeiss cat#000830-19).240μL of RLT Lysis Buffer (Qiagen cat#1015750) was then added to the capturedtissue
Cold active protease (CAP), was prepared and stored on ice (5mMCaCl2, Sigma cat#21115, 10mg/mL Bacillus Licheniformis protease, Sigma cat#P5459, 12.5U/mLDNAse, Sigma cat#4716728001). Mice were perfused with 20 mL of CAP using a small veininfusion set (Kawasumi cat#D3K2-23G) and two 10 mL syringes per mouse. Bladders weredissected and immediately put in a 60mm x 15mm petri dish (Fisherbrand cat#FB0875713A)containing CAP on ice for 10 min. The bladders were then transferred to HBSS media(ThermoFisher cat#14170-112) containing 1% Bovine Serum Albumin (Sigma cat#A2058) and0.1% glucose, where they were inverted and the urothelium was manually separated from thestroma. The cell suspension was then collected into a 1.5mL Eppendorf tube on ice and gentlytriturated until the cells were in a single cell suspension
The libraries were prepared using the SMART-Seq® v4Ultra® Low Input RNA Kit for Sequencing (TaKaRa) followed by Nextera XT (Illumina), bothaccording to manufacturer's instructions

treatment_protocol: N-butyl-N-(4-hydroxybutyl)-nitrosamine(BBN) (0.05%; Sigma cat#B8061  -1G) was administered in the water supply daily  for 3.5–24 weeks to induce bladder cancer. Mice were euthanized at 3.5 or 24 weeks

value: 5M BBN

tag: genotype

tag: disease state

value: Cancer


title: Adult10 Positive Interval1

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1.
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads.
Genome_build: GRCh38.96
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text file includes raw counts measurements.

source_name: whole blood

extract_protocol:
RNA extraction was performed automatically via the PAXgene Blood miRNA Kit and the QIAcube instrument (Qiagen) following the manufacturer’s protocol. RNA concentration and quality were assessed by using the Qubit instrument (Invitrogen) and the Agilent 2100 Bioanalyzer, respectively.
The Stranded Total RNA Ribo-Zero Plus kit from Illumina was used for the library preparation with 100 ng of total RNA as input. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM for clustering and sequenced on an Illumina HiSeq 4000 sequencer for a minimum of 30 million single-end 100 reads per sample.

value: whole blood

tag: sars-cov-2 infection

value: Positive

tag: age (years)

tag: time point

value: POS interval 1


title: P26_iPSC_ARID1B

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

library_source: genomic

data_processing:
ChIP-seq and ATAC-seq data were aligned to hg19 using BWA-mem
ATAC-seq and CHIP-seq peaks were called with MACS2
For input bigwig was made with Deeptools
Genome_build: Hg19
Supplementary_files_format_and_content: peak text files (ChIP-seq, ATAC-seq), Bigwig for input of Chip-seq

molecule: genomic DNA

growth_protocol: The iPSC lines were expanded in feeder-free, serum-free mTeSR™1 medium (STEMCELL Technologies). Cells were passaged ~1:10 at 80% confluency using ReLeSR (STEMCELL Technologies) and small cell clusters (50–200 cells) were subsequently plated on tissue culture dishes coated overnight with Geltrex™ LDEV-Free hESC-qualified Reduced Growth Factor Basement Membrane Matrix (Fisher-Scientific).

extract_protocol:
RNA-seq Cells were lysed in Tri-reagent (Zymo research) and total RNA was extracted using Quick-RNA Miniprep kit (Zymo research).
RNA libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® and NEBNext® UltraTM II DNA Library Prep Kit for Illumina® according to the manufacturer’s instructions (New England Biolabs). 1 μg of total RNA input was used for each library
ATAC-seq: 50000 cells per condition were processed as described in the original ATAC-seq protocol paper (Buenrostro et al 2013)
ChIP-seq: Barcoded libraries were made with NEB ULTRA II DNA Library Prep Kit for Illumina, and sequenced on Illumina NextSeq 500, producing 75bp SE reads.

treatment_protocol: Stem cells were differentiated in CNCC using a previously published protocol (Prescot et al.2015). iPSCs were treated with CNCC Derivation media: 1:1 Neurobasal medium/D-MEM F-12 medium,B-27 supplement, N-2 supplement, 20 ng/ml bFGF, 20 ng/ml EGF, 5 µg/ml bovine insulin and 1× Glutamax-I supplement. Three days after the appearance of the migratory CNCC, cells were detached using accutase and placed into geltrex-coated plates. The early migratory CNCCs were then transitioned to CNCC early maintenance media: 1:1 Neurobasal medium/D-MEM F-12 medium, B-27 supplement, N2 supplement , 20 ng/ml , 20 ng/ml EGF, 1 mg/ml bovine serum albumin and 1× Glutamax-I supplement

tag: antibodies

value: ARID1B Abcam ab57461


title: input_AKM26

first: Jun

last: Kim

address: 100 Washington Square East 1009 Silver Center

department: Biology

institute: NYU

data_processing:
Basecalls were performed using CASAVA version 1.8.
We aligned 50-75bp single-end ChIP-seq reads to C. elegans genome version WS220 using bowtie2 2.3.2 with default parameters (Langmead & Salzberg, 2012). Bam files were then sorted and indexed using samtools version 2.1.1 (Ramirez-Gonzalez, Bonnal, Caccamo, & Maclean, 2012). ChIP enrichment was normalized by either subtracting or dividing it by the input using DeepTools bamCompare using the following parameters: CPM, bin-size of 10bp, ignore duplicates, extend reads to 200bp, exclude chrM and remove blacklisted regions (Ho et al., 2014).For analyzing ChIP-seq data across the X chromosomal repeat block, --very sensitive option was used in bowtie2 and --minMappingQuality was removed for bamCompare.
MACS2 version 2.1.1 was used for fragment size prediction and for peak calling. For single replicate peak calling a minimum false discovery rate of .05 was used and for merged replicates a minimum false discovery rate of .01 was used to call significant peaks. Bedtools intersect was used to determine overlapping peaks between replicates and only those present in the majority of the replicates were chosen as final peaks.
Genome_build: WS220
Supplementary_files_format_and_content: ChIP to input CPM normalized ratio bigwig files for each replicate
Supplementary_files_format_and_content: ChIP to input CPM normalized ratio bigwig files averages
Supplementary_files_format_and_content: ChIP subtracted by input CPM normalized bigwig files for each replicate
Supplementary_files_format_and_content: ChIP subtracted by input CPM normalized bigwig files averages
Supplementary_files_format_and_content: Bed files containing ChIP-seq peaks called by MACS2

organism: Caenorhabditis elegans

source_name: whole worms

extract_protocol:
Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of embryo extract and 3-5 ug of antibody was used per ChIP. Half of the ChIP DNA were ligated to Illumina or home-made multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: developmental stage

value: mixed embryo

tag: chip antibody


title: P26_iPSC_ARID1A

value: ARID1A GeneTex GTX129433


title: P26_H3K27ac_CNCC9_rep1

value: H3K27ac Abcam ab4729


title: HCT116-J1-siCoilin-1-RiboMethSeq

city: New Orleans

first: Tina

middle: M

last: O'Grady

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

data_processing:
Adapter sequences were removed using Trimmomatic (0.36; LEADING:30 TRAILING:30 SLIDINGWINDOW:4:15 MINLEN:17 AVGQUAL:30). Only reads shorter than 90 nt were used for the analysis based on the length distribution of reads after adapter trimming.
Reads in the forward direction were mapped to an artificial genome containing ribosomal RNA sequences using bowtie2 (2.3.3.1; sensitive).
Mapped reads were analysed using the ‘R’ package ‘RNAmodR.RiboMethSeq’ and the Score C/RiboMethScore was used as a measurement for 2’-O methylation
Genome_build: hg19
Supplementary_files_format_and_content: .ends.csv: number of protected ends
Supplementary_files_format_and_content: .score.csv: scores per position

growth_protocol: Cell were maintained in DMEM + 10% heat-inactivated FBS, at 37°C with 5% CO2

extract_protocol:
TRIzol
150 ng RNA was used to construct RiboMethSeq libraries using the procedure of Marchand et al. (PMID 27302133)
RiboMethSeq

treatment_protocol: Cells were mock-transfected or transfected with 40 nM of non-targeting siRNA, siCoilin #1 or siCoilin #2 and maintained for 1, 2 or 3 days before RNA extraction.

tag: day


title: input_LAS35


title: P1269RMC

tag: pair


title: 4M K5VP16;Pparg Luminal Tumor Top rep1


title: P1259LM

value: M

tag: age

value: L


title: 4M Basal Tumor rep3

description:
DESeq2_kallisto_CT111_CT113_CT115_vs_CT126_CT128_CT132_CT140_CT143_counts_table_normalized
DESeq2_kallisto_CT111_CT113_CT115_vs_CT128_CT143_CT148_counts_table_normalized

value: wild type


title: P26_ARID1B_CNCC5


title: P19_iPSC_ATAC_rep2


title: P26_H3K27ac_CNCC7_rep1


title: input_LAS20


title: 4M Basal Tumor rep1


title: P1259LMC

value: Colon Organoid

tag: polyp


title: input_LAS36


title: 1M BBN Urothelium rep4

description: DESeq2_kallisto_CT103_CT104_CT105_CT106_vs_CT097_CT098_CT100_CT101_counts_table_normalized

value: 1M BBN

value: Pre-Disease


title: 4M Basal Tumor rep2


title: P1263RM

tag: cell type

value: F

value: R

value: Yes


title: P1263RMC

tag: Sex

value: Control


title: input_AKM27


title: P1269RM

tag: treatment

value: Treated


title: 1M BBN Urothelium rep3


title: P19_iPSC_ARID1B


title: P19_iPSC_ATAC_rep1


title: input_SE244


title: 1M BBN Urothelium rep2


title: input_LAS21


title: P1248RMC

tag: tissue

value: No


title: P1248RM


title: P1183RM


title: input_AKM193

tag: genotype

value: X;V


title: P19_H3K27ac_CNCC9_rep1


title: P19_H3K27ac_CNCC7_rep1


title: P19_iPSC_ARID1A


title: WT Urothelium rep4

value: untreated

tag: disease state

value: Homeostasis


title: input_AKM190


title: P1183RMC


title: WT Urothelium rep3


title: P19_ARID1B_CNCC5

value: ARID1B Abcam ab57461


title: P1102RM


title: P1102RMC


title: CTRL_LINE2_iPSC_ATAC_rep2

source_name: Control_Line_2 (GM23716 line)


title: input_AKM63


title: input_SE277

value: mixed embryo


title: input_AKM191


title: WT Urothelium rep1


title: CTRL_LINE2_iPSC_ARID1B


title: CTRL_LINE2_iPSC_ATAC_rep1


title: input_AKM113


title: 4D Mut Urotheliium rep4

description:
DESeq2_kallisto_CT063_CT065_CT066_CT067_vs_CT070_CT071_CT074_CT076_CT078_counts_table_normalized
DESeq2_kallisto_CT065_CT066_CT067_vs_CT071_CT074_CT078_counts_table_normalized


title: CTRL_LINE2_CNCC5_ARID1A

value: ARID1A GeneTex GTX129433


title: 4D Mut Urotheliium rep5


title: P1171LMC

value: M

value: L


title: P1145LM

value: Colon Organoid


title: 4D Mut Urotheliium rep3


title: input_AKM111


title: 4D Mut Urotheliium rep2


title: WT Urothelium rep2

value: wild type


title: input_AKM192


title: CTRL_LINE2_iPSC_ARID1A


title: P1145LMC


title: CTRL_LINE2_ARID1B_CNCC5


title: 4D Mut Urotheliium rep1

description: DESeq2_kallisto_CT063_CT065_CT066_CT067_vs_CT070_CT071_CT074_CT076_CT078_counts_table_normalized


title: CTRL_LINE1_iPSC_ATAC_rep2

source_name: Control_Line_1 (SV20 line)


title: P1116LM


title: input_AKM65


title: P1116LMC


title: CTRL_LINE1_iPSC_ATAC_rep1


title: DPY27-GFP_MK14_emb_AKM02_input_AKM26

description:
DPY-27GFP_MK14_emb_v9_avg_LAS14_LAS25_AKM02_inputsubt_v9.bw
DPY-27GFP_MK14_emb_v9_avg_LAS14_LAS25_AKM02_ratio_v9.bw

growth_protocol: Embryos were isolated by bleaching gravid adults grown on plates at 20C.

