title: KO_0h_15

source_name: Selenow knock-out BMDMs, 0 h


title: Skin_DR_723_day_0

status: Public on Dec 28 2022

type: SRA

city: Vienna

first: Georg

last: Stary

address: Spitalgasse 23

department: Dermatology

country: Austria

institute: Medical University of Vienna

library_source: transcriptomic

data_processing:
Single-end reads were trimmed for low quality bases and removal of low-quality reads using ReadTools
Trimmed reads were mapped to the Homo sapiens genome (GRCh38.92 assembly) using STAR (v2.5.3a) mapper
The reads mapped in multiple genomic locations were eliminated by using Samtools (v1.4)
Read counts for features (exons) were generated using the featureCounts function from the Subread package (v 1.22.1)
Assembly: hg38
Supplementary files format and content: Raw gene count matrix was generated using featureCounts function from the Subread package (v 1.22.1) with Ensembl Known Gene models (version GRCh38.92) as reference annotations

molecule: total RNA

organism: Homo sapiens

source_name: Mononuclear phagocytes

growth_protocol: freshly isolated cells from human tissue

extract_protocol:
cells were isolated from skin biopsies using collagenase IV + mesh filtering
Illumina
SMART-seq

tag: tissue

value: Skin

tag: time

value: Day 0 (day of transplantation)


title: 103627-001-105

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
The reads obtained were aligned to human genome (GRCh38 build 99) using STAR aligner (version 020201) and mapped reads were counted using HTSeq-count (version 0.9.0)
Genome_build: GRCh38 build 99
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: non-lesion

extract_protocol:
Skin samples were derived from 4mm punch biopsies were embedded in Tissue-Tek® and directly snap-frozen in liquid nitrogen, until further processing. Sections were cut (20µm) and dissolved and lysed in RLT plus (+BME) buffer. Samples were vortexed and homogenized by pipets before RNA isolation. RNA isolation was performed using a Qiagen Universal Kit, according to manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: diagnosis

value: Psoriatic Arthritis

tag: age

tag: Sex

value: Male


title: KO_0h_13

city: State College

first: Sougat

last: Misra

state: PA

address: 107 Shortlidge Road

department: Veterinary and Biomedical Sciences

country: USA

institute: The Pennsylvania State University

data_processing:
The data was mapped to the reference genome using Hisat2.
Reads mapped to the genes were counted using featureCounts
Normalization of raw gene counts and differential expresssion analysis were performed using DESeq2 package in R
Assembly: Mus_musculus.GRCm38 genome build
Supplementary files format and content: Tab delimited file with gene-level raw read counts

organism: Mus musculus

extract_protocol:
RNeasy Plus Mini Kit (Qiagen) with on column DNase treatment
100 base pair paired end reads were sequenced.

value: Bone marrow-originated

tag: cell type

value: bone marrow-derived macrophages

tag: genotype

value: Selenow knock-out

tag: treatment


title: Skin_DR_728_day_0


title: E13.5_Dnd1-cKO_rep3

type: RNA

city: Yokohama

first: Atsuki

last: Imai

state: Japan

country: Japan

institute: Yokohama National University

hyb_protocol: Cy3-labelled cDNA was fragmented, hybridized to SurePrint G3 Mouse GE 8x60K v2 Microarray (Agilent technologies) for 17hr at 65℃.

scan_protocol: After hybridization, the arrays were washed using Gene Expression Hybridization Kit and Gene Expression Wash Pack (Agilent technologies). The microarray was scanned by Agilent SureScan G2600D.

data_processing: The scan image data was analyzed with Feature Extraction (ver. 11.5.1.1) software. Further analysis was performed using limma package (ver. 3.50.0) on R (ver. 4.1.1). After log2 transformation and normalization, differential gene expression analysis was performed using 'lmFit' and 'eBayes' functions. Gene expression changes of >1.5-fold and p.value<0.05 were considered as significant.

source_name: E13.5, Dnd1-cKO, replicate 3

label_protocol: Labelling of cDNA by cyanine-3 were performed using Low Input Quick Amp Labeling Kit (One-Color) (Agilent technologies) from 100ng of total RNA.

extract_protocol: Total RNA was extracted from sorted 120,000 PGCs in testes of control and Dnd1-cKO embryos at E12.5 and E13.5 by RNeasy plus Micro kit (Qiagen, Netherlands) according to the manufactures’ instruction.

treatment_protocol: Single-cell suspensions were prepared from testes of control and Dnd1-cKO embryos by incubation with accutase (SF006, Merck Millipore, MA) at 37℃ for 40 min. Then, FACS was performed on a Cell Sorter (MoFlo Astrios, BeckmanCoulter, CA). Sorted PGCs were stored at -80 degree until total RNA extraction.

value: Male germ cell


title: 103627-001-106

source_name: normal skin

value: Ankylosing Spondylitis

value: Female


title: Skin_DR_727_day_0


title: 103627-001-104

source_name: lesion


title: Skin_DR_722_day_0


title: E13.5_Dnd1-cKO_rep2

source_name: E13.5, Dnd1-cKO, replicate 2


title: WT_24h_12

source_name: Wild-type BMDMs, 24 h

value: Wild-type

value: LPS (100 ng/ml)


title: E13.5_control_rep3

source_name: E13.5, control, replicate 3

value: Dnd1flox/flox; Nanog-EGFP


title: 103627-001-103


title: E13.5_control_rep2

source_name: E13.5, control, replicate 2


title: E13.5_Dnd1-cKO_rep1

source_name: E13.5, Dnd1-cKO, replicate 1


title: Skin_DR_721_day_0


title: WT_24h_11


title: E13.5_control_rep1

source_name: E13.5, control, replicate 1


title: E12.5_Dnd1-cKO_rep3

source_name: E12.5, Dnd1-cKO, replicate 3


title: 103627-001-102


title: KO_0h_14


title: WT_24h_10


title: E12.5_Dnd1-cKO_rep2

source_name: E12.5, Dnd1-cKO, replicate 2


title: WT_8h_9

source_name: Wild-type BMDMs, 8 h


title: 103627-001-101


title: WT_8h_8


title: Skin_DR_717_day_0


title: 103627-001-100


title: WT_8h_7


title: Skin_DR_713_day_0


title: 103627-001-099


title: Caco-2 cells, WT-rep2

city: Tongliao

first: Jingbo

last: Zhai

address: 996 Xilamulun Ave, Horqin District

country: China

institute: Inner Mongolia Minzu University

data_processing:
For RNA-seq, use Fastp software to filter low-quality sequences, undetected sequences and linker sequences. Use Hisat2 algorithm for genome alignment. Using HTSeq, select the FPKM standardization method to count the gene expression.The DESeq2 algorithm is used for differential screening to obtain differential genes that meet the Fold Change and FDR thresholds. Based on the differential screening results and the FPKM or RPKM of the sample, Volcano Plot analysis and cluster map analysis (Heatmap) are performed.
Assembly: hg38
Supplementary files format and content: For RNA-seq, a text file includes filtered reads fpkm values for each sample.The first row indicates the name of each sample.

growth_protocol: Caco-2 cells were cultured in DMEM (Thermo Fisher, Cat. No.: 11965-092) supplemented with 10% fetal bovine serum (FBS) and kept in a humid incubator at 37°C and supplemented with 5% CO2.

extract_protocol:
For RNA-seq, total RNA was extracted using TRIZOL.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
After depleting rRNA,  RNA samples were further fragmented into 150-200 bp using divalent cations at 94 °C for 8 min. The cleaved RNA fragments were reverse-transcribed into double-strand cDNA. The resulting cDNA fragments were end-repaired, A-tailed and ligated with indexed adapters. Target bands were harvested through VAHTSTM DNA Clean Beads. The products were purified and enriched by PCR to create the final cDNA libraries and quantified by Agilent 2200. The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina HiSeq Xten by NovelBio Corp. Laboratory, Shanghai.

treatment_protocol: cGAS-KO cells were constructed using CRISPR/Cas9.

tag: cell line

value: fibroblast

value: wildtype


title: Skin_DR_728_day_7

value: Baseline


title: WT_4h_6

source_name: Wild-type BMDMs, 4 h


title: 103627-001-098


title: E12.5_control_rep2

source_name: E12.5, control, replicate 2


title: 103627-001-097

value: Psoriasis


title: Caco-2 cells, cGAS-KO-rep2

value: cGAS knockout


title: Skin_DR_727_day_7

value: Skin


title: Caco-2 cells, WT-rep1


title: Skin_DR_719_day_0

value: Day 0 (day of transplantation)


title: WT_4h_4


title: 03N

city: Tokyo

first: Daisuke

last: Ohki

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

department: Department of Gastroenterology, Graduate School of Medicine

institute: The University of Tokyo

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263.