treatment_protocol: Embryos were treated with 2% formaldehyde for 30 minutes, washed with M9, and collected by centifugation and freezing at -80C until extract preparation.

tag: antibody target

tag: antibody antigen

value: Recombinant full length protein corresponding to GFP. Green fluorescent protein (GFP) from Aequorea victoria.

tag: matching input


title: P1114RM


title: 4D WT Urothelium rep3


title: input_AKM64


title: P1081RM


title: input_AKM112


title: DPY27-GFP_MK14_emb_LAS14_input_LAS20


title: 4D WT Urothelium rep2


title: CTRL_LINE1_iPSC_ARID1B

tag: antibodies


title: CTRL_LINE1_iPSC_ARID1A


title: P1171LM


title: DPY27-GFP_MK14_emb_LAS25_input_LAS35

tag: strain


title: DPY27-GFP_KB01_emb_LAS26_input_LAS36

description:
DPY-27GFP_KB01_emb_v9_avg_LAS15_LAS26_AKM04_inputsubt_v9.bw
DPY-27GFP_KB01_emb_v9_avg_LAS15_LAS26_AKM04_ratio_v9.bw

tag: developmental stage


title: CTRL_LINE1_H3K27ac_CNCC9_rep1

value: H3K27ac Abcam ab4729


title: CTRL_LINE1_H3K27ac_CNCC7_rep1


title: P1081RMC

value: R


title: 4D WT Urothelium rep1


title: DPY27-GFP_KB01_emb_AKM04_input_AKM27

tag: chip antibody


title: Spleen-WT_scRNA-seq

city: Shenzhen

first: Jiacheng

last: Bi

address: 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, P.R.China

country: China

institute: Shenzhen Institute of Advanced Technology

data_processing:
Raw FASTQ files were processed with Cell Ranger software (v1.3.1) for alignment, filtering, barcode counting and UMI counting.
Further analysis was performed with Seurat, by selecting highly variable genes using FindVariableGenes functions with default parameters, reduced the dimensionality by PCA, and clustered the cells using FindNeighbors and FindClusters.
We applied RunUMAP for visualization.
For comparison of splenic NK cells from NK-specific TIPE2 deficient mice or control mice, the data including 4270 NK cells from NK-specific TIPE2 deficient mice, and 4488 NK cells from control mice were merged for analysis.
Genome_build: mm10
Supplementary_files_format_and_content: processed seurat object files

source_name: Spleen

extract_protocol:
Mononuclear cells are isolated from the spleen following red blood cell lysis. NK cells are enriched by Magnetic Cell Sorting (Miltenyi) for library construction.
The 10x Genomics Chromium single-cell 3’ v4 kit and protocol was used to prepare the library.

value: Spleen

value: post natal week 6


title: Spleen-KO_scRNA-seq

value: Tnfaip8l2 flox/flox; NKp46iCre+


title: P1074RM

value: Treated

value: No


title: P1114RMC

value: Control


title: 4D WT Urothelium rep4

value: untreated

value: Homeostasis


title: P1074RMC


title: MV4-11_AC220_rep1

city: Gainesville

first: Petr

last: Starostik

state: Florida

institute: University of Florida

description: MV4-11 cells were treated with AC220 for 24 hours_rep1

data_processing:
Reads were aligned to human genome (UCSC hg19) using RNA-Seq aligner STAR (version 2.4.0) .
DESeq2 (version 1.1.0) was used to identify differentially expressed genes after filtering out genes with low reads, resulting in average 35 M reads per sample. Genes with adjusted P value < 0.05 and |log2 (fold change)|≥ 1 were considered as having a significantly altered expression.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: csv files showing the compared gene expression

source_name: peripheral blood

growth_protocol: All cells were cultured in RPMI media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin maintained at 5% CO2 and 37°C. Cells were expanded and frozen at low passage number and were passaged <20 times before thawing a fresh vial.

extract_protocol:
RNA was isolated using miRNeasy Mini Kit (Qiagen) with genomic DNA depletion
NEBNext® Poly (A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® were used for library preparation.   RNA-Seq 150bp paired-end libraries were sequenced on NextSeq 500 or NovaSeq6000 (Illumina, San Diego, CA).

treatment_protocol: Both MOLM14 and MV4-11 cells were treated with DMSO, 2 nM gilteritinib, 2 nM crenolanib or 2 nM AC220 for 24 hours. The RNA-seq experiments were performed triplicates.

tag: cell line

value: acute myeloid leukemia cell line

value: hemizygous FLT3-ITD mutation

value: AC220 for 24 hours


title: CTRL_LINE1_CNCC5_ARID1A

value: ARID1A GeneTex GTX129433


title: E13_MGE_multi_atac

city: Cambridge

first: Kathryn

last: Allaway

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Disease

institute: Broad Institute

description: ATAC from the same barcoded cells as Gene expression (RNA) sample

data_processing:
Raw multiomic data was processed using the Cell Ranger ARC v1.0.0 pipeline (10x Genomics). Reads were aligned to the GRCm38 (mm10) mus musculus genome.
Read filtering, alignment, and barcode counting were performed using cellranger-arc count.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv file containing cell barcodes  present in the corresponding expression matrix.
Supplementary_files_format_and_content: features.tsv file containing gene IDs and names present in the corresponding expression matrix.
Supplementary_files_format_and_content: matrix.mtx file is sparse matrix containing feature-barcode matrices.
Supplementary_files_format_and_content: The fragments.tsv.gz file is  a tabular file where each line represents a unique ATAC-seq fragment. Duplicate reads are collapsed into a single fragment record.
Supplementary_files_format_and_content: The per_barcode_metrics.csv file contains QC information associated with each barcode for cell-calling.

source_name: medial ganglionic eminence

extract_protocol:
E13.5 embryos were harvested from timed pregnant CD-1 mice  and the MGE was dissected in ice-cold Leibovitz's L-15 medium. Pooled tissue from several embryos were dissociated using the Neural Tissue Dissociation Kit (T) (Miltyeni Biotec, PN-130-093-231) according to the manufacturer’s instructions. Dissociated cells were then filtered through a 70 um filter, and centrifuged at 300xg for 5 min at 4C. Nuclei then were isolated as described in the 10x Genomics demonstrated protocols ‘Nuclei Isolation from Embryonic Mouse Brain for Single Cell Multiome ATAC + Gene Expression Sequencing ’ for fresh tissue for input to single-cell Multiome library preparation.
Single-cell multiomic (ATAC + Gene Expression) libraries were prepared on the 10x Genomics platform using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (PN-1000285), Chromium Next GEM Chip J Single Cell Kit (PN-1000230), Single Index Kit N Set A (Pn- PN-1000212) and Dual Index Kit TT Set A (PN-1000215) as instructed by the manufacturer. Libraries were sequenced using the Nova-Seq 100 cycle kit (ATAC library) and Next-Seq 150 cycle kit (Gene Expression library) (Illumina) by Broad Institute Genomic Services.
Dual scRNA/scATAC-seq

value: MGE cells


title: DPY-26_MK14_emb_LAS29_LAS35

description:
DPY-26_MK14_emb_v9_avg_LAS16_LAS29_AKM03_inputsubt_v9.bw
DPY-26_MK14_emb_v9_avg_LAS16_LAS29_AKM03_ratio_v9.bw

value: mixed embryo


title: DPY27-GFP_KB01_emb_LAS15_input_LAS21

value: Recombinant full length protein corresponding to GFP. Green fluorescent protein (GFP) from Aequorea victoria.


title: P2_Mef2c_cKO_Cortex_ATAC

data_processing:
Raw sequencing data were passed through the Cell Ranger ATAC pipeline (10X Genomics, v1.1.0). FASTQ files were generated from BCL files using cellranger-atac mkfastq.
Read filtering, alignment, and barcode counting were performed using cellranger-atac count.
Genome_build: mm10
Supplementary_files_format_and_content: The fragments.tsv.gz file contains  a tabular file where each line represents a unique ATAC-seq fragment. Duplicate reads are collapsed into a single fragment record.
Supplementary_files_format_and_content: The singlecell.csv file contains QC information associated with each barcode for cell-calling.

source_name: Whole Cortex

extract_protocol:
For embryonic timepoints, male hemizygous Dlx6a-Cre mice (Jax stock #008199) were crossed with female homozygous Ai9 or Ai14 mice (Rosa-LSL-tdtomato, Jax stock # 007909 or 007914) and checked daily for the presence of a vaginal plug, with the morning a plug was found being considered embryonic day 0. Embryos were screened using a fluorescent microscope for the presence of tdTomato. For embryonic timepoints using wild-type mice, timed pregnant CD-1 mice were used (Charles River #022). For postnatal timepoints, male hemizygous Dlx6a-Cre mice were crossed with female homozygous INTACT mice (flox-Sun1-eGFP, Jax stock #021039) to yield Dlx6a-Cre;INTACT offspring. For the P2 Mef2c conditional knockout (Mef2c_cKO), mice with the Lhx6-iCre (Jax stock #026555) and Mef2c-Fl/+ (Jax stock #025556) alleles were crossed with mice with the Mef2c-Fl/Fl and INTACT alleles to yield Lhx6-iCre;INTACT;Mef2c-Fl/Fl offspring. For embryonic timepoints, embryos were harvested from pregnant dams and relevant brain regions were dissected in ice-cold Leibovitz's L-15 medium. Pooled tissue from several embryos were dissociated using the Neural Tissue Dissociation Kit (T) (Miltyeni Biotec, PN-130-093-231) according to the manufacturer’s instructions. Dissociated cells were then filtered through a 70 um filter, centrifuged at 300xg for 5 min at 4C, and, where cell-sorting was required, resuspended in 1% BSA in PBS for cell sorting of tdTomato+ cells. For postnatal timepoints, brains were harvested, sectioned coronally on a stainless-steel mouse brain slicer (Zivic Instruments), and regions of interest were dissected in ice cold ACSF. Tissue was then transferred to a dounce homogenizer containing Lysis Buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, and 0.01% IGEPAL CA-630, 0.001% Digitonin). Tissue was homogenized with 10 strokes of pestle A, 10 strokes of pestle B, and incubated for 5 minutes on ice before being filtered through a 30 μm filter and centrifuged at 500xg for 10 minutes at 4C. The pellet was resuspended in 1% BSA in PBS for sorting for GFP+ nuclei. For all timepoints, cells or nuclei were sorted into Diluted Nuclei Buffer (10x Genomics) on a Sony SH800S cell sorter with a 100 µm chip.
scATAC-seq libraries were prepared using the Chromium Single Cell ATAC Solution v1 (10X Genomics). Libraries were sequenced using a Nova-Seq 100 cycle kit (Illumina).