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: Human colorectal normal mucosa

label_protocol: Cyanine-3 (Cy3) labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit.

extract_protocol: Total RNA was extracted (miRNeasy Mini kit, Qiagen) from tissue samples, and its integrity was verified by Nanodrop 1000 spectrometer.

treatment_protocol: One biopsy sample was obtained from each tumor and surrounding normal mucosa.

value: normal tissue

tag: gender

value: F


title: E12.5_control_rep1

source_name: E12.5, control, replicate 1


title: E12.5_control_rep3

source_name: E12.5, control, replicate 3


title: 103627-001-096


title: E12.5_Dnd1-cKO_rep1

source_name: E12.5, Dnd1-cKO, replicate 1


title: Caco-2 cells, cGAS-KO-rep1


title: Skin_DR_723_day_7

source_name: Mononuclear phagocytes


title: Skin_DR_718_day_0


title: WT_0h_3

source_name: Wild-type BMDMs, 0 h

value: Bone marrow-originated

value: bone marrow-derived macrophages


title: Skin_DR_722_day_7


title: 103627-001-094

source_name: non-lesion

value: Psoriatic Arthritis

value: Male


title: Skin_DR_721_day_7


title: WT_0h_2


title: Young_4

city: Daejeon

first: Yea Eun

last: Kang

address: 282Munhwa-ro, Jung-gu Daejeon

department: Department of Endocrinology and Metabolism

country: South Korea

institute: Chungnam National

data_processing:
Single-cell RNA-seq data were mapped, and counts of molecules per barcode were quantified using the 10x software package cellranger (version 3.0.2) and GRCh38 reference genome supplied by 10x Genomics.
To exclude low quality or doublets, we performed Scrublet, doublet detection algorithm with expected doublet rate parameter of 0.1, filtered cells with fewer than 200 genes or cells with 25% or higher mitochondrial proportion with Seurat R package (v3.2.0).
Each gene UMI count was normalized by total UMI counts in the corresponding cell, multiplied by scale factor 10,000 and transformed to the natural log scale plus 1.
For accurate identification of cell types, we removed clusters identifying doublet and repeated these steps.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-deliminated text file containing the raw gene expression for QC filtered cells.

molecule: polyA RNA

source_name: Normal thyroid

extract_protocol:
Thyroid tissues were minced in HBSS for 5 min and digested with 400 unit/ml Collagenase type 4 (CLS-4, Worthington) dissolved in RPMI media at 37 °C for 60 min. Cells were centrifuged at 4000 rpm for 5 min at 4°C, and the pellet was resuspended with RPMI medium with 10% FBS. After mechanical dissociation, the cell suspension was filtered through 70 μM cell strainer and centrifuged for 5 min at 4°C. The pellet was incubated with red blood cell lysis buffer (11814389001, Roche) for 10 min on ice. After centrifugation, the cell pellet was resuspended with FBS-free RPMI media, filtered through a 40 μM cell strainer, and processed on the 10x Chromium platform.
The concentration of cell suspension was counted with using automated cell counter and adjusted to capture 10,000 cells per sample. Cells were loaded according to the standard protocol of the Chromium Single Cell 3’ Kit (v3 chemistry) or 5' Kit (v1.1 chemistry). All the following steps were performed according to the standard manufacturer’s protocol.

value: Female

tag: pathologic diagnosis

value: PTC, classical type

tag: alternative name


title: Old_3

extract_protocol:
Thyroid tissues were minced in HBSS for 5 min and digested with 400 unit/ml Collagenase type 4 (CLS-4, Worthington) dissolved in RPMI media at 37 °C for 60 min. Cells were centrifuged at 4000 rpm for 5 min at 4°C, and the pellet was resuspended with RPMI medium with 10% FBS. After mechanical dissociation, the cell suspension was filtered through 70 μM cell strainer and centrifuged for 5 min at 4°C. The pellet was incubated with red blood cell lysis buffer (11814389001, Roche) for 10 min on ice. After centrifugation, the cell pellet was resuspended with FBS-free RPMI media, filtered through a 40 μM cell strainer, and processed on the 10x Chromium platform.
The concentration of cell suspension was counted with using automated cell counter and adjusted to capture 10,000 cells per sample. Cells were loaded according to the standard protocol of the Chromium Single Cell 3’ Kit (v3 chemistry). All the following steps were performed according to the standard manufacturer’s protocol.


title: WT_0h_1

value: Wild-type


title: Old_2


title: Skin_DR_719_day_7


title: WT_4h_5

value: LPS (100 ng/ml)


title: Skin_DR_718_day_7


title: 103627-001-092

source_name: normal skin

value: Ankylosing Spondylitis


title: Old_1

value: Follicular adenoma


title: Skin_DR_717_day_7

value: Baseline


title: 103627-001-091

value: Psoriasis


title: Skin_DR_713_day_7


title: Young_2

value: Thy 05


title: Young_3


title: 103627-001-090

source_name: lesion

value: Skin


title: 103627-001-089


title: MCF7_shEZH2A_rep2

city: San Antonio

first: Kexin

last: Xu

state: Texas

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

data_processing:
Basecalls were performed using Illumina Casava software.
Reads were aligned to hg19 genome assembly using STAR 2.5.2b. Refseq transcripts were supplied in GTF format file.
featureCounts package was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by DESeq2 with FDR thresold 0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each Sample

growth_protocol: MCF7 cells were grown in high glucose DMEM meidum with 10% FBS and 1% P/S

extract_protocol:
total RNA was extracted by Trizol Reagent from Invitrogen (Cat no 15596026).
RNA library was prepared by the KAPA Stranded mRNA-Seq kit (KK8421), according to the manufacturer’s instructions.

treatment_protocol: MCF7 cells were transduced with shEZH2 or shControl. Or Syngeneic BALB/c mice implanted with 67NR cells were treated with EZH2 inhibitor

tag: transfection


title: 103627-001-088


title: C48Skm-2

city: Lanzhou City

first: lu

last: zhao

state: Gansu Province

address: Yintan Road Street

institute: Gansu Agricultural University

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: GCF_002163495.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Oncorhynchus mykiss

source_name: skin tissues

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin tissues

value: control

tag: phenotype

value: wild-type


title: T48Skm-1

value: IHNV infection


title: 103627-001-095


title: C48Skm-3


title: MCF7_shEZH2A_rep1


title: T48Skm-3


title: Young_1

value: Thy 04


title: 103627-001-093

value: Psoriatic Arthritis


title: 103627-001-087

value: Male


title: MCF7_shEZH24_rep2


title: Mifepristone_4

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

data_processing:
RNA-seq reads were aligned with STAR-aligner using the genome build Ensembl CanFam3.1 Release 88.1.
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: Ensembl Canis familiaris CanFam3.1 Release 88
Supplementary files format and content: Tab-delimited .txt files include 2 columns: Ensembl feature identifier and raw count number.

organism: Canis lupus familiaris

source_name: Mifepristone

extract_protocol:
Total RNA was isolated with TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Dog Uterine Stromal (DUS) cells

value: 1uM Mifepristone (6h) after decidualization


title: Mifepristone_5


title: 103627-001-086


title: MCF7_shEZH24_rep1


title: T48Skm-2


title: 1387-3890-3

city: Nanning

first: Di

last: Tian

address: DaXue east road

institute: College of Life Science and Technology,GuangXi university

data_processing:
The original file sequenced by the MGI high-throughput sequencer is an image file. After base calling and Bcl2Fastq conversion, the original sequenced reads in FASTQ (fq for short) format can be obtained, which is called raw data or raw reads.
The original sequencing data will contain linker information, low-quality bases, and undetected bases (represented by N). These information will cause great interference to subsequent information analysis. These interference information will be removed by fine filtering methods. The final data is valid data, we call it Clean data or Clean read.
Use SOAPnuke software (v2.1.0) to filter Raw reads to get Clean reads. The main parameters are: –lowQual=20, –nRate=0.005, –qualRate=0.5, other parameters are default. The steps of data processing are as follows: 1) Filter out the paired reads containing the linker sequence.2) Remove paired reads with a ratio of N (N means that the base information cannot be determined) greater than 0.5%.3) Remove low-quality paired reads (reads with Qphred<=20 bases accounting for more than 50% of the entire read length).
Image recognition, decontamination, and adapter removal of sequencing results. Statistical results include the number of sequencing reads, data yield, Q20 content, Q30 content, GC content, etc
Assembly: HISAT2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Penicillium oxalicum

source_name: Mycelium

growth_protocol: Penicillium oxalicum strains were cultured on PDA at 28°C for 4 days, and the spores were washed with 0.2% Tween-80 to obtain fresh spore fluid.

extract_protocol:
RNA was extracted with Trizol,  the purity of RNA (OD260/280) was detected by Nanodrop2000. The integrity of RNA were accurately detected by Agilent 2100,the detection indicators include: RIN value, 28S/18S, whether the map baseline is raised, 5S peak, and electrophoresis to detect whether the RNA sample is diffuse or has a genome DNA contamination.
After the sample is qualified, the library is constructed. The main process is as follows: 1) mRNA enrichment for total RNA by mRNA enrichment method: Enrich mRNA with polyA tail using magnetic beads with Oligo dT. 2) Fragment the RNA obtained by interrupting the buffer, perform reverse transcription with random N6 primers, and synthesize the double-stranded cDNA to form double-stranded DNA. 3) Fill in the end of the synthesized double-stranded DNA and phosphorylate the 5' end, form a sticky end with a protruding "A" at the 3' end, and then connect a bubbling linker with a protruding "T" at the 3' end. 4) The ligation product is amplified by PCR with specific primers. 5) The PCR product is thermally denatured into single-stranded DNA, and then a single-stranded circular DNA library is obtained by circularizing the single-stranded DNA with a bridge primer.

treatment_protocol: Fresh spore fluid was inoculated into the glucose medium for 24 hours and then transferred to the enzyme-producing medium containing raw starch as the only carbon source for 24 hours.

value: Mycelium

value: Deletion of PoxCxrC and overexpression of POX_f08097 in TE4-10

value: Culture in enzyme production medium with raw starch after transfer 24h


title: Mifepristone_3


title: Mifepristone_2


title: MCF7_shCtrl_rep2

value: shCtrl


title: 103627-001-084

value: Ankylosing Spondylitis


title: MCF7_shCtrl_rep1


title: Mifepristone_1


title: 1387-3890-2


title: shEZH2_input

library_source: genomic

data_processing:
Basecalls performed using Illuminal CASAVA software.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v1.1.2 with only uniquely mapped reads retained.
Peaks were called using MACS2 with q-value less than 1e-5. The peaks overlapped with the blacklist regions downloaded from UCSC were removed
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file

molecule: genomic DNA

growth_protocol: Cells were grown in high glucose DMEM meidum with 10% FBS and 1% P/S

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody conjugated magnet beads pull-down.
The extracted ChIP DNA was ligated to specific adaptors of ThruPLEX DNA-seq kit (R400427), according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with EZH2 inhibitor or transduced with shEZH2 or shControl.