value: cortical interneurons


title: MV4-11_Gilteritinib_rep1

description: MV4-11 cells were treated with gilteritinib for 24 hours_rep1

value: gilteritinib for 24 hours


title: P1157RM

value: Colon Organoid

value: M

tag: pair

value: R


title: P1229LM

value: F

value: Treated

tag: age

value: L


title: P1229LMC

value: Control

tag: polyp

value: No


title: MV4-11_DMSO_rep1

description: MV4-11 cells were treated with DMSO for 24 hours_rep1

tag: cell type

value: acute myeloid leukemia cell line

value: DMSO for 24 hours


title: P1157RMC

tag: Sex


title: MV4-11_Crenolanib_rep1

description: MV4-11 cells were treated with crenolanib for 24 hours_rep1

value: hemizygous FLT3-ITD mutation

tag: treatment

value: crenolanib for 24 hours


title: P10_Dlxpos_ALM_ATAC

source_name: Cortex - ALM


title: DPY-26_MK14_emb_AKM03_input_AKM26


title: P10_Dlxpos_V1_ATAC

source_name: Cortex - V1


title: DPY-26_KB01_emb_LAS30_input_LAS36

description:
DPY-26_KB01_emb_v9_avg_LAS17_LAS30_AKM05_inputsubt_v9.bw
DPY-26_KB01_emb_v9_avg_LAS17_LAS30_AKM05_ratio_v9.bw


title: DPY-26_MK14_emb_LAS16_input_LAS20


title: P28_Dlxpos_ALM_ATAC


title: P1174RMC

tag: tissue


title: P1174RM


title: DPY-26_KB01_emb_AKM05_AKM27

tag: genotype


title: MOLM14_Gilteritinib_rep2

description: MOLM14 cells were treated with gilteritinib for 24 hours_rep2

value: heterozygous FLT3-ITD mutation


title: P2_Dlxpos_Cortex_ATAC


title: DPY26_KB01_emb_LAS17_input_LAS21

value: mixed embryo


title: MOLM14_Crenolanib_rep2

description: MOLM14 cells were treated with crenolanib for 24 hours_rep2


title: E14_Cortex_ATAC

value: cortical cells


title: E18_Dlx6pos_Cortex_ATAC

value: cortical interneurons


title: P1119RM

value: Yes


title: P1119RMC

value: Colon Organoid


title: MOLM14_DMSO_rep2

description: MOLM14 cells were treated with DMSO for 24 hours_rep2


title: E14_CGE_2_ATAC

source_name: Caudal Ganglionic Eminence

value: pan-CGE cells


title: MOLM14_AC220_rep1

description: MOLM14 cells were treated with AC220 for 24 hours_rep1

value: AC220 for 24 hours


title: DPY27_sir2_emb_SE275_input_SE277


title: DPY27_set4xv_L3_AKM187_input_AKM193

value: X;V


title: E14_CGE_1_ATAC


title: DPY27_sir2_emb_SE242_input_SE244


title: MOLM14_AC220_rep2

description: MOLM14 cells were treated with AC220 for 24 hours_rep2


title: P1153RMC

value: M

value: R


title: MOLM14_Crenolanib_rep1

description: MOLM14 cells were treated with crenolanib for 24 hours_rep1


title: E13_MGE_Dlx6neg_2_ATAC

source_name: Medial Ganglionic Eminence

value: MGE progenitor cells


title: E13_MGE_Dlx6pos_2_ATAC

value: MGE postmitotic cells


title: P1170LM

value: F

value: Treated

value: L

value: No


title: P1153RM


title: MOLM14_Gilteritinib_rep1

description: MOLM14 cells were treated with gilteritinib for 24 hours_rep1

value: acute myeloid leukemia cell line

value: heterozygous FLT3-ITD mutation

value: gilteritinib for 24 hours


title: CTRL_LINE1_H3K27ac_iPSC

data_processing:
ChIP-seq and ATAC-seq data were aligned to hg19 using BWA-mem
RNA-seq data were aligned to hg19 using STARR-2pass
ATAC-seq peaks were called with MACS2.  CHIP-seq peaks for ARID1A/ARID1B/SOX2/NANOG were called with HOMER (findpeaks function). ChIP-seq peaks for H3K27ac were called using MACS2
RNA-seq gene expression was quantified using Kallisto
For input bigwig was made with Deeptools
Genome_build: Hg19
Supplementary_files_format_and_content: peak text files (ChIP-seq, ATAC-seq), Kallisto quantification (spreadsheet) for RNA-seq. Bigwig for input of Chip-seq

extract_protocol: Barcoded libraries were made with NEB ULTRA II DNA Library Prep Kit for Illumina, and sequenced on Illumina NextSeq 500, producing 75bp SE reads.

value: H3K27ac  Abcam ab4729


title: E13_MGE_Dlx6neg_1_ATAC


title: DPY27_set4xv_L3_AKM60_input_AKM63


title: DPY27_jmjxv_L3_AKM185_input_AKM191


title: P1155LM


title: DPY27_set4xv_L3_AKM108_input_AKM111


title: E13_MGE_Dlx6pos_1_ATAC


title: DPY27_set4xv_L3_AKM184_input_AKM190


title: P1155LMC

value: Control


title: DPY27_jmjxv_L3_AKM110_input_AKM113


title: MOLM14_DMSO_rep1

description: MOLM14 cells were treated with DMSO for 24 hours_rep1

value: DMSO for 24 hours


title: P26_RNA_CNCC5_rep2

source_name: Patient-26 line


title: P26_SOX2_CNCC5_rep1

value: SOX2  Active Motif 39843


title: P1122LM

value: Colon Organoid

value: Yes


title: P26_RNA_CNCC5_rep1


title: P28_V1_Dlxpos_RNA

data_processing:
Raw scRNA-seq data was processed using the standard CellRanger v3.0.0 pipeline (10x Genomics). FASTQ files were generated from BCL files using cellranger mkfastq.
Read filtering, alignment, and barcode counting were performed using cellranger count. For single-nuclei RNA-seq datasets, a custom pre-mRNA reference from the mm10 genome was generated allowing intronic sequences to be included in gene counts.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv files are tsv files containing cell barcodes  present in the corresponding expression matrix.
Supplementary_files_format_and_content: features.tsv files are tsv files containing gene IDs and names present in the corresponding expression matrix.
Supplementary_files_format_and_content: matrix.mtx files are sparse matrix files containing feature-barcode matrices.

extract_protocol:
For embryonic timepoints, male hemizygous Dlx6a-Cre mice (Jax stock #008199) were crossed with female homozygous Ai9 or Ai14 mice (Rosa-LSL-tdtomato, Jax stock # 007909 or 007914) and checked daily for the presence of a vaginal plug, with the morning a plug was found being considered embryonic day 0. Embryos were screened using a fluorescent microscope for the presence of tdTomato. Embryos were harvested from pregnant dams and relevant brain regions were dissected in ice-cold Leibovitz's L-15 medium. Pooled tissue from several embryos were dissociated using the Neural Tissue Dissociation Kit (T) (Miltyeni Biotec, PN-130-093-231) according to the manufacturer’s instructions. Dissociated cells were then filtered through a 70 um filter, centrifuged at 300xg for 5 min at 4C, and, where cell-sorting was required, resuspended in 1% BSA in PBS for cell sorting of tdTomato+ cells. Sorting was performed on a Sony SH800S cell sorter with a 100 µm chip.  For postnatal timepoints, male hemizygous Dlx6a-Cre mice were crossed with female homozygous INTACT mice. Nuclei for scRNA-seq were isolated as described previously with some modifications. Briefly, brains were harvested, sectioned coronally on a stainless steel mouse brain slicer (Zivic Instruments), and regions of interest were dissected in ice cold Homogenization Buffer (HB) (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, 1mM DTT, 0.15mM spermine, 0.5mM spermidine). Dissected tissue was then transferred to a 2 ml dounce homogenizer containing HB + 0.3% IGEPAL-CA630 + 0.2U/µl RNAse inhibitor and homogenized with 10 strokes of pestle A and 10 strokes of pestle B. Nuclei were then filtered through a 30 μm filter and centrifuged at 500xg for 5 minutes at 4C. The pellet was resuspended in 1% BSA + 0.2U/µl RNAse inhibitor in PBS and centrifuged again at 500xg for 5 minutes at 4C. The pellet was then again resuspended in 1% BSA + 0.2U/µl RNAse inhibitor in PBS an filtered through a 40 μm filter for sorting of GFP+ nuclei on a Sony SH800S cell sorter with a 100 µm chip. Nuclei were collected in 1% BSA + 0.2U/µl RNAse inhibitor for input to 10X Genomics scRNA-seq.  (flox-Sun1-eGFP, Jax stock #021039) to yield Dlx6a-Cre;INTACT offspring.
scRNA-seq libraries were prepared using the Chromium Single Cell 3' Solution v3 (10X Genomics). Libraries were sequenced using a Nova-Seq S2 100 cycle kit (Illumina).

value: cortical interneurons


title: DPY27_jmjxv_L3_AKM109_input_AKM112


title: P28_ALM_Dlxpos_RNA

source_name: Cortex-ALM


title: DPY27_N2xv_L3_AKM62_input_AKM65

value: X;V


title: P26_NANOG_CNCC5_rep1

value: NANOG  R&D Systems AF1997


title: P26_RNA_iPSC_rep1


title: P1082LMC


title: P10_V1_Dlxpos_RNA


title: DPY27_N2xv_L3_AKM61_input_AKM64


title: P26_CNCC5_H3K27ac_rep1


title: P10_ALM_Dlxpos_RNA


title: P1055LM


title: P2_Cortex_Mef2c_cKO_RNA

source_name: Cortex

value: MGE-derived cortical interneurons


title: P26_CNCC5_ARID1A

value: ARID1A GeneTex GTX129433


title: P26_ATAC_CNCC5_rep2


title: E13 MGE_Dlx6neg_RNA

value: MGE progenitor cells


title: P26_ATAC_CNCC5_rep1


title: P1236RM

source_name: Colon Organoid

value: M

value: Treated

value: R


title: E13 MGE_Dlx6pos_RNA

value: MGE postmitotic cells


title: DPY27_N2xv_L3_AKM186_input_AKM192


title: P1122LMC

value: F

value: L


title: single cell RNA_KO

city: San Antonio

first: Peng

last: Zhang

state: TX

address: 8403 Floyd Curl Drive

institute: UT Health San Antonio

data_processing:
Sequencing results from 10x Genomics were demultiplexed and converted to FASTQ format by cellranger  with a parameter of mkfastq
The FASTQ data was aligned to mouse reference genome and quantified using cellranger with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: h5 files of raw counts for all genes in each cell

source_name: Bone marrow

extract_protocol:
Cells were pooled from two different mice for each genotype
The libraries for each single cell sample were prepared using the Chromium Single Cell Gene Expression 3’ Version 3 Kit (10X Genomics) with the Chromium Controller.

treatment_protocol: BM c-Kit+ cells from Mx1Cre+ Ints11 flox/fox and WT littermates were purified by sorting 4 days after poly(I:C) injection

value: cKit+ bone marrow cells


title: P19_SOX2_CNCC5_rep1

source_name: Patient-19 line


title: P1236RMC

value: Control

value: No


title: P1082LM

value: Colon Organoid


title: P1170LMC


title: P1210RM


title: P19_RNA_CNCC5_rep2


title: P1210RMC


title: P1055LMC


title: 1M BBN Urothelium rep1

description: DESeq2_kallisto_CT103_CT104_CT105_CT106_vs_CT097_CT098_CT100_CT101_counts_table_normalized

source_name: Urothelium

value: 1M BBN

value: wild type

tag: disease state

value: Pre-Disease


title: P2_Cortex_Dlxpos_RNA

value: cortical interneurons


title: P1181LM

value: Yes


title: P1181LMC


title: P1218LM


title: HuRKO_DZ_MDM_19 [DZ_KO3]

city: Toulouse

first: Manuel

middle: D

last: Diaz-Munoz

address: CHU Purpan, BP3028

country: France

institute: INSERM

description:
processed data file:
DESeq2_Normalised_counts.csv
DESeq2_KO_DZ_WT_DZ.csv
lane5681_ACCACTGT_HuRKO_DZ_MDM_19
lane5719_CCACTGT_HuRKO_DZ_MDM_19
lane5718_CCACTGT_HuRKO_DZ_MDM_19

data_processing:
Sample demultiplexing (all samples were loaded in 3 different lane). Data from each sample was then merged.
Raw sequence reads were trimmed to remove both barcodes and adapters using Trim Galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (v0.4.4). Example: command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC lane2_L1_CGATGT_L002_R1.fastq.gz
Remaining sequences were and aligned to the mouse genome (GRCm38) with HiSat (v2.1.0)
Bam files were merged using SamTools (v1.8) and counted using FeatureCounts (v1.6.3), Mus_musculus.GRCm38.89.gtf annotation and default parameters.
R (v3.4.1) and DESeq2 (v1.24.0) was used for differential expression analysis. NA omit. Cut off: padj<0.05
Differential alternative splicing (AS) was analysed with rMATS (v4.0.2) after reprocessing sequencing data as follow.  Data trimmed with Flexbar (v3.0) and SamTools (v1.8) and remapped using STAR (v 2.5.1b), an splicing aware tool (Python (v2.7.2)). Read length was 101, parameter -paired and annotation  Mus_musculus.GRCm38.90.gtf. Differentially spliced events in pairwise comparison were considered significant if FDR<0.05 and have an absolute inclusion level of >0.1.
Genome_build: mm10
Supplementary_files_format_and_content: csv files. DESeq2 results, DESeq2 normalized gene counts, rMATs results.

source_name: DZ GC B cells

extract_protocol:
Total RNA from FACs-sorted DZ and LZ GC B cells was isolated using the Rneasy Microkit from Qiagen.
Libraries were generated using 10 ng of total RNA and the SureSelect Strand Specific RNA-Seq Library Preparation kit for the Illumina platform (Agilent)

tag: genotype/variation

value: HuRfl/fl AIDCre (HuR KO)

tag: cell type source

value: dark zone (DZ, CD19+ IgD- CD38- CD95+ CXCR4+ CD86- cells)

value: primary germinal centre B cells

tag: illumina index

value: ACCACTGT


title: WT_DZ_MDM_17 [DZ_WT3]

description:
processed data file:
DESeq2_Normalised_counts.csv
DESeq2_KO_DZ_WT_DZ.csv
lane5681_ATCATTCC_WT_DZ_MDM_17
lane5719_TCATTCC_WT_DZ_MDM_17
lane5718_TCATTCC_WT_DZ_MDM_17

value: HuRfl/fl (control WT)

value: ATCATTCC


title: D5_5h_3

city: West Lafayette

first: Vikki

last: Weake

state: Indiana

address: 175 S University St

department: Biochemistry

institute: Purdue University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence with Trimmomatic, then mapped to dm6 whole genome using Hisat2  with parameters -p 8 --rna-strandness FR -x
Counts were identified for each gene using Htseq-count (v0.11.1) with default parameters.
Genome_build: dm6
Supplementary_files_format_and_content: raw counts

organism: Drosophila melanogaster

source_name: Immunoenriched Drosphila photoreceptor nuclei

extract_protocol:
Bead bound nuclei were added to 300ul of Trizol. RNA was extracted using Direct-zol RNA microPrep (Zymo Research)
Universal Plus™ Total RNA-Seq (Tecan) with Drosophila specific rRNA depletion

value: immunoenriched R1-R6 photoreceptor nuclei

value: Five hours of blue light


title: D5_8h_3

value: Eight hours of blue light


title: D5_8h_2


title: D5_8h_1


title: single cell RNA_WT

value: cKit+ bone marrow cells


title: D5_5h_2


title: P1212RM

value: M

value: Treated

value: R


title: HuRKO_DZ_MDM_11 [DZ_KO1]

description:
processed data file:
DESeq2_Normalised_counts.csv
DESeq2_KO_DZ_WT_DZ.csv
lane5681_AAACATCG_HuRKO_DZ_MDM_11
lane5719_AACATCG_HuRKO_DZ_MDM_11
lane5718_AACATCG_HuRKO_DZ_MDM_11

value: AAACATCG


title: D5_5h_1


title: D5_3h_3

value: Three hours of blue light


title: P19_RNA_CNCC5_rep1


title: P19_CNCC5_HK27ac_Rep1

tag: antibodies

value: H3K27ac  Abcam ab4729


title: P19_ATAC_CNCC5_Rep2


title: P19_NANOG_CNCC5_rep1

value: NANOG  R&D Systems AF1997


title: P19_iPSC_RNA_rep1


title: P1212RMC

value: Colon Organoid

value: Control

value: Yes


title: P19_CNCC5_ARID1A

value: ARID1A GeneTex GTX129433


title: WT_DZ_MDM_13 [DZ_WT2]

description:
processed data file:
DESeq2_Normalised_counts.csv
DESeq2_KO_DZ_WT_DZ.csv
lane5681_CGAACTTA_WT_DZ_MDM_13
lane5719_GAACTTA_WT_DZ_MDM_13
lane5718_GAACTTA_WT_DZ_MDM_13

tag: strain

value: HuRfl/fl (control WT)

value: dark zone (DZ, CD19+ IgD- CD38- CD95+ CXCR4+ CD86- cells)

value: primary germinal centre B cells

value: CGAACTTA


title: HuRKO_DZ_MDM_15 [DZ_KO2]

description:
processed data file:
DESeq2_Normalised_counts.csv
DESeq2_KO_DZ_WT_DZ.csv
lane5681_AAGGACAC_HuRKO_DZ_MDM_15
lane5719_AGGACAC_HuRKO_DZ_MDM_15
lane5718_AGGACAC_HuRKO_DZ_MDM_15

value: HuRfl/fl AIDCre (HuR KO)

value: AAGGACAC


title: P1208LM

value: F

value: L

value: No


title: CTRL_LINE2_SOX2_CNCC5_rep1

source_name: Control_Line_2 (GM23716 line)

value: SOX2  Active Motif 39843


title: EVs replica 1

city: Valencia

first: Imelda

last: Ontoria-Oviedo

address: Avda Fernando Abril Martorell 106

department: Regeneration and Heart transplantation Unit

country: Spain

institute: Instituto de Investigación Sanitaria La Fe

data_processing:
quality of sequencing reads was analyzed using the software FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/] and MultiQC [Ewels, et al., Bioinformatics (2016)].
sequences were filtered and trimmed using the cutAdapt tool [http://journal.embnet.org/index.php/embnetjournal/article/view/200]
reads were aligned to the transcriptome (http://www.mirbase.org/) using Bowtie2 to obtain the matrix of counts
Supplementary_files_format_and_content: Matrix table with raw miRNA counts for every miRNA and every sample

source_name: Evs, rep1, miRNA-seq

extract_protocol:
Total RNA was isolated through the miRNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard strand specific total RNA seq Illumina protocols
smallRNA Tailor mix

value: dental pulp

value: mesenchymal stem cells

tag: sample type

value: EVs


title: P1208LMC

value: Colon Organoid


title: P19_ATAC_CNCC5_rep1


title: D5_3h_2

value: immunoenriched R1-R6 photoreceptor nuclei

value: Three hours of blue light


title: EVs replica 2

source_name: Evs, rep2, miRNA-seq


title: P1218LMC

value: Control


title: P1168RMC

value: M

value: R

value: Yes


title: D30_2

value: aged to D30


title: D5_3h_1


title: CTRL_LINE2_RNA_CNCC5_rep2


title: WT_DZ_MDM_9 [DZ_WT1]

description:
processed data file:
DESeq2_Normalised_counts.csv
DESeq2_KO_DZ_WT_DZ.csv
lane5681_AGCAGGAA_WT_DZ_MDM_9
lane5719_GCAGGAA_WT_DZ_MDM_9
lane5718_GCAGGAA_WT_DZ_MDM_9

value: HuRfl/fl (control WT)

value: dark zone (DZ, CD19+ IgD- CD38- CD95+ CXCR4+ CD86- cells)

value: primary germinal centre B cells

value: AGCAGGAA


title: CTRL_LINE2_RNA_CNCC5_rep1


title: Caco2 cells - Sample3_day 16

city: Nantes

first: Aurelie

last: Thedrez

address: 8 quai Moncousu

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 was used for base-calling
Raw fastq pairs matched the following criteria: the 16 bases of the first read correspond to 6 bases for a designed sample-specific barcode and 10 bases for a unique molecular identifier (UMI). The second read (104 bases) corresponds to the captured poly(A) RNAs sequence.
Primary analysis was performed using a snakemake pipeline  (https://bio.tools/3SRP) running with  Python: 3.6.6, bwa: 0.7.17-r1188, samtools: 1.9,  FastQC: v0.11.5, multiQC: 1.6, R: 3.5.1 (2018-07-02) , DESeq2: ‘1.20.0’ and limma: ‘3.36.5’. Briefly, samples demultiplexing was performed with a python script. Raw paired-end fastq files were transformed  into a single-end fastq file for each sample. Alignment on RefSeq human mRNA sequences (hg19) , available from the UCSC download site, was performed using bwa 0.7.17-r1188 with non-default parameter “-l 24”. Aligned reads were parsed and UMIs were counted for each gene in each sample to create an expression matrix containing the absolute abundance of mRNAs in all samples. Reads aligned on multiple genes or containing more than 3 mismatches with the reference were discarded. Samples containing less than 5000 genes or less than 200000 reads assigned were discarded.
Secondary analysis  was done using  R studio software  v1.2.5042.  First, genes with no read in at least 4 samples were filtered out from expression matrix. Filtered expression matrix was normalized, rLog transformed and differentially expressed genes (DEGs) at day 16 compared to day 8 were searched using DESeq2 package (v 1.28.1). Genes with a p value adjusted with Benjamini-Hochberg procedure < 0.05 and a fold change ≤ 0.6 or ≥ 0.6 were considered as DEGs.
Genome_build: hg19
Supplementary_files_format_and_content: NTS-192_CaCO2.unq.refseq.umi.txt - matrix table with raw gene counts for every gene and every sample
normalized_counts.txt - matrix table with normalized counts from Dseq2 analysis for every filtered gene and every sample
rld.txt - matrix table with regularized log transformed counts from DESeq2 analysis  for every filtered gene and every sample
Dseq2analysis.txt  - matrix table with results from differential gene expression analysis from DESeq2 library  for every filtered gene

source_name: enterocyte like-Caco2 cells

growth_protocol: Caco2 cells were maintained in TPP® tissue culture flasks in DMEM containing 4.5 g/L glucose and pyruvate (Gibco™) and supplemented with 10% decomplemented FBS (Corning™), 2 mM glutamine, 100 U/mL penicillin, and 100 mg/mL streptomycin. Once 80 % confluence was reached, cells were detached with trypsin-EDTA (Sigma Aldrich, Saint Quentin Fallavier, France) and diluted for the differentiation protocol. Caco2 cells were seeded at a density of 0.1 x 106 cells/0.33 cm2 onto polycarbonate micropore membranes (0.4 mm pore size) in Transwell® inserts (Costar, Cambridge, MA) and maintained for 8 or 16 days. Medium from apical and basolateral compartments was changed every two days. At day 8 and day 16 of culture in transwells, cells were finally detached with trypsin-EDTA 1X,  washed in cold PBS, flashed frozen on dry ice and stored at -80°C.