tag: chip antibody


title: Control_5

source_name: Control (non-decidualized)

value: Control


title: shEZH2_pSTAT2


title: Control_3


title: C48Skm-1


title: 103627-001-081

value: Psoriasis


title: TE4-10-3

value: WT


title: TE4-10-1


title: 1387-3890-1


title: TE4-10-2


title: 103627-001-083

value: Skin


title: Control_1


title: shCtrl_input


title: 103627-001-085


title: ctl_y3

city: Nan Jing

first: js

last: wang

address: tian yuan

institute: Nanjing Medical University

description: total RNA

data_processing:
BD Rhapsody analysis pipeline was used to process sequencing data with default parameters
Seurat (version 3.1.5) was used to process expression matrix
Cells filtered with < 301 expressed genes or > 30% UMIs originating from mitochondrial
Genome_build: GENCODE v29
Supplementary_files_format_and_content: tab-delimited text files include expression matrix and cell type metadata

source_name: Cells form lung

extract_protocol:
Lung tissue was cut into pieces and incubated with 2 mg/ml collagenase I, 2 mg/ml collagenase IV and 0.2 mg/ml DNase I (Roche) in RPMI 1640 for 40 min at 37℃ with 150 rpm shaking. The resulting cell suspension was filtered through a 70-μm sterile nylon strainer and centrifuged at 400 g for 5 min at 4℃. The cell pellet was resuspended in 1 ml RBC lysis buffer (0.15 mol/l NH4Cl, 10 mmol/l KHCO3, 0.1 mmol/l EDTA) and lysed for 10 min at room temperature. Cells were centrifuged at 400 g for 5 min at 4℃. The cell pellet was resuspended in 400 μl PBS for cell sorting by Countstar (IC1000).
Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual microwells. Reverse transcription was performed on a ThermoMixer® C (Eppendorf) at 1,200 rpm and 37°C for 45 minutes. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200. scRNA-seq libraries were constructed using BD Rhapsody™ WTA Amplification Kit (BD, 633801). The libraries were sequenced on Illumina Novaseq6000 sequencer for at least 50,000 150 bp pair-end reads per cell.

value: lung

tag: disease

value: healthy

tag: group

value: non-smoker


title: ctl_y1

description: total RNA

tag: tissue


title: MCF7_Input


title: cAMP_4

source_name: cAMP

value: Decidualization induced with 0.5mM dbcAMP for 72h


title: cAMP_5


title: ctl_y2

description: total RNA


title: cAMP_2


title: CUTLL1_Empty-V_SET2_DMSO

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

description: CUTLL1 cells constitutively expressing an Empty Vector (Empty-V) and treated with DMSO

hyb_protocol: Samples were then hybridized ON, washed, stained, and scanned using the GeneChip Hybridization Oven 640, Fluidic Station 450.

scan_protocol: Scanner 3000 7G (Thermo Fisher Scientific) were used to generate the raw data files (.CEL files) according to the manufacturer's instruction.

data_processing: Quality control and normalization of CEL files were performed using Transcriptome Analysis Console (TAC) software v4.0 (Thermo Fisher Scientific) by performing “Gene level SST-RMA” summarization method with human genome version hg38. The analyses were performed in two independent biological experiments and gene expression data were Log2 transformed before analyses.

label: biotin

source_name: cell line, infected with an empty vector as control, DMSO treated

label_protocol: RNA samples have been amplified, fragmented, and labeled for array hybridization according to the manufacturer’s instruction (GeneChip® Human Clarion S Array; ThermoFisher Scientific).

growth_protocol: CUTLL1 human T-ALL cell line was cultured in RPMI 1640 medium supplemented with 10% FBS, 1 mM sodium pyruvate, 2 mM L-glutamine, and antibiotics (Invitrogen). Cells were maintained at 37°C and 5% CO2 in a humidified incubator. Cells were routinely verified as free of mycoplasma contamination.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany), treated with DNase-RNase free (Qiagen, Hilden, Germany) and quantified by Nanodrop (Thermo Fisher Scientific).

treatment_protocol: Lentivirus was produced by transient co-transfection of 293T cells with pCMVΔR8.74 and pCMV-VSV-G packaging/envelope and viral transduction performed by spinfection in the presence of polybrene. Virally transduced cells were sorted by flow cytometry. Empty-V and miR-17/92 constructs were based on pRRLsin.cPPTcts.MNDU3.PGK.GFP.WPRE backbone. Lentiviral miR-17/92 construct was derived from MSCV-mir-17-92 plasmid (cat. #64100, Addgene). Cells were subsequently sorted with FACS and then cultured  in the presence of gamma-secretase inhibitor GSI (1uM final) for 2 days, or DMSO as control.

value: T-cell lymphoma cell line with t(7;9) rearrangement


title: MCF7_H3K27me3


title: shCtrl_pSTAT2


title: ctl_o3

description: total RNA


title: 103627-001-082

value: Male


title: MCF7_EZH2

value: EZH2 (Proteintech, #21800-1-AP)


title: CUTLL1_Empty-V_SET1_DMSO


title: ctl_o1

description: total RNA

value: smoker


title: GSK_STAT2


title: Aglepristone_5

source_name: Aglepristone

value: Dog Uterine Stromal (DUS) cells

value: 1uM Aglepristone (6h) after decidualization


title: GSK_input


title: Aglepristone_4


title: ctl_o2

description: total RNA


title: COPD3

description: total RNA

value: COPD


title: DMSO_STAT2

value: DMSO


title: Aglepristone_2


title: DMSO_input


title: Aglepristone_1


title: COPD2

description: total RNA


title: CUTLL1_Empty-V_SET2_GSI1uM

description: CUTLL1 cells constitutively expressing an miR-17-92 cluster Empty Vector (Empty-V) and treated with GSI (1uM)

source_name: cell line, infected with an empty vector as control, GSI treated


title: CUTLL1_Empty-V_SET1_GSI1uM


title: CUTLL1_miRNA17-92_SET2_DMSO

description: CUTLL1 cells constitutively expressing the miR-17-92 cluster and treated with DMSO

source_name: cell line, miRNA17-92 overexpressing, DMSO treated


title: scATAC-seq-mESC_pb_2_cell85

status: Public on Dec 27 2022

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

description: Single-cell-ATAC-seq

data_processing:
The raw fastq files were aligned to mm9 genome using STAR aligner. Peaks were called on the read-count on the peak was calculated for every cell.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data is in bed format. For every cell the read-counts on its on scATAC-seq peaks is given

source_name: Cell-culture

growth_protocol: E14 mESC were cultured in 6-well dishes, pre-coated with 0.1% gelatin and in Serum+LIF media containing DMEM knockout (Gibco #10829), 15% FBS (Gibco #10270), 1xPen-Strep- Glutamine (Gibco #10378), 1xMEM (Gibco #11140), 1xB-ME (Gibco #21985) and 1000 U/ml LIF (Merck #ESG1107).

extract_protocol:
Briefly, mESCs were trypsinised, washed in 1X DPBS, counted  used for plate-based scATAC-seq analysis, as previously described (Chen et al, PMID: 30559361 and   PMID: 34282334).
Single cell ATAC-seq

value: embryonic stem cell


title: Aglepristone_3


title: scATAC-seq-mESC_pb_2_cell84

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell79

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell80

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell81

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell77

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell78

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell83

description: Single-cell-ATAC-seq


title: CUTLL1_miRNA17-92_SET2_GSI1uM

description: CUTLL1 cells constitutively expressing the miR-17-92 cluster and treated with GSI (1uM)

source_name: cell line, miRNA17-92 overexpressing, GSI treated


title: CUTLL1_miRNA17-92_SET1_GSI1uM


title: scATAC-seq-mESC_pb_2_cell76

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell68

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell70

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell73

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell74

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell71

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell75

description: Single-cell-ATAC-seq


title: CUTLL1_miRNA17-92_SET1_DMSO


title: scATAC-seq-mESC_pb_2_cell72

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell63

description: Single-cell-ATAC-seq


title: COPD1

description: total RNA


title: scATAC-seq-mESC_pb_2_cell64

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell65

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell67

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell66

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell69

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell82

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell62

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell54

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell61

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell58

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell57

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell56

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell53

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell59

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell60

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell55

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell49

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell50

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell52

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell48

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell43

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell44

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell46

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell45

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell47

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell42

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell41

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell40

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell38

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell39

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell37

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell36

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell35

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell32

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell33

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell34

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell51

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell28

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell27

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell26

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell25

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell30

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell31

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell23

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell29

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell20

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell24

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell19

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell22

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell18

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell16

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell17

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell15

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell14

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell13

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell12

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell11

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell08

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell09

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell10

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell06

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell02

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell03

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell05

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell01

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell21

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell00

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell97

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell99

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell95

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell96

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell98

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell93

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell9

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell90

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell88

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell85

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell92

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell87

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell84

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell86

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_2_cell07

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell82

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell81

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell8

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell77

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell76

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell94

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell75

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell80

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell79

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell74

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell72

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell89

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell91

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell78

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell70

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell7

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell71

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell83

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell69

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell66

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell65

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell63

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell62

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell61

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell60

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell6

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell57

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell64

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell59

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell58

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell73

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell56

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell54

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell55

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell53

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell51

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell52

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell50

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell5

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell48

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell47

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell67

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell44

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell43

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell42

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell49

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell68

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell41

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell40

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell4

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell35

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell37

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell36

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell33

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell34

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell31

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell30

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell29

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell28

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell46

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell27

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell26

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell22

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell24

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell23

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell21

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell19

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell25

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell18

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell39

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell13

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell14

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell15

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell16

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell17

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell12

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell11

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell32

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell09

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell20

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell08

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell10

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell06

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell07

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell05

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell04

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell03

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell01

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell02

description: Single-cell-ATAC-seq


title: scATAC-seq-mESC_pb_1_cell00

description: Single-cell-ATAC-seq


title: Human colonoid line, replicate5, 5% WRN

city: New York

first: Judy

last: Cho

state: NY

address: 1470 Madison Avenue, 8th Fl., Box 1498;

department: Pathology, Molecular and Cell-Based Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Tophat2 and Cufflinks were used for mapping and quantification of reads
FastQC was used to evaluate read/mapping quality
HTSeq was used to quantify raw reads mapped to each gene region
Assembly: hg19
Supplementary files format and content: Bulk_HumanOrganoidCells_RawReadCounts.csv

source_name: Proximal colon

growth_protocol: human colonoid line were generated from colonic biopsies of IBD, UC or healthy donor. Colonoid lines were maintained at 37C incubator with 5% Co2.