extract_protocol:
Total RNA were extracted from cell samples with the Nucleospin RNA II kit from Macherey Nagel (Hoerdt, France) following manufacturer’s instructions.
The libraries were prepared from 10 ng of total RNA in 4µl. The mRNA poly(A) tails were tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcriptase. Barcoded cDNAs from multiple samples were then pooled, amplified and tagmented using a transposon-fragmentation approach which enriches for 3′ends of cDNA : 100ng of full-lentgth cDNAs were used as input to the Nextera DNA Sample Prep kit (ref FC-121-1030, Illumina) which enriches for 3′ends of cDNA. Size library was controlled on 2200 Tape Station Sytem (Agilent Technologies). A library of 350–800 bp length was run on an Illumina HiSeq 2500 using a Hiseq Rapid SBS Kit v2-50 cycles (ref FC-402-4022) and a Hiseq Rapid PE Cluster Kit v2 (ref PE-402-4002) according to manufacturer’s protocol (Denaturing and Diluting Libraries for the HiSeq® and GAIIx, Part # 15050107 v03 protocol, Illumina).
3' DGE RNA-seq

value: Human Caco2 cell line

tag: differentiation stage

value: mature

tag: time

value: 16 days post-seeding in transwell


title: D15_3

value: aged to D15


title: Caco2 cells - Sample1_day 16

tag: cell line


title: Caco2 cells - Sample2_day 16


title: CTRL_LINE2_iPSC_RNA_rep1


title: CTRL_LINE2_NANOG_CNCC5_rep1

value: NANOG  R&D Systems AF1997


title: D30_1


title: input_CNCC5

source_name: Control_Line_1 (SV20 line)


title: P1151LMC

description: OUTLIER REMOVED IN PAPER

data_processing:
Base calls were generated in real-time on the NovaSeq6000 instrument (RTA 3.1.5); (2) demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4); (3) sequence read and base quality are checked using the FASTX-toolkit (v0.0.13); (4) sequences are aligned to GRCh38 with reference transcriptome GENCODE release 29 using STAR (v2.6.1d
Briefly, 100bp paired-end reads were trimmed and aligned to the GENCODE reference transcriptome using STAR and reads were quantified using HT-Seq. Gene counts were generated for each sample and collated into a singular matrix for mixed-effects regression model in Dream.
Genome_build: GrCh38, GENCODE release 29
Supplementary_files_format_and_content: "Pheno.csv" contains sample metadata, "counts.csv" contains raw counts, "SummaryStats.csv" contains the number and percentages of reads mapped for each sample

extract_protocol:
For RNA isolation, media was gently removed and 300μl RNA lysis Solution RA1 + 6μl TCEP (Machery-Nagel; Cat No: 740902.50) was added to each well. The lysate was collected in a 1.5ml Eppendorf tube. Each tube was vortexed vigorously and placed on ice. Further steps were carried out according to manufacturer’s protocol of the Machel-Nagel RNA XS kit. RNA was checked for quality using the Agilent 4200 Tapestation. Samples with RIN > =8.5 were considered for library preparation and sequencing using the Illumina NovoSeq
Total RNA is normalized to 7.5ng/ul in a total volume of 50ul on the Perkin Elmer Janus Workstation (Perkin Elmer, Janus II).  Poly-A selection and cDNA synthesis are performed using the TruSeq Stranded mRNA kit as outlined by the manufacturer (Illumina, cat#RS-122-2103).  All steps are automated on the Perkin Elmer Sciclone NGSx Workstation to reduce batch to batch variability and to increase sample throughput.  Final RNASeq libraries are quantified using the Quant-it dsDNA High Sensitivity assay, and library insert size distribution is checked using a fragment analyzer (Advanced Analytical; kit ID DNF474).  Samples where adapter dimers constitute more than 4% of the electopherogram area are failed prior to sequencing.  Technical controls (K562,Thermo Fisher Scientific, cat# AM7832), are compared to expected results to ensure that batch to batch variability is minimized.  Successful libraries are normalized to 10nM for submission to sequencing.

value: Colon Organoid

tag: pair

tag: age

value: L

value: No


title: P1152LM

tag: cell type

value: F

value: Treated

tag: polyp


title: Caco2 cells - Sample4_day 8

value: immature

value: 8 days post-seeding in transwell


title: D30_3

value: immunoenriched R1-R6 photoreceptor nuclei

tag: treatment

value: aged to D30


title: P1168RM

tag: Sex

value: M

tag: tissue

value: R

value: Yes


title: P1152LMC

value: Control


title: Caco2 cells -Sample4_day 16

value: Human Caco2 cell line

value: mature


title: CTRL_LINE2_ATAC_CNCC5_rep2


title: D15_1

value: aged to D15


title: D15_2


title: CTRL_LINE2_CNCC5_H3K27ac_rep1

value: H3K27ac  Abcam ab4729


title: Caco2 cells - Sample2_day 8


title: P1138LM

value: Colon Organoid


title: P1151LM

description: OUTLIER REMOVED IN PAPER

value: L


title: D5_3

value: aged to D5


title: P1138LMC

value: F

value: No


title: CTRL_LINE2_ATAC_CNCC5_rep1


title: Caco2 cells -Sample3_day 8

value: immature


title: P1128LM

value: Treated


title: D5_2

value: immunoenriched R1-R6 photoreceptor nuclei


title: D5_1


title: CTRL_LINE1_SOX2_CNCC5_rep1

value: SOX2  Active Motif 39843


title: DGM-13471_sm (Demographics_Drop-seq)

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
The position of the barcodes in R1 reads are bases 1 - 12 and the UMI is 13 - 20.
The clustering algorithm was performed using Seurat, a R package for single cell analysis.  Raw digital expression matrices that contain integer counts of number of transcripts for each gene in each cell were generated separately for each sequence.
All the genes expressed in at least 10 cells and all the cells with at least 200 detected genes were analyzed. Cells were filtered out that had unique gene counts over 104 or <200 and the % mitochondrial genes for each cell >0.25.
The total 11,702 cells for the 6 samples were merged together in a matrix and normalized by the total number of unique molecular identifiers (UMIs) per cells, multiplying by a scale factor (104) and then log transformed. Cell-cell variation was regressed out in gene expression driven by number of detected molecules per cell as well as the % mitochondrial gene content.
Principal component analysis (PCA) was assessed on the datasets from 11,702 cells. Highly variable genes wereidentified and used as input to the PCA to ensure robust identification of the primary structure in the data. Twenty statistically significant PCs were calculated. The PCs were used to project cells onto a two dimensional map using t-Distributed Stochastic Neighbor Embedding with perplexity parameter set to 30, allowing cells with simi-lar expression signature genes and similar PCs loading to localize near each other. The clustering algorithm, K-nearest neighbor (KNN) graph based on the euclidean distance in PCA space was constructed to iteratively group cells together. The resolution parameter in FindClusters function in Seurat package was set to 0.5. With this approach, 11 district clusters were identified.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text files include the Ensembl unique gene symbol and UMI values for all samples.

source_name: small airway epithelium brushing

extract_protocol:
Single cell capture, RNA extraction and cDNA preparation were performed on the Drop-seq system following the manufacturer’s protocol. In all cases, >80% of the cells were single cells, with 70 to 80% cell viability. Cell suspensions were filtered through a 35 µm nylon mesh cell strainer snap cap and loaded on an Influx™ cell sorter.  The single viable cells were sorted, resuspended in PBS/0.01% BSA and the sorted single cell suspension counted using Countess™ Automated Cell Counter adjusted to the final concentration of 100 to 120 cells/µl.
The single cell suspension, barcoded beads, and droplet generation oil were running through a microfluidics device to form droplets.  Droplets containing both a single cell and barcoded bead were immediately lysed and the released mRNA hybridized to the primers on the surface of the beads.
The single cell libraries were pooled and sequenced with paired end clustering and 101x2 cycles sequencing on the Illumina Hiseq 2500

tag: smoking status

value: smoker

tag: gender

value: M

tag: ethnicity

value: Hispanic

value: small airway epithelium (SAE)


title: Caco2 cells - Sample1_day 8

value: Human Caco2 cell line

value: 8 days post-seeding in transwell


title: DGM-00384_sm (Demographics_Drop-seq)

value: African


title: Infected 10d replicate 6

city: Utrecht

first: Arnar Kari

last: Sigurdarson Sandholt

address: Yalelaan 2

department: IRAS

country: Netherlands

institute: Utrecht University

description:
TF-2585-7
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

data_processing:
Base calling with Illumina basecaller
Reads were trimmed to get rid of adapters and low-quality parts with Trimmomatic v. 0.36, using the standard Illumina adapter library, SLIDINGWINDOW:4:20 and MINLEN:50
Reads were mapped to a merged version of the reference genomes (effectively mapping to both at the same time as if they were a single genome) with STAR v. 2.7.2b, using default settings
Reads mapping to features were counted using HTSeq v. 0.9.1, with strandedness set on reverse, i.e. -s reverse, and otherwise default settings
Read counts loaded into R and, using edgeR, each sample was CPM normalized with regards to library size and genes filtered out that had few/no reads mapping to them across samples
Genome_build: GRCg6a/Eth001
Supplementary_files_format_and_content: comma separated text files containing raw gene counts for each gene and sample, one for the chicken data and one for E. tenella
Supplementary_files_format_and_content: comma separated text files containing CPM normalized read counts for each organism, with low expressed genes across time points filtered out along with samples without chicken data, for the chicken dataset, and samples without E. tenella data, for the E. tenella dataset

organism: Gallus gallus

source_name: Chicken caecum

growth_protocol: A pure E. tenella Houghton strain (Chapman & Shirley, 2003) isolate was maintained by twice yearly passage in chickens and sporulated oocysts were prepared as according to earlier described protocols (Wattrang et al., 2016). For this study, 36 female Dekalb White Leghorn-type laying chickens (in Sweden marketed under the name Bovans Robust) purchased from a commercial hatchery were used. An additional group of 6 chickens from the same batch not included in the present study were infected in parallel and data for oocyst excretion and caecal lesion scoring of these chickens are presented herein. All chickens were reared from day-old under SPF-conditions at the National Veterinary Institute animal facilities and were group housed in cages in rooms under negative pressure ventilation.

extract_protocol:
At 1, 2, 3, 4 and 10 days after infection all chickens in one of the infected groups and one or two of the uninfected control chickens were killed by cervical dislocation and the two caeca were collected. Approximately 1 cm of the proximal part of the caeca containing the caecal tonsils was cut off. The remaining caeca were cut open longitudinally and caecal contents were thoroughly rinsed off with ice cold PBS. Ceacal tissues were cut into 0.5 cm wide strips and the tissue from the two caeca from each bird where pooled in 5 ml RNAlater (RNAlater® stabilization solution, Invitrogen, ThermoFisher Scientific). Samples in RNAlater were subsequently stored at 4°C for 24 h and thereafter stored at -20°C until RNA isolation.   Caecal tissues stored in RNAlater were thawed, removed from the solution and briefly air-dried. Tissues were then added to test tubes containing 10 ml of TRIzol and a 1:1 mixture of 2 mm ø and 0.5 mm ø XX beads (XX). Tubes were placed in a XX and shaken three times for 60 s at 6.2 m/s. After this treatment all mucosal tissue but not all connective tissue was dissolved. Samples were then stored at – 70°C until RNA isolation. For RNA isolation 1 ml from each of the caecal samples homogenised in TRIzol was used and RNA was extracted using chloroform according to the TRIzol manufacturer’s RNA isolation protocol. The Isolated RNA was subsequently treated with DNase (TURBO™ DNase, 2U/ul, ThermoFisher Scientific) according to the manufacturers protocol (Pub. No. MAN0001271) and further purified using reagents and the “RNA cleanup” protocol of the RNeasy Mini kit (Qiagen) protocol. RNA concentration and quality was then assessed using the Agilent RNA 6000 Nano kit on a 2100 Bioanalyzer Instrument (Agilent) and the RNA stored at -70°C until further analysis.
Sequencing libraries were prepared from 500ng total RNA using the TruSeq stranded mRNA library preparation kit (Cat# 20020594/5, Illumina Inc.) including polyA selection.The library preparation was performed according to the manufacturers’ protocol (#1000000040498). NovaSeq 6000 S4 flowcell, paired-end 150bp read length, v1 sequencing chemistry.