extract_protocol:
Total RNA were extracted from treated human colonoid lines using Trizol method according to mamanufacturer’s instructions.
Sequencing library was generated by using TruSeq stranded RNA seq library prep kit with Ribo-Zero depletion (lllumina)

treatment_protocol: human colonoid lines were treated with 50% or 5% WRN (L-cell expressing Wnt3a, Rspondin3 and Noggin) culture medium

value: Proximal colon

value: colonoid

value: epithelial cells

tag: disease state

value: UC


title: Human colonoid line, replicate6, 5% WRN

source_name: distal colon

value: distal colon


title: Human colonoid line, replicate7, 5% WRN

value: Heathy donor


title: Human colonoid line, replicate4, 5% WRN

value: IBD


title: Human colonoid line, replicate2, 5% WRN


title: Human colonoid line, replicate1, 5% WRN


title: Human colonoid line, replicate5, 50% WRN

value: 50% WRN


title: Human colonoid line, replicate3, 5% WRN


title: Human colonoid line, replicate6, 50% WRN


title: Human colonoid line, replicate4, 50% WRN


title: Human colonoid line, replicate2, 50% WRN


title: Human colonoid line, replicate1, 50% WRN


title: Os 60 min. heat shock, 3 g/g SWC, rep 1

city: Winnipeg

first: Olivia

last: Wilkins

state: Manitoba

address: 66 Chancellors Cir

department: Biological Sciences

country: Canada

institute: University of Manitoba

data_processing:
Adapters/low-quality sequences were trimmed using Trimmomatic, default settings
Trimmed reads were aligned to MSU v7.0 Oryza sativa reference genome using HISAT2
Gene counts from aligned reads were obtained using featureCounts
Assembly: Oryza sativa japonica MSU v7.0
Supplementary files format and content: comma-separated values file containing gene counts from all samples

organism: Oryza sativa

source_name: Whole shoot

growth_protocol: Nipponbare rice seeds germinated for 3 days at 30°C, then planted in pots with Sungro Sunshine Mix #4 (7 per pot). Soil was dried andt measured amounts of water were readded to get exact soil water contents. Plants were grown for 10 days in a Conviron growth chamber with 12/12hr light/dark, 30°C/27°C temperature, 90% humidity. Pots were rewatered to target weight daily.

extract_protocol:
Total RNA was extracted with a Qiagen RNeasy Plant Mini Kit
Library construction and QC carried out by Genome Quebec; mRNA stranded library with NEBNext Library Prep Kit

treatment_protocol: Drought treatments were carried out as above. For heat treatments, at day 10, wet/control pots were moved to a 40°C chamber for 30min or 60 min before collection. All treatments were collected at midday (6hr after dawn). Whole shoots were flash frozen in liquid nitrogen and stored at -80°C.

value: Whole shoot

value: Nipponbare

value: Heat

tag: heat shock_length_(minutes)


title: Os 30 min. heat shock, 3 g/g SWC, rep 2


title: Os 60 min. heat shock, 3 g/g SWC, rep 2


title: Os 60 min. heat shock, 3 g/g SWC, rep 3


title: Human colonoid line, replicate3, 50% WRN


title: Os wet/control, 3 g/g SWC, rep 3

value: Drought


title: Os 30 min. heat shock, 3 g/g SWC, rep 3


title: Os wet/control, 3 g/g SWC, rep 2


title: Human colonoid line, replicate7, 50% WRN


title: Os mild drought, 1.5 g/g SWC, rep 3


title: Os mild drought, 1.5 g/g SWC, rep 1


title: Os mild drought, 1.5 g/g SWC, rep 2


title: Os severe drought, 1.25 g/g SWC, rep 3


title: Os severe drought, 1.25 g/g SWC, rep 2


title: Os 30 min. heat shock, 3 g/g SWC, rep 1


title: 0 hours post IAV infection, strain 5001A

city: Tel-Aviv

first: Gal

last: Yankovitz

address: Haim Levanon

department: The Shmunis School of Biomedicine and Cancer Research

country: Israel

institute: Tel-Aviv University

data_processing:
We applied a joint alignment of sequencing reads for both the mouse genome and the influenza virus genome (using the Bowtie2 software), and then applied a joint quantification of both the virus and mouse transcripts. For this quantification, we applied an FPKM-normalization using the RSEM software.
We filtered out duplicate genes by choosing the first appearance of each gene.
Genome_build: mm9, NC_002016, NC_002017, NC_002018, NC_002019, NC_002020, NC_002021, NC_002022, NC_002023
Supplementary_files_format_and_content: comma-delimited csv file including FPKM normalized reads (includes both mouse and IAV genes)

organism:
Mus musculus
Influenza A virus (A/Puerto Rico/8/1934(H1N1))

source_name: Lungs

extract_protocol:
Murine lungs were harvested immediately after the time of sacrifice, sliced into small pieces, homogenized using BeadBlaster Microtube Homogenizer (90sec, 4000rpm) in the presence of QIAzol. RNA isolation was then performed according to miRNeasy kit protocol (Qiagen).
mRNA quality was checked using the Agilent 2100 Bioanalyzer according to the manufacturer’s instructions. All RNA Integrity Numbers (RINs) were higher than 8. cDNA libraries were prepared using 2µg of isolated RNA according to the manufacturer’s instructions of the SENSE mRNA-Seq Library Prep Kit V2 for Illumina (Lexogen). DNA size and quality were checked using the Agilent 2100 Bioanalyzer, according to the manufacturer’s instructions. Libraries were quantified by using the Qubit DNA HS Assay kit (Invitrogen). The amplified libraries, each sample having its own index primer, were pooled at a total concentration of 2 nM and sequenced using the Illumina HiSeq platform (Technion Genome Center, Israel).

tag: strain

value: Lungs

tag: infection

value: IAV

tag: time

value: 0 hours post IAV infection


title: 0 hours post IAV infection, strain 5005A


title: 0 hours post IAV infection, strain 5023A


title: 6 hours post IAV infection, MLE-12 cells, control

data_processing:
We applied a joint alignment of sequencing reads for both the mouse genome and the influenza virus genome (using the STAR software), and then applied a joint quantification of both the virus and mouse transcripts. For this quantification, we applied normalization using the DSEQ2 software.
We filtered out duplicate genes by choosing the first appearance of each gene.
Genome_build: mm9
Supplementary_files_format_and_content: comma-delimited csv files including DESEQ2 normalized reads.

growth_protocol: Immortalized mouse Lung Epithelial Type I (LET1) (BEI Resources, NIAID, NIH, NR-42941) and mouse lung type II epithelial (MLE-12) cell lines were maintained in Dulbecco’s modified Eagle’s medium (DMEM, high glucose) supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine, 1% penicillin/streptomycin (all from Biological Industries, Kibbutz Beit-Haemek, Israel). All cells were grown at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from cells using the Direct-zol RNA Miniprep kit (ZYMO Research)
mRNA quality was checked using the Agilent 2100 Bioanalyzer according to the manufacturer’s instructions. All RNA Integrity Numbers (RINs) were higher than 8. cDNA libraries were prepared using 0.5µg of isolated RNA according to the manufacturer’s instructions of the SENSE mRNA-Seq Library Prep Kit V2 for Illumina (Lexogen). DNA size and quality were checked using the Agilent 2100 Bioanalyzer, according to the manufacturer’s instructions. Libraries were quantified by using the Qubit DNA HS Assay kit (Invitrogen). The amplified libraries, each sample having its own index primer, were pooled at a total concentration of 2 nM and sequenced using the Illumina HiSeq platform (Technion Genome Center, Israel).

treatment_protocol: Influenza A virus strain A/PR/8/34 (H1N1) propagated by allantoic inoculation of 10-days-old chicken embryonated eggs and stored at −80°C. Viral titers were determined using MDCK cells and expressed as median tissue culture infective dose (TCID50). For infection experiments, 24-well plates were seeded with LET1 (50000 cells/well) or MLE-12 (100000 cells/well) cells. After 24h, cells were washed with PBS and infected with IAV (MOI=5), in a serum-free medium for 1hr with gentle rocking. Following infection, the inoculum was removed and cells were incubated in OptiMEM I reduced medium