treatment_protocol: At 12 days of age blood samples were collected and analysed for maternal antibodies to E. tenella using an in house ELISA as previously described (Wattrang et al., 2016). Chickens were then allocated to six groups, n=6, with respect to an even distribution of maternal antibodies. One group was kept as uninfected controls and at 17 days of age chickens in the remaining five groups were inoculated orally with 1000 live E. tenella oocysts per bird. Viability of oocysts was estimated based on our experience that approx. 12 % of oocysts loose infectivity per month of storage in 2 % dichromate at 4 °C and oocysts used in this experiment had been stored for 3 months. From day 5 to day 9 (120 h to 218 h) after infection all faeces produced by chickens were collected and numbers of oocysts per gram faeces (OPG) were determined as described earlier (Wattrang et al., 2016; Wattrang et al., 2019).

tag: agent

value: Eimeria tenella

tag: infection status

value: Infected

tag: sample time post-infection [days]

tag: breed

value: Dekalb White Leghorn-type laying chicken/Bovans Robust

tag: e. tenella strain

value: Houghton


title: DGM-13434_sm (Demographics_Drop-seq)

value: Asian-Pacificlslander


title: CTRL_LINE1_RNA_CNCC5_rep2

extract_protocol:
RNA-seq Cells were lysed in Tri-reagent (Zymo research) and total RNA was extracted using Quick-RNA Miniprep kit (Zymo research).
RNA libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® and NEBNext® UltraTM II DNA Library Prep Kit for Illumina® according to the manufacturer’s instructions (New England Biolabs). 1 μg of total RNA input was used for each library
ATAC-seq: 50000 cells per condition were processed as described in the original ATAC-seq protocol paper (Buenrostro et al 2013)
ChIP-seq: Barcoded libraries were made with NEB ULTRA II DNA Library Prep Kit for Illumina, and sequenced on Illumina NextSeq 500, producing 75bp SE reads.


title: CTRL_LINE1_RNA_CNCC5_rep1


title: P1109RM

value: Colon Organoid

value: F

value: R

value: No


title: Infected 10d replicate 5

description:
TF-2585-36
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv


title: P1096RM

value: Treated


title: CTRL_LINE1_NANOG_CNCC5_rep1

tag: antibodies

value: NANOG  R&D Systems AF1997


title: CTRL_LINE1_CNCC5_H3K27ac_rep1

value: H3K27ac  Abcam ab4729


title: DGM-13451_sm (Demographics_Drop-seq)

value: nonsmoker


title: CTRL_LINE1_iPSC_RNA_rep1


title: P1109RMC

value: Control


title: Infected 10d replicate 4

description:
TF-2585-34
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv


title: P1096RMC

value: M


title: CTRL_LINE1_CNCC4_H3K27ac_rep1


title: DGM-13427_sm (Demographics_Drop-seq)

value: small airway epithelium (SAE)


title: DGM-13460_sm (Demographics_Drop-seq)

value: Caucasian


title: Infected 10d replicate 3

description:
TF-2585-31
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

value: Eimeria tenella


title: P1128LMC

value: L


title: Infected 10d replicate 2

description:
TF-2585-28
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

value: Infected

value: Dekalb White Leghorn-type laying chicken/Bovans Robust


title: CTRL_LINE1_CNCC3_H3K27ac_rep1


title: P1083RMC


title: 312

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

institute: East Carolina University

data_processing:
Kallisto for pseudo-alignment to Ensembl transcriptome of GRCm38
DESeq2 for differential gene expression
Genome_build: GRCm38
Supplementary_files_format_and_content: A .csv file including TPM of each gene for all 24 samples

source_name: skeletal muscle from NIA aging colony

growth_protocol: Mice were individually housed and feeded ad libitum.

extract_protocol:
Skeletal muscle was homogenized with QIAzol using MP Bio FastPrep-24 (5G) disruptor. Qiagen RNeasy Mini kit was used for the following RNA extraction
Illumina TruSeq Stranded Total RNA Library Prep Kit was used with polyA pull-down strategy

treatment_protocol: laparotomy was conducted in experimental mice.

value: soleus muscle

tag: strain

value: male

value: laparotomy

value: 24 months

tag: performance result

value: low functioning


title: 314

tag: age


title: Infected 4d replicate 6

description:
TC-2484-43
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

value: Houghton


title: CTRL_LINE1_CNCC2_H3K27ac_rep1

tag: cell type


title: CTRL_LINE1_ATAC_CNCC5_rep2.gz


title: Infected 4d replicate 4

description:
TC-2484-17
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv


title: siGI3_3

data_processing:
Reads were mapped to the human genome (hg19) using STAR v2.5.2a. Transcript abundance was quantified at the gene level with Ensembl 75 annotation using the STAR option --quantMode GeneCounts
Genome_build: hg19
Supplementary_files_format_and_content: STAR output tab-delimited ReadsPerGene.out.tab files, listing reads per gene. Column 4: sense reads. Column 3: antisense reads.

source_name: HeLa

growth_protocol: Cells were maintained at 37°C in the presence of 5% CO2 in Dulbecco's Modified Eagle's Medium supplemented with 10% heat-inactivated fetal bovine serum.

extract_protocol:
RNA was isolated using a Nucleospin kit from Macherey/Nagel.
Illumina TruSeq stranded mRNA protocol

treatment_protocol: Cells were plated 24h before transfection and then transfected using the Calcium phosphate method at a confluence of ~50% with either siDHX15 or siGl3 (control: targeting Gl3 luciferase) with a final concentration of 40 nm.

tag: sirna


title: Infected 4d replicate 5

description:
TC-2484-29
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv


title: 306

tag: treatment

value: high functioning


title: Infected 4d replicate 3

description:
TC-2484-14
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv


title: CTRL_LINE1_ATAC_CNCC5_rep1


title: siDHX15_1


title: 309

tag: Sex

value: control


title: ARID1B_WT_ATAC_CNCC5


title: 311

tag: tissue


title: 310


title: P1083RM

first: Matthew

last: Devall

value: Colon Organoid

value: Treated

tag: pair

value: R

tag: polyp

value: No


title: Infected 4d replicate 2

description:
TC-2484-1
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv


title: ARID1B_WT_CNCC5_H3K27ac_rep1

value: ARID1B  Abcam ab57461


title: ARID1B_KD_CNCC5_H3K27ac_rep1


title: Infected 10d replicate 1

description:
TF-2585-27
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

value: Eimeria tenella


title: siGI3_2


title: Infected 3d replicate 5

description:
TC-2483-4
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv


title: siGI3_1


title: 316


title: siDHX15_2


title: siDHX15_3


title: ARID1B_KD_ATAC_CNCC5


title: HCT116-siDHX15-2-RiboMethSeq

data_processing:
Library strategy: RiboMeth-seq
Adapter sequences were removed using Trimmomatic (0.36; LEADING:30 TRAILING:30 SLIDINGWINDOW:4:15 MINLEN:17 AVGQUAL:30). Only reads shorter than 90 nt were used for the analysis based on the length distribution of reads after adapter trimming.
Reads in the forward direction were mapped to an artificial genome containing ribosomal RNA sequences using bowtie2 (2.3.3.1; sensitive).
Mapped reads were analysed using the ‘R’ package ‘RNAmodR.RiboMethSeq’ and the Score C/RiboMethScore was used as a measurement for 2’-O methylation
Genome_build: hg19
Supplementary_files_format_and_content: .ends.csv: number of protected ends
Supplementary_files_format_and_content: .score.csv: scores per position

extract_protocol:
TRIzol
150 ng RNA was used to construct RiboMethSeq libraries using the procedure of Marchand et al. (PMID 27302133)

treatment_protocol: Cells were mock-transfected or transfected with 40 nM of non-targeting siRNA, siTFIP11 #1, siTFIP11 #2, siDHX15 #1 or siDHX15 #2 and maintained for 3 days before RNA extraction.

tag: cell line

tag: transfection


title: 307


title: 315


title: Infected 3d replicate 6

description:
TC-2483-8
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

tag: agent

tag: infection status


title: Infected 3d replicate 4

description:
TC-2483-32
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

tag: sample time post-infection [days]

tag: breed


title: HCT116-siDHX15-1-RiboMethSeq


title: ARID1B_CTRL_LINE1_rep3

tag: antibodies


title: 308

tag: strain


title: ARID1B_CTRL_LINE2_rep1

source_name: Control_Line_2 (SV20 line)


title: 302

tag: performance result


title: Infected 3d replicate 3

description:
TC-2483-30
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

tag: e. tenella strain


title: HCT116-siTFIP11-1-RiboMethSeq


title: HCT116-siTFIP11-2-RiboMethSeq


title: Infected 3d replicate 2

description:
TC-2483-3
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv


title: 303

tag: age


title: 530

value: 20 months


title: HCT116-Mock-RiboMethSeq

value: mock


title: HCT116-siCtr-RiboMethSeq

value: control siRNA


title: 528

value: soleus muscle


title: Adipocyte 12

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

country: Germany

institute: Quantitative Biology Center (QBiC)

data_processing:
The data was processed with the RNA-Seq Nextflow (release 1.3) workflow, which can be found at https://github.com/nf-core/rnaseq.
Quality control was done with FASTQC (v0.11.8) and adapter trimming was performed by Trim Galore (v0.5.0).
STAR (v2.6.1) was used for aligning the reads to the human reference genome GRCh38 Ensembl release 92.
Evaluation of the RNA-seq experiment was performed with RSeQC (v2.6.4).
Read counting on features (e.g. genes) was performed with featureCounts (v1.6.2)
For the differential expression analysis the raw read count table resulting from featureCounts was used and fed into the R package DESeq2 (v2.7.R).
Genome_build: GRCh38 Ensembl release 92
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample. Gene Names and Ensembl gene IDs are given as first two columns in this file

source_name: Human pancreatic fat

growth_protocol: Preadipocytes were isolated from human pancreatic fat pads obtained during pancreatic surgery. Connective tissue and blood vessels were manually removed. Tissue was minced with scissors and digested at 37°C for 30 min in a water bath shaker with collagenase solution containing: 1% (w/v) collagenase type I, 1.5% (w/v) BSA; (in mmol/L): 100 HEPES, 120 NaCl, 50 KCl, 1 CaCl2, 5 glucose. The suspension was passed through a 100 µm nylon filter and centrifuged at 12,000 rpm for 1 min, after which floating adipocytes were removed. Afterwards, the remaining suspenstion was passed through a 40 µm nylon filter. Cells were sedimented by centrifugation at 1,800 rpm for 7 min and resuspended in preadipocyte expansion medium. Exclusion of contamination by other cells types was performed by fluorescence activated cell sorting (FACS) analysis with antibodies against CD31 (endothelial cells) and CD68 (macrophages). Isolated preadipocytes were expanded in DMEM/Ham’s mixture F12 (1:1) containing: 2 mmol/L glutamine, 20% (v/v) FCS, 1% (v/v) chicken embryo extract (Sera Laboratories International), 1% (v/v) antibiotics, and 0.5 mg/ml amphotericin B. Adipocyte differentiation was achieved after 14 days cultivation in DMEM/Ham’s mixture F12 (1:1) containing (in mmol/L): 2 glutamine, 17 pantothenate, 1 biotin, 10 troglitazone, 0.001 insulin; (in mg/ml): 2 apotransferin, 0.5 amphotericin; 5% (v/v) FCS and 1% (v/v) antibiotics. During the first 7 days of differentiation, medium was supplemented with (in mmol/L): 0.5 3-isobutyl-1-methyl-xanthine, 1 cortisol and 50 indomethacin. During the second week of differentiation adipocytes were cultured in DMEM/Ham’s mixture F12 without supplements.

extract_protocol:
Aliquots of cultured preadipocytes and their respective in vitro differentiated adipocytes were used for RNA extraction using NucleoSpin® RNA (Macherey-Nagel). RNA integrity (RIN ≥ 9) was measured with Bioanalyzer 2100 (Agilent Technologies).
mRNA was isolated from 1 µg RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module. After fragmentation, the samples were subjected to the workflow for strand-specific RNASeq library preparation (Ultra Directional RNA Library Prep II, NEB) and 75 bp single read sequencing was performed on Illumina NextSeq500.

tag: sample id

tag: cell type

value: In vitro differentiated adipocytes

tag: individual

value: Donor #13

value: Male

value: 70 years old


title: Adipocyte 11

value: Donor #14

tag: Sex

value: 48 years old


title: Uninfected replicate 6

description:
TC-2482-9
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv

value: Uninfected

value: Dekalb White Leghorn-type laying chicken/Bovans Robust


title: siBCKDK#2 [MDA_574]

city: Saint John

first: Thomas

last: Pulinilkunnil

state: New Brunswick

address: 100 Tucker park road

department: Biochemistry and Molecular Biology

country: Canada

institute: Dalhousie University

data_processing:
Paired-end reads were pseudoaligned to the Homo sapiens GRCh38 transcriptome and quantified using kallisto
Transcripts were summarized to gene-level counts with the R package tximport and testing for differential gene expression was completed with DESeq2. Testing for differential expression was conducted only on genes with an average estimated count of greater than 0.3.
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene-level normalized counts for each sample as determined by tximport and DESeq2

source_name: Breast Cancer Cells

growth_protocol: MDA-MB-231 cells were grown in DMEM High Glucose + 9% FBS prior to treatment

extract_protocol:
RNA was extracted using the Qiagen RNeasy mini kit according to the manufacturer’s instructions
Libraries were constructed using NEBNext DNA Library Prep Master Mix Set for Illumina accroding to manufacturers instructions

treatment_protocol: Cells were transfected for 48 hours with 10 nM of either control siRNA or two separate siRNA's targeting BCKDK using 2µL Lipofectamine RNAiMAX per plate and diluted in Opti-MEM

tag: sirna


title: Infected 3d replicate 1

description:
TC-2483-18
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

value: Infected

value: Houghton


title: ARID1B_CTRL_LINE1_rep1

first: Marco

last: Trizzino


title: Infected 2d replicate 5

description:
TC-2482-5
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv


title: 511

tag: tissue

value: male

tag: treatment

value: laparotomy


title: Infected 2d replicate 4

description:
TC-2482-44
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

value: Eimeria tenella


title: siBCKDK#2 [MDA_573]


title: Adipocyte 10

value: Donor #17

value: 82 years old


title: 519

value: control

value: 20 months


title: Infected 2d replicate 6

description:
TC-2482-6
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv


title: siBCKDK#2 [MDA_572]


title: Adipocyte 6

value: In vitro differentiated adipocytes

value: Donor #7

value: 58 years old


title: siBCKDK#1 [MDA_570]


title: 512

value: soleus muscle


title: Adipocyte 8

value: Donor #6

value: Male

value: 55 years old


title: siBCKDK#1 [MDA_569]


title: Infected 1d replicate 4

description:
TC-2482-40
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

value: Dekalb White Leghorn-type laying chicken/Bovans Robust


title: siBCKDK#1 [MDA_571]


title: 513


title: Infected 1d replicate 6

description:
TC-2482-42
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

value: Infected


title: 38

value: 3 months


title: Infected 1d replicate 5

description:
TC-2482-41
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

value: Houghton


title: Adipocyte 4

value: Donor #4

value: 73 years old


title: Adipocyte 9

value: Donor #16

value: 64 years old


title: Uninfected replicate 5

description:
TC-2482-35
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv

value: Uninfected


title: 27

value: male

value: laparotomy


title: Infected 1d replicate 3

description:
TC-2482-26
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

value: Eimeria tenella


title: siCTRL [MDA_562]

value: siCTRL


title: 32

value: soleus muscle


title: Adipocyte 5

value: In vitro differentiated adipocytes

value: Donor #10

value: 77 years old


title: siCTRL [MDA_561]


title: 26

value: control


title: Adipocyte 2

value: Donor #1

value: Male

value: 59 years old


title: Adipocyte 1

value: Donor #3

value: 65 years old


title: Adipocyte 3

value: Donor #5

value: 70 years old


title: siCTRL [MDA_559]


title: siCTRL [MDA_560]


title: 29

value: 3 months


title: Uninfected replicate 4

description:
TC-2482-22
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv

value: Uninfected

value: Dekalb White Leghorn-type laying chicken/Bovans Robust


title: 24

value: male


title: Infected 1d replicate 2

description:
TC-2482-21
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

value: Eimeria tenella

value: Infected

value: Houghton


title: TVA1_Ven_2

city: Philadelphia

first: Ruitao

state: PA

address: 2930 Chestnut St. Apt. 1709-B

department: Pediatrics

institute: Children's Hospital of Philadelphia

data_processing:
Sequencing reads were aligned to the human genome hg38 reference sequence using STAR v3.5.3a
Gene-based FPKM and read count matrices were performed with Cufflinks v2.2.1 and featureCounts v1.3.6.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: leukemia cell line

growth_protocol: B-cell acute lymphoblastic leukemia cell lines MHHCALL4, MUTZ5, and TVA1 were grown in suspension typically 10-20 × 106 cells into a T75 flask in RPMI 1640 (31870-025; Invitrogen) supplemented with 20% FBS, 1% Glutamax, 1% HEPES, 1% NEAA, and 100 unit/ml penicillin/streptomycin (MUTZ5 and MHH-cALL4) or RPMI supplemented with 10% FBS and 100 unit/ml penicillin/streptomycin (TVA1).

extract_protocol:
Total RNA was extracted using RNeasy Micro kit (Qiagen) and treated with DNAse, and SMART-seq v4 Ultra Low input RNA kit (Takara) and Nextera XT DNA library prep kit (Illumina) were used for library preparation using 10 ng of total RNA as input.
RNA libraries were prepared for sequencing using standard Illumina protocols
Paired-end sequencing was performed using the Illumina NovaSeq 6000 platform with a 150-bp read length

treatment_protocol: Two technical replicates per condition were treated with 0.1% DMSO vehicle, venetoclax, tyrosine kinase inhibitor (ruxolitinib or dasatinib), or combination for 72 hours

value: B cell precursor leukemia


title: Preadipocyte 11

value: Isolated preadipocytes

value: Donor #14

value: 48 years old


title: Bp

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

data_processing:
reads demultiplexed and bcl to fastq conversion using cellranger mkfastq v2.1.0
reads aligned and counted using cellranger count v2.1.0
Samples were process in R v3.6.2 using Seurat V3.1.5
Genome_build: mm10
Supplementary_files_format_and_content: Genes.tsv, Barcodes.tsv, and Matrix.mtx (set of 3 files)

source_name: whole lung tissue

growth_protocol: Mice were inoculated intranasally with 1X10e5 CFU of Bordetella pertussis D420, 150 CFU of f. tularensis subspecies holarctica Live Vaccine Stratin (LVS), or PBS only.

extract_protocol:
Cells were processed through the 10X Genomics Chromium using the V2 3' selection beads
Libraries were constructed following the 10X Genomics V2 3' sequencing library prep kit

treatment_protocol: Samples of whole lung were digested via a combination and enzymatic digestion and manual disaccociation.

value: B. pertussis

value: whole lung


title: Preadipocyte 12

value: Donor #13

value: Male


title: Preadipocyte 9

value: Donor #16

value: 64 years old


title: Preadipocyte 10

value: Donor #17

value: 82 years old


title: Infected 2d replicate 2

description:
TC-2482-16
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

value: Dekalb White Leghorn-type laying chicken/Bovans Robust


title: Uninfected replicate 3

description:
TC-2482-19
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv

value: Uninfected


title: TVA1_Das_2


title: LVS

value: F. tularensis live vaccine strain


title: Infected 2d replicate 3

description:
TC-2482-24
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

value: Eimeria tenella

value: Infected


title: Uninfected replicate 2

description:
TC-2482-13
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv


title: TVA1_Das_1

value: B cell precursor leukemia


title: Knockout 3-C692

first: Mark

last: Kahn

address: 3400 Civic Center Blvd

department: Cardiovascular Institute

institute: University of Pennsylvania

data_processing:
Illumina software used for basecalling.
CellRanger used for raw processing
Seurat R-package used for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: A xlsx spreadsheet containing normalized expression of genes based on cluster and group

source_name: Kidney Cortex

extract_protocol:
Kidneys were perfused with HBSS and stored in RNALater at -80C. A 2 mm3 section of tissue was rinsed briefly with PBS and minced before adding 1 mL of lysis buffer containing 20 mM Tris-HCl (pH 8), 320 mM sucrose, 5 mM CaCl2, 3 mM MgAc2,  0.1 mM EDTA, and 0.1% TritonX-100. The tissue was initially dissociated by pipetting up and down ~10X with a p-1000 tip and then being passed through a 25G syringe ~10X. The tissue was incubated on ice for 10 minutes and then passed through a 30 µm CellTrics filter. Nuclei were pelleted by centrifugation (5 min, 500g, 4°C) and washed with PBS after removal of supernatant. Nuclei were pelleted again and resuspended in 1 mL of PBS containing 0.04% BSA and RNAse inhibitor (0.2u/µL) before counting by hemocytometer.  Nuclei were then diluted and prepared using the 10X Chromium System according to the manufacturer’s instructions (10X Genomics).
RNA libraries were prepared for sequencing using standard 10X Genomics and Illumina protocols

tag: genotype

value: Podocin-Cre Klf4 fl/fl

value: FVB/N

value: kidney cortex

tag: rna fraction

value: nuclear RNA

tag: preparation

value: Single nuclei


title: TVA1_Ven_1


title: TVA1_DMSO_2


title: Uninfected replicate 1

description:
SH-2259-20_S1
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv

tag: infection status

tag: sample time post-infection [days]


title: Preadipocyte 7

value: Isolated preadipocytes

value: Donor #9

value: 62 years old


title: TVA1_DMSO_1


title: Knockout 2-C691


title: Control 2-A152

value: Klf4 fl/fl


title: Preadipocyte 6

value: Donor #7

value: Male

value: 58 years old


title: Preadipocyte 5

value: Donor #10

value: 77 years old


title: Naive

value: whole lung


title: Preadipocyte 8

value: Donor #6

value: 55 years old


title: Control 3-A156


title: Infected 2d replicate 1

description:
SH-2259-12_S3
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

tag: agent

value: Eimeria tenella

value: Infected

tag: breed

value: Dekalb White Leghorn-type laying chicken/Bovans Robust

value: Houghton


title: RdsA depletion.rep.3

city: Cuernavaca

first: David

last: Romero

state: Morelos

address: Ave. Universidad 2001. Col. Chamilpa

department: Center for Genomic Sciences

country: Mexico

institute: National Autonomous University of Mexico

data_processing:
Quality checking of the sequencing raw reads was done using fastq.gzC
Sequence reads were trimmed using Trimmomatic v.0.36
Paired-end reads were mapped towards R. etli CFN42 reference genome (GenBank accession number GCF_000092045.1) using Bowtie2 aligner v.2.2.6.
Read counts were generated using featureCounts software. The hit counts were summarized using the gene_id for the total CDS features of the reference genome (6226), allowing MultiMapping and MultiOverlap reads
Determination of differential gene expression was done using NOISeqBIO with TMM normalization
Genome_build: R. etli CFN42 (GenBank accession number GCF_000092045.1)
Supplementary_files_format_and_content: Excel Workbook, a single file for all samples containing: the number of raw and normalized mean reads (TMM) for each gene, as well as, the differential expression analysis using NOISeqBIO

organism: Rhizobium etli

source_name: Bacterial cells

growth_protocol: Uninduced R. etli strains were grown in minimal medium Y (MMY) supplemented with biotin at 1 mg l-1. MMY at 30°C to an A620 of 0.5 (9 h)

extract_protocol:
Cell pellets (10^8 cells) were stored on RNAlater (Thermo-Fisher).  Further RNA extraction, rRNA depletion, was done by GeneWiz (South Plainfield, NJ, USA).
cDNA library was made according to the protolocols of GeneWiz (South Plainfield, NJ, USA).