value: FVB/N-Tg(SFTPC-TAg)5.1Jaw transgenic


title: Os wet/control, 3 g/g SWC, rep 1

tag: genotype


title: 0 hours post IAV infection, strain 5007A


title: 2 hours post IAV infection, MLE-12 cells, Arhgdia knockout


title: 0 hours post IAV infection, strain 5021A


title: Mock, MLE-12 cells, control

description: Mock, MLE-12 cells, control


title: 6 hours post IAV infection, MLE-12 cells, Arhgdia knockout


title: 0 hours post IAV infection, strain 5020A


title: 2 hours post IAV infection, MLE-12 cells, control


title: 0 hours post IAV infection, strain 5004A


title: 0 hours post IAV infection, strain 5003A


title: Os severe drought, 1.25 g/g SWC, rep 1

tag: treatment


title: 6 hours post IAV infection, LET1 cells, Arhgdia knockout


title: 0 hours post IAV infection, strain 5012A


title: Mock, LET1 cells, Arhgdia knockout

description: Mock, LET1 cells, Arhgdia knockout


title: 6 hours post IAV infection, LET1 cells, control


title: Mock, MLE-12 cells, Arhgdia knockout

description: Mock, MLE-12 cells, Arhgdia knockout


title: 0 hours post IAV infection, strain 6009A


title: 0 hours post IAV infection, strain 3912A


title: Mock, LET1 cells, control

description: Mock, LET1 cells, control


title: 0 hours post IAV infection, strain 4141A


title: 0 hours post IAV infection, strain 1488A


title: 2 hours post IAV infection, LET1 cells, Arhgdia knockout


title: 0 hours post IAV infection, strain 2750A


title: 0 hours post IAV infection, strain 5022A


title: 0 hours post IAV infection, strain 3348A


title: 0 hours post IAV infection, strain 211B


title: Uninfected Vero 3

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

data_processing:
Basecalling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and alignment (Cutadapt v2.5, STAR v2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Genome_build: Chlorocebus sabeus ChlSab1.1 and Rickettsia canadensis str CA410 ASM28391.1
Supplementary_files_format_and_content: Tab delimited file (tsv) for raw hit counts

organism: Chlorocebus sabaeus

source_name: Vero cells

growth_protocol: ~1x10^4 Vero cells and ~1x10^5 R. canadensis pRAM18dRGA+ were seeded in 100 uL DMEM+10% FBS in a 96 well format, and allowed to grow for 48 hours at 37degrees Celsius and 5% CO2

extract_protocol:
Media was aspirated and replaced by addition of 200uL cellstripper for 15 minutes, followed by scraping to resuspend the cells. The suspension was spun at 17000 RPM for 5 minutes, aspirated, and the pellet resuspended in 100uL RNALater. Extraction was performed using RNeasy extraction kits.
Extracted RNA was ribo-depleted using the Ribo-Zero Gold Epidemiology rRNA removal kit, followed by NEBNext Ultra RNA library prep.

treatment_protocol: At 48 hours, each respective compound was added at 10x observed IC90 values. Cultures were continued for an additional 24 hours to then harvest.

tag: infected

value: Uninfected

tag: drug

value: No Drug


title: HSD fibroblast H19

city: Brescia

first: Nicola

last: Chiarelli

state: Lombardy

address: Viale Europa 11

department: Molecular and Translational Medicine

institute: University of Brescia

data_processing:
Raw sequences were aligned and processed by Torrent Suite 5.12.3 according to standard analysis procedures. Output normalized counts (in read per milion) were generated (*.chp files ).   Differentially expressed genes (DEGs) were identified by using the Transcriptome Analysis Console (TAC) software (version 4.0.2) with the ampliSeqRNA plugin (Thermofisher Scientific) and applying an ANOVA test with a fold-change threshold of ±1.5 and an FDR-adjusted p-value ≤ 0.01.
Assembly: hg19_AmpliSeq_Transcriptome_21K_v1.transcript
Supplementary files format and content: Output normalized counts (in read per milion) were generated (*.chp files ).

source_name: dermis

growth_protocol: Control and patient fibroblasts were grown between 1st and 4th in vitro passage at 37 °C in a 5% CO2 atmosphere in Earle's Modified Eagle Medium supplemented with 2 mM L-glutamine, 10% FBS, and 100 µg/ml penicillin and streptomycin

extract_protocol:
Total RNA was purified from patient and control cells grown for 72 hours at 70-80% of confluency using the miRNeasy kit (Qiagen). Sample quality and quantity were evaluated with the Agilent 2100 Bioanalyzer (Agilent Technology) and the Qubit fluorometer (Thermofisher Scientific), respectively.
To improve statistical power, RNA samples from all experimental groups were sequenced twice as biological replicates (BR) (at the 2nd and 4th in vitro passage, respectively) plus 20 technical replicates (TR) for control fibroblasts and 10 for both hEDS and HSD cells. Reverse transcription and library preparation were achieved following the standard protocol of the Ion Ampliseq Transcriptome Human Gene Expression Kit (Thermofisher Scientific), which targets by multiplexed PCR 18,574 protein-coding and 2,228 non-coding RNAs (mRNAs/ncRNAs). Libraries were quantified with the Ion qPCR Library Quantification Kit, diluted to 100 pM and pooled equally, with 8 samples per pool, followed by emulsion PCR and enrichment with the Ion OneTouch2 with ES system. Libraries were then loaded onto an Ion 540 chip and sequenced on the Ion S5 instrument.
RNA-seq, targeted transcriptome sequencing

value: dermis

tag: cell type

value: Skin fibroblasts

value: HSD

value: affected


title: HSD fibroblast H20_biological replicate


title: HSD fibroblast H18


title: HSD fibroblast H20


title: 0 hours post IAV infection, strain 72A


title: 0 hours post IAV infection, strain 111A


title: HSD fibroblast H19_biological replicate


title: Uninfected Vero 2


title: HSD fibroblast H18_biological replicate


title: 3 hours post IAV infection, strain 5023A

value: 3 hours post IAV infection


title: HSD fibroblast H17_biological replicate


title: 0 hours post IAV infection, strain 1912A


title: 0 hours post IAV infection, strain 188A


title: Uninfected Vero 1


title: 3 hours post IAV infection, strain 2513A


title: 0 hours post IAV infection, strain 2513A


title: scATAC-seq-mESC_pb_1_cell38

description: Single-cell-ATAC-seq

value: embryonic stem cell

tag: cell line


title: 2 hours post IAV infection, LET1 cells, control


title: HSD fibroblast H17


title: 48 hours post IAV infection, strain B6

value: 48 hours post IAV infection


title: JSF-3204 Treated 1

organism:
Rickettsia canadensis
Chlorocebus sabaeus

source_name: Vero cells infected with R. canadensis

value: R. canadensis infected


title: HSD fibroblast H16_biological replicate


title: 48 hours post IAV infection, strain 72A


title: 48 hours post IAV infection, strain 6018A


title: HSD fibroblast H16


title: 48 hours post IAV infection, strain 6020A


title: Chloramphenicol Treated 2

value: Chloramphenicol


title: JSF-3204 Treated 2


title: Chloramphenicol Treated 1


title: 48 hours post IAV infection, strain 6012A


title: 48 hours post IAV infection, strain 57B


title: Duartin Treated 2

value: Duartin


title: Doxycycline Treated 1

value: Doxycycline


title: Doxycycline Treated 2


title: HSD fibroblast H15


title: HSD fibroblast H14_biological replicate


title: HSD fibroblast H15_biological replicate


title: 48 hours post IAV infection, strain 6009A

value: Lungs


title: 48 hours post IAV infection, strain 5020A

value: IAV


title: Duartin Treated 1


title: HSD fibroblast H14


title: 48 hours post IAV infection, strain 5008A


title: 48 hours post IAV infection, strain 5011A


title: 48 hours post IAV infection, strain 5012A


title: 48 hours post IAV infection, strain 5005A


title: 48 hours post IAV infection, strain 5023A


title: Rifampin Treated 2

value: Rifampin


title: 48 hours post IAV infection, strain 5004A


title: HSD fibroblast H13_biological replicate


title: 48 hours post IAV infection, strain 5003A


title: HSD fibroblast H13


title: Rifampin Treated 1


title: 48 hours post IAV infection, strain 5001A


title: 48 hours post IAV infection, strain 5021A


title: 24 hours post IAV infection, strain 6020A

value: 24 hours post IAV infection


title: HSD fibroblast H12_technical replicate


title: 48 hours post IAV infection, strain 5022A


title: Infected Control 3


title: 24 hours post IAV infection, strain B6


title: HSD fibroblast H12_biological replicate


title: HSD fibroblast H12


title: 24 hours post IAV infection, strain 5007A


title: 24 hours post IAV infection, strain 5011A


title: 24 hours post IAV infection, strain 5008A


title: 24 hours post IAV infection, strain 5020A


title: Infected Control 1


title: 24 hours post IAV infection, strain 5003A


title: 24 hours post IAV infection, strain 5022A


title: 24 hours post IAV infection, strain 6009A


title: HSD fibroblast H11_technical replicate


title: HSD fibroblast H11


title: HSD fibroblast H11_biological replicate


title: 48 hours post IAV infection, strain 4438A


title: 48 hours post IAV infection, strain 4141A


title: HSD fibroblast H10_biological replicate


title: Infected Control 2


title: HSD fibroblast H10


title: 48 hours post IAV infection, strain 3912A


title: w1118, 5.5-6h,H1, rep2

city: Göttingen

first: Ufuk

last: Günesdogan

address: Justus-von-Liebig Weg 11

country: Germany

institute: University of Göttingen

data_processing:
Nextera Transposase adapter and low quality bases were eliminated using TrimGalore v0.6.6 and Cutadapt v1.17.
Reads were mapped to the Drosophila melanogaster reference genome dm6 (FlyBase Dmel Release 6.23) assembly using bowtie2 v2.3.4.2.
Mapped pairs were further filtered to maintain mapping quality above 10, as well as FR orientation concordant alignments, using custom scripts and samtools v1.9
PCR duplicates and mitochondrial reads were removed by sambamba v0.6.7 as well as reads blacklisted by the ENCODE project
NarrowPeak representation was used for histone marks H3K4me3, H2K27ac with following settings: -f BAMPE --keepdup all -p 5e-4 --call-summits. For histone marks enriched in broad domains including H3K36me3, H3K27me3, H2AK9ac, and H2BK16ac, the broadPeak representation was used applying following settings: -f BAMPE --keepdup all -p 5e-4 -b 0.01.
bigwig files required for coverage tracks as well as heatmaps were generated using Deeptools v3.3.1
Assembly: dm6
Supplementary files format and content: bigWig, bed containing peaks
Library strategy: CUT&Tag