value: rdsA gene under the control of a cumate inducible promoter

tag: depletion time

value: 9 hours

tag: strain


title: Infected 4d replicate 1

description:
SH-2259-11_S5
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv

tag: e. tenella strain


title: Infected 1d replicate 1

description:
SH-2259-15_S2
chicken_counts.csv
eimeria_counts.csv
chicken_counts_norm.csv
eimeria_counts_norm.csv


title: Preadipocyte 2

tag: sample id

value: Isolated preadipocytes

value: Donor #1

tag: age

value: 59 years old


title: TVA1_Combo_2

tag: cell type

value: B cell precursor leukemia


title: RdsA depletion.rep.1


title: Preadipocyte 1

tag: individual

value: Donor #3

tag: Sex

value: Male

value: 65 years old


title: jmjC rep2

city: New York

first: Jun

last: Kim

address: 100 Washington Square East 1009 Silver Center

institute: NYU

data_processing:
Basecalls were performed using CASAVA version 1.8.
Paired end Illumina sequence reads were mapped using default parameters of the juicer pipeline (version=1.5.7) as described in (Durand et al., 2016). For insertions and fusion strains, the reference genome was modified to match the genetic changes. For downstream analysis, inter_30.hic outputs from juicer pipeline were converted to h5 file to be used in HiCExplorer (version=3.5.1)(Ramirez et al., 2018; Wolff et al., 2018). Matrices of replicates were combined using hicSumMatrices. Each replicate or each summed matrix were normalized to match the depth of the smallest matrix in comparison using hicNormalize with the option --smallest. The replicate and summed matrices were ICE normalized using hicCorrectMatrix with the following parameters: --correction_method ICE, -t 1.7 5, --skipDiagonal, --chromosomes I II III IV V X or I II III IV XV for X-V fusion.
The insulation scores were computed using the 10kb-binned normalized matrix function hicFindTADs with the following parameters: --correctForMultipleTesting fdr, --minDepth 80000, --maxDepth 200000, --step 40000. For 2kb-binned normalized matrix, the following parameters were used: --correctForMultipleTesting fdr, --minDepth 16000, --maxDepth 40000, --step 8000. Output score.bedgraph was compared between experimental conditions. The bedgraph file was converted to bigwig using BedgraphToBigwig utility provided from UCSC website (Kent, Zweig, Barber, Hinrichs, & Karolchik, 2010).
Genome_build: WS220
Supplementary_files_format_and_content: hic matrix files
Supplementary_files_format_and_content: bedgraphs containing insulation scores

source_name: whole worms

extract_protocol:
Frozen embryos were then resuspended in and crosslinked with 2% formaldehyde in M9 for another 30 mins. The embryos were spun down at 6000g for 30 sec and washed once with 100mM Tris Cl pH 7.5 and twice with M9. The pellet was resuspended in Nuclei Buffer A (15 mM Tris–HCl pH 7.5, 2 mM MgCl2,0.34 M Sucrose,0.15 mM Spermine, 0.5 mM Spermidine, 1 mM DTT,0.5 mM PMSF (1X Calbiochem Protease Inhibitor cocktail I), 0.25% NP-40, 0.1% Triton X-100), centrifuged at 1000g for 5 minutes at 4C then resuspended in 1.5 mL Nuclei Buffer A. The embryos were then dounced 10X with a loose pestle and 10X with a tight pestle. The nuclei were separated from the cellular debris through spinning down the dounced material at 200G, then collecting the supernatant containing the nuclei into a separate tube. The pellet was resuspended in 1.5mL and the douncing process was repeated four times. Each individual supernatant containing nuclei was checked for quality by DAPI staining and those without debris were pooled and spun down at 1000G for 10 mins at 4C. Approximately 20 ul nuclei pellet were used to proceed to Arima Hi-C per the manufacturer’s instructions.
 Library preparation was performed using the KAPA Hyper Prep Kit using the protocol provided by Arima.

value: jmjC

tag: developmental stage

value: mixed embryo

value: dpy-21(y607 JmjC)


title: Preadipocyte 4

value: Donor #4

value: 73 years old


title: dpy21 rep2

description:
DJ62_DJ63_minus_DJ73_DJ74_10000_score.bedgraph
DJ62_DJ63_10000_score.bedgraph

extract_protocol:
Approximately 50 ul of the embryo pellet was resuspended and crosslinked a second time using the same conditions, washed once with 50 mL 100mM Tris-Cl pH 7.5 and twice with 50 mL M9. The embryo pellet was resuspended in 1 ml embryo buffer (110 mM NaCl, 40 mM KCl, 2 mM CaCl2, 2 mM MgCl2, 25 mM HEPES-KOH pH 7.5) containing 1 unit chitinase (Sigma) and digested approximately 15 minutes. Blastomeres were then washed with embryo buffer twice by spinning at 1000g 5 min. The pellet was resuspended in 1 mL Nuclei Buffer A (15 mM Tris   HCl pH 7.5, 2 mM MgCl2, 0.34 M Sucrose, 0.15 mM Spermine, 0.5 mM Spermidine, 1 mM DTT, 0.5 mM PMSF, 1xCalbiochem Protease Inhibitor cocktail I, 0.25% NP-40, 0.1% Triton X-100), centrifuged at 1000 g for 5 minutes at 4  C then resuspended in 1.5 mL Nuclei Buffer A. The embryos were dounced ten times with a loose pestle A and ten times with a tight pestle B. The cellular debris was spun down 1 min at 200 g. The supernatant containing nuclei was kept on ice. The pellet was resuspended in 1.5 mL Nuclei Buffer A, and the douncing process was repeated four times. Each supernatant was checked for absence of debris by DAPI stain and pooled and spun down at 1000 g for 10 mins at 4  C. Approximately ~20   l of nuclei were used to proceed to Arima Hi-C kit, which uses two 4-base cutters DpnII (^GATC) and HinfI (G^ANTC)
Library preparation was performed using the KAPA Hyper Prep Kit using the protocol provided by Arima.


title: MUTZ5_Ven_2


title: HeLa siTFIP11-3 snRNA-seq

city: New Orleans

first: Tina

last: O'Grady

address: 1430 Tulane Ave., SL79

institute: Tulane Health Sciences Center

data_processing:
Adapters, polyA tails and the 3 most 5' bases were removed, and reads < 15 nt removed, using Cutadapt
Transcript expression (GENCODE v. 26 annotation) was quantified using Salmon v0.8.2
Genome_build: hg19
Supplementary_files_format_and_content: transcript level quant.sf files from Salmon output

extract_protocol:
RNeasy Mini Kit (QIAGEN)
Clontech SMARTer smRNA-Seq Kit for Illumina protocol, with size selection to enrich for transcripts in the snRNA/snoRNA size range

treatment_protocol: Cells were plated 24h before transfection and then transfected using the Calcium phosphate method at a confluence of ~50% with either siTFIP11 or siGl3 (control: targeting Gl3 luciferase) with a final concentration of 40 nm.

tag: cell line

value: HeLa

tag: treatment


title: Lung-Normal 2

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren St, Rm# W250.Q

department: New Jersey Medical School,

institute: Rutgers Biomedical and Health Sciences, Rutgers The State University of NJ

data_processing:
QuantSeq FWD followed by Trimming using reference 'polyA' and "truseq"
The STAR aligner (Spliced Transcripts Alignment to a Reference) is Lexogens aligner of choice for aligning reads which were generated in a QuantSeq FWD or QuantSeq REV experiment.
The STAR aligner aligns reads directly to a reference genome via the utilization of a pre-generated index of the reference. A reference consists of sequences in FASTA format and, optionally, information about genes and transcripts stored in a GFF/GTF file. The reads are provided in a text file in the FASTQ format, which is then aligned by the tool. The results of this alignment are the aligned reads in SAM or binary SAM (BAM) format, optionally the unmapped reads in SAM/BAM format and mapping statistics for the alignment.
The STAR aligners key feature is that it maps reads directly against the reference in notable short time, with an inherent drawback of requiring a relatively high amount of short term memory (RAM) compared to other alignment tools to do so.
The differential expression analysis was performed with DESeq2. DESeq2 is a bioconducter package implemented in R.
Genome_build: OryCun2.0 (GCA_000003625.1)
Supplementary_files_format_and_content: There are 3 groups; Group-1=Singles; Group-2=Aggregates; Group-3=Normal  (control). Group 1 and 2 were normalized to Group-3 (control) and the resulting data (log2 fold change) is presented as Differentially Expressed list of entities in Excel file

organism: Oryctolagus cuniculus

source_name: Lung

extract_protocol:
Total RNA from uninfected, Mtb-SC and -AG-infected rabbit lungs was isolated (n=3) at T=24 h time point. Briefly, portions of frozen lung tissue (0.5g) were thawed in the presence of 10x volume (wt/vol) of TRIzol reagent (Life Technologies, Grand Island, NY, USA) and homogenized on ice. RNA was extracted once with 0.1 volumes (vol/vol) of BCP solution (Molecular Research Center Inc, Cincinnati, OH, USA), and the aqueous phase, containing RNA, was mixed with an equal volume of 70% ethanol and passed through mini spin columns from the Qiagen RNeasy Mini Kit (Qiagen Inc, Germantown, MD, USA).  Following on-column digestion of the contaminating DNA using DNaseI, RNA was purified and eluted with sterile water, as described by the manufacturer.  The quality and quantity of the purified RNA were assessed by using the NanoDrop instrument (NanoDrop products, Wilmington, DE, USA), and by Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).
RNAseq experiment was performed by Lexogen (Lexogen, Inc, Greenland, NH, USA). Briefly, cDNA libraries were prepared using Lexogen QuantSeq 3′mRNA-Seq Library Prep Kit FWD for Illumina using standard protocols (Lexogen, Inc, Greenland, NH, USA), and sequencing was performed with NextSeq protocol. The quality of sample reads, mapping, alignment, and read counts were performed using the STAR (Spliced Transcripts Alignment to a Reference) tool and the RSEQC quality control package (Lexogen, Inc, Greenland, NH, USA). After removing genes without reads in all the tested samples, data normalization and differential expression of transcripts were performed with DESeq2 from the Bioconductor package implemented in R. The output data were filtered to select transcripts with Benjamini-Hochberg adjusted p <0.05 using FASTQ/MULTIQC tool (Lexogen, Inc, Greenland, NH, USA).

value: NZW

tag: tissue

value: Lung

tag: time point

value: 24 hrs post infection


title: MUTZ5_Ven_1

last: Zhang


title: RdsA depletion.rep.2

tag: genotype

value: rdsA gene under the control of a cumate inducible promoter

value: 9 hours


title: Preadipocyte 3

value: Isolated preadipocytes

value: Donor #5

value: 70 years old


title: MUTZ5_DMSO_1

value: B cell precursor leukemia


title: Adipocyte 7

value: In vitro differentiated adipocytes

value: Donor #9

value: Male

value: 62 years old


title: jmjC rep1

value: jmjC

value: mixed embryo

value: dpy-21(y607 JmjC)


title: HeLa siGL3-2 snRNA-seq

value: HeLa


title: MUTZ5_Rux_2


title: dpy21 rep1