organism: Drosophila melanogaster

source_name: whole embryo

growth_protocol: Experimental design: Flies were raised on apple agar petri dishes in acrylic cages for 30 minutes for egg laying at 25°C, petri dishes were exchanged with new ones and embryos were further incubated at 25°C for 3.5, 4.5 or 5.5 hours

extract_protocol:
Embryos were washed with PBST and dechorionated in 50% bleach, mutant embryos were identified by eYFP expression. Nuclei were extracted following Kaya-Okur et al., 2019
Libraries were constructed following Kaya-Okur et al., 2019, using the listed antibodies, libraries were generated using Epicypher 15-1017-EPC and 15-1018-EPC

treatment_protocol: Maintaining flies used for embryo collection: controlled light conditions (24h light on), new apple agar plates were provided with yeast twice a day, raised at 25°C

value: whole embryo

value: Drosophila embryo 5.5-6h AEL

tag: antibody

value: H1 (Active Motif, #61786)


title: HisC, 4.5-5h,H3K27me3, rep2

description:
HisC_5h_H3K27me3.merged.bw
HisC_5h_H3K27me3.broadPeak.nobl.3cols.bed

value: Drosophila embryo 4.5-5h AEL

value: H3K27me3 (Active Motif, #39157)


title: w1118, 5.5-6h,H1, rep3


title: 48 hours post IAV infection, strain 2750A


title: 48 hours post IAV infection, strain 3348A


title: HSD fibroblast H9_technical replicate

value: dermis

value: Skin fibroblasts

value: HSD

value: affected


title: w1118, 5.5-6h,H1, rep1


title: 24 hours post IAV infection, strain 6018A


title: 48 hours post IAV infection, strain 2513A

value: 48 hours post IAV infection


title: 48 hours post IAV infection, strain 21B


title: HisC, 5.5-6h, H1, rep3


title: HSD fibroblast H9


title: HisC, 5.5-6h, H1, rep2


title: HisC, 5.5-6h, H1, rep1


title: 48 hours post IAV infection, strain 211B


title: 24 hours post IAV infection, strain 4141A


title: HSD fibroblast H8_technical replicate


title: 48 hours post IAV infection, strain 1912A


title: HSD fibroblast H9_biological replicate


title: 48 hours post IAV infection, strain 5000A


title: w1118, 5.5-6h,H3K27me3, rep2

description:
w1118_6h_H3K27me3.merged.bw
w1118_6h_H3K27me3.broadPeak.nobl.3cols.bed


title: 24 hours post IAV infection, strain 5012A


title: 24 hours post IAV infection, strain 2750A


title: 48 hours post IAV infection, strain 2126A


title: HisC, 4.5-5h,H3K27me3, rep1


title: w1118, 4.5-5h,H3K27me3, rep2

description:
w1118_5h_H3K27me3.merged.bw
w1118_5h_H3K27me3.broadPeak.nobl.3cols.bed


title: 24 hours post IAV infection, strain 3348A


title: HSD fibroblast H8_biological replicate


title: HSD fibroblast H8


title: w1118, 5.5-6h,H3K27me3, rep1


title: 24 hours post IAV infection, strain 5004A


title: w1118, 4.5-5h,H3K27me3, rep1


title: 24 hours post IAV infection, strain 57B


title: 24 hours post IAV infection, strain 111A


title: 24 hours post IAV infection, strain 211B


title: 24 hours post IAV infection, strain 2126A


title: HSD fibroblast H7_technical replicate


title: HSD fibroblast H7_biological replicate


title: 24 hours post IAV infection, strain 72A


title: w1118, 5.5-6h, RNAP2 ser2, rep2

value: RNAPII phospho S2 (Abcam, ab5095)


title: 24 hours post IAV infection, strain 2513A


title: 48 hours post IAV infection, strain 188A


title: HSD fibroblast H7


title: w1118, 5.5-6h, RNAP2 ser2, rep1


title: 48 hours post IAV infection, strain 111A


title: 48 hours post IAV infection, strain 1488A


title: HSD fibroblast H6_biological replicate


title: w1118, 4.5-5h, RNAP2 ser2, rep2


title: 48 hours post IAV infection, strain 111B


title: w1118, 4.5-5h, RNAP2 ser2, rep1


title: 96 hours post IAV infection, strain 72A

value: 96 hours post IAV infection


title: HSD fibroblast H6


title: 96 hours post IAV infection, strain 6020A


title: HSD fibroblast H5_technical replicate


title: HisC, 5.5-6h, RNAP2 ser2, rep1


title: 96 hours post IAV infection, strain 6012A


title: 96 hours post IAV infection, strain 57B


title: 96 hours post IAV infection, strain 6009A


title: 96 hours post IAV infection, strain 6018A


title: HSD fibroblast H5_biological replicate


title: HisC, 4.5-5h, RNAP2 ser2, rep1


title: 24 hours post IAV infection, strain 4438A


title: HSD fibroblast H5


title: HisC, 4.5-5h, RNAP2 ser2, rep2


title: 24 hours post IAV infection, strain 3912A


title: HSD fibroblast H4_technical replicate


title: 96 hours post IAV infection, strain B6


title: HSD fibroblast H6_technical replicate


title: 24 hours post IAV infection, strain 5021A


title: CyO, 5.5-6h, H3K4me3, rep2

value: CyO

value: H3K4me3 (Active Motif, #91264)


title: HSD fibroblast H4_biological replicate


title: CyO, 4.5-5h, H3K4me3, rep2


title: 24 hours post IAV infection, strain 5000A

value: Lungs

value: IAV


title: HSD fibroblast H4


title: 24 hours post IAV infection, strain 5001A

value: 24 hours post IAV infection


title: 24 hours post IAV infection, strain 1912A


title: CyO, 5.5-6h, H3K4me3, rep1

value: whole embryo


title: 24 hours post IAV infection, strain 188A


title: 24 hours post IAV infection, strain 5023A


title: HSD fibroblast H3_biological replicate


title: 24 hours post IAV infection, strain 1488A


title: CyO, 4.5-5h, H3K4me3, rep1


title: 96 hours post IAV infection, strain 5022A


title: 24 hours post IAV infection, strain 6012A


title: 24 hours post IAV infection, strain 5005A


title: HSD fibroblast H2_biological replicate


title: 96 hours post IAV infection, strain 5023A


title: wm, 6.5-7h, STRIPEseq, rep3

description: 5'capped mRNA

data_processing:
Quality of STRIPEseq data sets was analyzed using FastQC v0.11.5
STRIPEseq read files were processed and aligned to Drosophila melanogaster reference genome dm6 (FlyBase Dmel Release 6.23) following the GoSTRIPES workflow (https://github.com/BrendelGroup/GoSTRIPES)
Reads counts were further calculated and TSSs were called using TSRchitect (https://www.bioconductor.org/packages/release/bioc/html/TSRchitect.html). The threshold for a TSS to be called was set to at least 5 raw counts that had to cluster into a TSR consistently in at least three of the analyzed replicates
Read counts were then normalized and differential TSR analysis was performed using DESeq2 with default settings. TSR shape analysis was accomplished using TSRexplorer. Annotation of TSSs and TSRs was done with ChIPseeker using a promoter window from -/+ 250bp of a TSS
Genome browser tracks in bigwig format were generated from merged replicates using deeptools bamCoverage
Assembly: dm6

growth_protocol: Experimental design: Flies were raised on apple agar petri dishes in acrylic cages for 30 minutes for egg laying at 25°C, petri dishes were exchanged with new ones and embryos were further incubated at 25°C for 5.5, 6.5 hours

extract_protocol:
Total mRNA was extracted using fresh or with  RNAlater (Invitrogen) preserved (at -80°C) embryos. mRNA is extracted using Qiagen RNeasy Plus Micro kit adjusting the protocol for small RNA species as described by the manufacturer
200ng total input RNA was used. Uncapped mRNA was digested by Terminator Exonuclease. Adapter and indices were added by template switching oligo PCR, the final library was amplified by PCR using NEB Ultra II Q5 PCR master mix M0544S (14 cycles) following the protocol published by  Policastro et al., 2020
STRIPE-seq, Policastro et al., 2020

treatment_protocol:
Maintaining flies used for embryo collection: controlled light conditions (24h light on), new apple agar plates were provided with yeast twice a day, raised at 25°C
Embryos were washed with PBST and dechorionated in 50% bleach, mutant embryos were identified by eYFP expression

value: Drosophila embryo 6.5-7h AEL


title: wm, 6.5-7h, STRIPEseq, rep5

description: 5'capped mRNA


title: 96 hours post IAV infection, strain 5018A


title: 96 hours post IAV infection, strain 5021A


title: 96 hours post IAV infection, strain 5012A


title: HSD fibroblast H2_technical replicate


title: 96 hours post IAV infection, strain 5020A


title: wm, 6.5-7h, STRIPEseq, rep4

description: 5'capped mRNA


title: 96 hours post IAV infection, strain 5008A


title: HSD fibroblast H2


title: 96 hours post IAV infection, strain 5007A


title: 96 hours post IAV infection, strain 5005A


title: wm, 6.5-7h, STRIPEseq, rep1

description: 5'capped mRNA


title: HSD fibroblast H3


title: HSD fibroblast H1_technical replicate


title: HSD fibroblast H1_biological replicate


title: HSD fibroblast H1


title: 0 hours post IAV infection, strain 4438A

value: 0 hours post IAV infection


title: 7 hours post IAV infection, strain 5003A

value: 7 hours post IAV infection


title: 7 hours post IAV infection, strain 5023A


title: 96 hours post IAV infection, strain 5011A


title: hEDS fibroblast P20_technical replicate

value: hEDS


title: HisC, 6.5-7h, STRIPEseq, rep5

description: 5'capped mRNA

value: Df(2L)HisC, P{GAL4-twi.2xPE}/ Df(2L)HisC, P{UAS:eYFP}AH2


title: HisC, 6.5-7h, STRIPEseq, rep4

description: 5'capped mRNA


title: wm, 6.5-7h, STRIPEseq, rep2

description: 5'capped mRNA


title: 7 hours post IAV infection, strain 5005A


title: 7 hours post IAV infection, strain 5021A


title: 7 hours post IAV infection, strain 5000A


title: 3 hours post IAV infection, strain 6020A

value: 3 hours post IAV infection


title: 7 hours post IAV infection, strain 5001A


title: HisC, 6.5-7h, STRIPEseq, rep1

description: 5'capped mRNA


title: hEDS fibroblast P20

value: dermis

value: Skin fibroblasts


title: HisC, 6.5-7h, STRIPEseq, rep2

description: 5'capped mRNA


title: hEDS fibroblast P19_biological replicate

value: affected


title: 3 hours post IAV infection, strain B6


title: 3 hours post IAV infection, strain 6012A


title: wm, 5.5-6h, STRIPEseq, rep3

description: 5'capped mRNA

value: Drosophila embryo 5.5-6h AEL


title: 3 hours post IAV infection, strain 5007A


title: 96 hours post IAV infection, strain 5004A

value: 96 hours post IAV infection


title: hEDS fibroblast P19


title: 3 hours post IAV infection, strain 188A


title: hEDS fibroblast P20_biological replicate


title: wm, 5.5-6h, STRIPEseq, rep4

description: 5'capped mRNA


title: 3 hours post IAV infection, strain 5004A


title: HisC, 6.5-7h, STRIPEseq, rep3

description: 5'capped mRNA


title: hEDS fibroblast P18


title: wm, 5.5-6h, STRIPEseq, rep2

description: 5'capped mRNA


title: HisC, 5.5-6h, STRIPEseq, rep3

description: 5'capped mRNA


title: 3 hours post IAV infection, strain 3348A


title: hEDS fibroblast P17_biological replicate


title: 0 hours post IAV infection, strain 57B


title: 96 hours post IAV infection, strain 4438A


title: 0 hours post IAV infection, strain 5000A


title: 3 hours post IAV infection, strain 5011A


title: 3 hours post IAV infection, strain 5008A


title: hEDS fibroblast P18_biological replicate


title: 96 hours post IAV infection, strain 4141A


title: hEDS fibroblast P17


title: 96 hours post IAV infection, strain 4052A


title: hEDS fibroblast P17_technical replicate


title: wm, 5.5-6h, STRIPEseq, rep1

description: 5'capped mRNA


title: 96 hours post IAV infection, strain 5001A


title: 7 hours post IAV infection, strain 6012A


title: HisC, 5.5-6h, STRIPEseq, rep1

description: 5'capped mRNA


title: hEDS fibroblast P16


title: 96 hours post IAV infection, strain 5000A


title: HisC, 5.5-6h, STRIPEseq, rep2

description: 5'capped mRNA


title: 0 hours post IAV infection, strain 2126A


title: 96 hours post IAV infection, strain 3912A


title: HisC, 5.5-6h, STRIPEseq, rep4

description: 5'capped mRNA


title: hEDS fibroblast P16_biological replicate


title: 96 hours post IAV infection, strain 2513A


title: 96 hours post IAV infection, strain 3348A


title: w1118, 5.5-6h, RNAP2, rep2

data_processing:
Nextera Transposase adapter and low quality bases were eliminated using TrimGalore v0.6.6 and Cutadapt v1.17.
Reads were mapped to the Drosophila melanogaster reference genome dm6 (FlyBase Dmel Release 6.23) assembly using bowtie2 v2.3.4.2.
Mapped pairs were further filtered to maintain mapping quality above 10, as well as FR orientation concordant alignments, using custom scripts and samtools v1.9
PCR duplicates and mitochondrial reads were removed by sambamba v0.6.7 as well as reads blacklisted by the ENCODE project
NarrowPeak representation was used for histone marks H3K4me3, H2K27ac with following settings: -f BAMPE --keepdup all -p 5e-4 --call-summits. For histone marks enriched in broad domains including H3K36me3, H3K27me3, H2AK9ac, and H2BK16ac, the broadPeak representation was used applying following settings: -f BAMPE --keepdup all -p 5e-4 -b 0.01.
bigwig files required for coverage tracks as well as heatmaps were generated using Deeptools v3.3.1
Assembly: dm6
Supplementary files format and content: bigWig, bed containing peaks

extract_protocol:
Embryos were washed with PBST and dechorionated in 50% bleach, mutant embryos were identified by eYFP expression. Nuclei were extracted following Kaya-Okur et al., 2019
Libraries were constructed following Kaya-Okur et al., 2019, using the listed antibodies, libraries were generated using Epicypher 15-1017-EPC and 15-1018-EPC
CUT&Tag

value: RNAP2 (Active Motif, #61668)


title: 96 hours post IAV infection, strain 2750A


title: w1118, 5.5-6h, RNAP2, rep1


title: HisC, 5.5-6h, RNAP2, rep2


title: hEDS fibroblast P15_biological replicate


title: hEDS fibroblast P14_biological replicate


title: 7 hours post IAV infection, strain 1912A


title: 96 hours post IAV infection, strain 21B


title: HisC, 5.5-6h, RNAP2, rep1


title: w1118, 5.5-6h, H3K4me3, rep3

value: H3K4me3 (Active Motif, #91264)


title: 7 hours post IAV infection, strain 4438A

value: Lungs


title: 7 hours post IAV infection, strain 5008A

value: IAV


title: 7 hours post IAV infection, strain 188A


title: 7 hours post IAV infection, strain 5011A


title: hEDS fibroblast P14


title: hEDS fibroblast P14_technical replicate


title: 7 hours post IAV infection, strain 1488A


title: 3 hours post IAV infection, strain 6009A


title: w1118, 5.5-6h, H3K4me3, rep1


title: 7 hours post IAV infection, strain 3912A


title: hEDS fibroblast P13_biological replicate


title: w1118, 5.5-6h, H3K4me3, rep2


title: hEDS fibroblast P15


title: hEDS fibroblast P13


title: 3 hours post IAV infection, strain 5003A


title: 3 hours post IAV infection, strain 5020A


title: w1118, 4.5-5h, H3K4me3, rep3

value: Drosophila embryo 4.5-5h AEL


title: hEDS fibroblast P12_biological replicate


title: 3 hours post IAV infection, strain 5022A


title: 3 hours post IAV infection, strain 4141A


title: w1118, 4.5-5h, H3K4me3, rep2

value: whole embryo


title: hEDS fibroblast P12


title: 3 hours post IAV infection, strain 2750A


title: w1118, 4.5-5h, H3K4me3, rep1


title: hEDS fibroblast P11_technical replicate


title: 3 hours post IAV infection, strain 211B


title: 3 hours post IAV infection, strain 5005A


title: w1118, 3.5-4h, H3K4me3, rep2

value: Drosophila embryo 3.5-4h AEL


title: 3 hours post IAV infection, strain 57B


title: 7 hours post IAV infection, strain 2126A


title: 7 hours post IAV infection, strain 57B


title: hEDS fibroblast P11


title: hEDS fibroblast P11_biological replicate


title: 7 hours post IAV infection, strain 2513A


title: hEDS fibroblast P10_biological replicate


title: HisC, 5.5-6h, H3K4me3, rep3


title: 7 hours post IAV infection, strain 72A


title: 96 hours post IAV infection, strain 2131A


title: 96 hours post IAV infection, strain 2126A


title: 3 hours post IAV infection, strain 5012A


title: hEDS fibroblast P10


title: HisC, 5.5-6h, H3K4me3, rep2


title: 96 hours post IAV infection, strain 211B


title: 96 hours post IAV infection, strain 1912A


title: hEDS fibroblast P9_technical replicate


title: 3 hours post IAV infection, strain 111A


title: w1118, 3.5-4h, H3K4me3, rep3


title: 96 hours post IAV infection, strain 188A


title: HisC, 5.5-6h, H3K4me3, rep1


title: 96 hours post IAV infection, strain 1513A


title: 96 hours post IAV infection, strain 1488A


title: w1118, 3.5-4h, H3K4me3, rep1


title: HisC, 4.5-5h, H3K4me3, rep3


title: 96 hours post IAV infection, strain 111B


title: 96 hours post IAV infection, strain 111A


title: HisC, 4.5-5h, H3K4me3, rep1


title: 96 hours post IAV infection, strain 1061A


title: hEDS fibroblast P8_biological replicate


title: HisC, 4.5-5h, H3K4me3, rep2


title: hEDS fibroblast P8


title: 7 hours post IAV infection, strain 6020A


title: HisC, 3.5-4h, H3K4me3, rep2


title: HisC, 5.5-6h, RNAP2 ser2, rep2

value: RNAPII phospho S2 (Abcam, ab5095)


title: hEDS fibroblast P7_technical replicate


title: 0 hours post IAV infection, strain 6012A

value: 0 hours post IAV infection


title: 7 hours post IAV infection, strain B6

value: 7 hours post IAV infection


title: HisC, 3.5-4h, H3K4me3, rep1

value: Df(2L)HisC, P{GAL4-twi.2xPE}/ Df(2L)HisC, P{UAS:eYFP}AH2


title: 0 hours post IAV infection, strain B6


title: hEDS fibroblast P7_biological replicate

value: hEDS


title: 7 hours post IAV infection, strain 6018A


title: w1118, 5.5-6h, H2BK16ac, rep2

value: H2BK16ac (Active Motif, #39122)


title: 7 hours post IAV infection, strain 5007A


title: hEDS fibroblast P7

value: dermis

value: Skin fibroblasts


title: hEDS fibroblast P9_biological replicate

value: affected


title: w1118, 5.5-6h, H2BK16ac, rep1

value: Drosophila embryo 5.5-6h AEL


title: hEDS fibroblast P9


title: 0 hours post IAV infection, strain 5011A


title: 0 hours post IAV infection, strain 6018A


title: w1118, 4.5-5h, H2BK16ac, rep2


title: 3 hours post IAV infection, strain 1488A

value: 3 hours post IAV infection


title: hEDS fibroblast P6_biological replicate


title: 3 hours post IAV infection, strain 3912A


title: hEDS fibroblast P6


title: w1118, 4.5-5h, H2BK16ac, rep1


title: 7 hours post IAV infection, strain 6009A


title: HisC, 5.5-6h, H2BK16ac, rep2


title: HisC, 5.5-6h, H2BK16ac, rep1


title: hEDS fibroblast P5_biological replicate


title: 3 hours post IAV infection, strain 5000A


title: 7 hours post IAV infection, strain 21B


title: 7 hours post IAV infection, strain 5022A


title: hEDS fibroblast P5


title: 7 hours post IAV infection, strain 5020A


title: hEDS fibroblast P4_biological replicate


title: 0 hours post IAV infection, strain 5008A


title: HisC, 4.5-5h, H2BK16ac, rep1


title: 7 hours post IAV infection, strain 4141A


title: 7 hours post IAV infection, strain 3348A


title: 7 hours post IAV infection, strain 2750A


title: hEDS fibroblast P4


title: 7 hours post IAV infection, strain 5012A


title: w1118, 5.5-6h, H2AK9ac, rep2

value: H2AK9ac (Active Motif, #39110)


title: 7 hours post IAV infection, strain 5004A

value: Lungs


title: HisC, 4.5-5h, H2BK16ac, rep2


title: 7 hours post IAV infection, strain 5011A.1

value: IAV


title: 7 hours post IAV infection, strain 211B


title: hEDS fibroblast P5_technical replicate


title: 7 hours post IAV infection, strain 111A


title: w1118, 5.5-6h, H2AK9ac, rep1


title: hEDS fibroblast P3_technical replicate


title: 3 hours post IAV infection, strain 5001A


title: w1118, 4.5-5h, H2AK9ac, rep3

value: Drosophila embryo 4.5-5h AEL


title: 3 hours post IAV infection, strain 4438A


title: hEDS fibroblast P3


title: hEDS fibroblast P2_technical replicate


title: 3 hours post IAV infection, strain 2126A


title: w1118, 4.5-5h, H2AK9ac, rep1

value: whole embryo


title: HisC, 5.5-6h, H2AK9ac, rep2


title: 3 hours post IAV infection, strain 1912A


title: HisC, 5.5-6h, H2AK9ac, rep3


title: RF_EC3

city: Boston

first: KLaus

last: Schmitz-Abe

state: MA

address: 300 Longwood Avenue

department: Asthma, Allergy and Immunology

institute: Children's Hospital Boston

description: BB

data_processing:
fastq file to bam file to count file: Rsubread (feature Counts): Default parameters
Count file to Gene differential expression file: edgeR (version 3.28) : Default parameters
Count file to Gene differential expression file: DESeq2 (version 1.26.0) : Default parameters
Count file to Gene differential expression file: Limma (version 3.42.2) : Default parameters
Join results: VExP Pipeline (Retnlb..Gene_expression.xlsx)
Assembly: GRCm38/mm10 (UCSC reference)
Supplementary files format and content: Retnlb..Counts.xlsx: Excel file; RNAseq Count Matrix for all samples.
Supplementary files format and content: Retnlb..Gene_expression.xlsx: Excel file; RNAseq Gene-differential expression Matrix for all samples.

source_name: Small Intestine

growth_protocol: Small intestinal epithelial cells were cell sorted using BD FACS Aria and Snap Freezed before RNA extraction.

extract_protocol:
Small intestinal epithelial cells from WT, Il4raF709 or Retnlb–/–Il4raF709 were stained with EPCAM-1, CD45 and Viability dye. Epithelial cells were cell sorted as live EPCAM1+ CD45-. The cells were then lysed using RLT buffer. The RNA was extracted using the Qiagen miniRNasy kit as per manufacturer's protocol.
RNA to cDNA was performed using the SMART-Seq v4 Ultra Low Input RNA kit using the manufacturer's protocol.

treatment_protocol: WT, Il4raF709 and Retnlb–/–Il4raF709 were treated with Ovalbumin together with SEB once weekly for 8 weeks. On week 9 small intestinal epithelial cells were cell sorted using BD FACS Aria and Snap Freezed before RNA extraction.

value: Small intestinal epithelial cells


title: WT_EC5

description: CC

value: WT


title: WT_EC2

description: CC


title: WT_EC4

description: CC


title: RF_EC2

description: BB


title: 3 hours post IAV infection, strain 72A


title: RF_EC5

description: BB


title: F_EC5

description: AA


title: HisC, 5.5-6h, H2AK9ac, rep1


title: hEDS fibroblast P1_biological replicate


title: hEDS fibroblast P2_biological replicate


title: hEDS fibroblast P3_biological replicate


title: hEDS fibroblast P2


title: hEDS fibroblast P1_technical replicate


title: HisC, 4.5-5h, H2AK9ac, rep2


title: hEDS fibroblast P1


title: SW480 cells, shNAT10, bio rep2 [SL2A_480]

city: Nanjing

first: Chi

last: Jin

address: Han Zhong Road

institute: Nanjing university school

data_processing:
Dr Tom II
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: DLD-1 and SW480 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using Trizol (TAKARA). RNA was used for the construction of sequencing libraries.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was  generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end  repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on  the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the  final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: DLD-1 and SW480 cells were treated with shControl or shNAT10 virus respectively.

value: Human colorectal cancer cells

value: NAT10 knockdown

value: shNAT10 virus


title: SW480 cells, shNAT10, bio rep1 [SL1A_480]


title: F_EC3

description: AA


title: SW480 cells, shControl, bio rep2 [NC2A_480]

value: shControl virus


title: w1118, 4.5-5h, H2AK9ac, rep2


title: F_EC2

description: AA


title: Control fibroblast C40_technical replicate

value: healthy donors

value: unaffected


title: SW480 cells, shControl, bio rep1 [NC1A_480]


title: Control fibroblast C40_biological replicate

value: dermis

value: Skin fibroblasts


title: w1118, 4.5-5h, H3K36me3, rep2

value: H3K36me3 (Active Motif, #61102)


title: w1118, 5.5-6h, H3K36me3, rep1

value: Drosophila embryo 5.5-6h AEL


title: Control fibroblast C39


title: HisC, 5.5-6h, H3K36me3, rep2

value: Df(2L)HisC, P{GAL4-twi.2xPE}/ Df(2L)HisC, P{UAS:eYFP}AH2


title: w1118, 4.5-5h, H3K36me3, rep1


title: Control fibroblast C40


title: M13-NT-(MEIS1ex) rep2

city: Cambridge

first: Sarah

middle: J

last: Horton

state: Cambridgeshire

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute - Department of Haematology

country: United Kingdom

institute: University of Cambridge

data_processing:
Paired end RNA-seq reads were quality filtered and adapter sequences were trimmed using TrimGalore package.
Trimmed sequence reads were mapped using STAR version=2.7.10a against the human genome (Hg38). Uniquely-mapping, high confidence reads were retained using the following flags (NH:i:1 and MAPQ=255).
Read counts were quantified with HTSeq version 1.99.2
Assembly: hg38
Supplementary files format and content: BigWig files of uniquely mappable, high-confidence reads for display in Genome Browser created using genomeCoverageBed from BAM to bedGraph, followed by conversion to BigWig using bedGraphToBigWig
Supplementary files format and content: tab-delimited text files containing read counts for each gene (in ENSEMBL IDs)

source_name: MLL-AF9 positive MOLM13

extract_protocol:
Total RNA was extracted from cells using RNeasy Plus mini (QIAGEN) kit following manufacturer’s instructions.
libraries were prepared using Illumina kit (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, Cat# E7760S) with RiboZero depletion following manufacturer’s instructions. Libraries were sequenced on Hiseq platform with PE150 reads length.

value: MLL-AF9 positive MOLM13

value: AML cell line


title: M13-NT-(MEIS1ex) rep4


title: Control fibroblast C38_technical replicate


title: Control fibroblast C39_biological replicate


title: M13-MEIS1-Cr-rep4


title: M13-NT-(MEIS1ex) rep1


title: HisC, 5.5-6h, H3K36me3, rep1


title: M13-NT-(MEIS1ex) rep3


title: Control fibroblast C38_biological replicate


title: DLD-1 cells, shControl, bio rep1 [NC1A_DLD]


title: M13-MEIS1-Cr-rep3


title: HisC, 4.5-5h, H3K36me3, rep2

value: Drosophila embryo 4.5-5h AEL


title: HisC, 4.5-5h, H2AK9ac, rep1

value: whole embryo

value: H2AK9ac (Active Motif, #39110)


title: DLD-1 cells, shControl, bio rep2 [NC2A_DLD]

value: WT


title: M13-MEIS1-Cr-rep2


title: Fibroblast_WGBS_rep2

city: Shanghai

first: Liao

last: Zhaodi

address: 500, Qiangye Road

department: Institute of Neuroscience

institute: Chinese Academy of Sciences

description: this sample contains sequencing data from a single lane

data_processing:
The raw sequencing reads were trimmed by fastp (version 0.23.2) with default parameters to remove low-quality bases and adapters in paired-end reads.
The fibroblast WGBS data were aligned to macFas5 using Bismark with default parameters.
The methylation level and coverage depth of each cytosine were extracted from the aligned reads with bismark_methylation_extractor.
HyperDMRs and hypoDMRs were identified using methpipe (version 3.4.3) and were further filtered requiring at least 25 CpG sites and at least 25% methylation difference.
Tiling window/region DNA methylation level was calculated by using methylKit package in the Bioconductor R program.
Assembly: macFas5
Supplementary files format and content: tab-delimited text files include CpG values for each Sample

organism: Macaca fascicularis x Macaca mulatta

source_name: fibroblast

extract_protocol:
Fibroblasts were seeded into lysis buffer by mouth pipette and subjected to bisulfite conversion using the EZ DNA Methylation Direct Kit.
A small amount of unmethylated Lambda DNA (Promega, D152A) was added to each sample before bisulfite conversion to serve as spike-in controls for evaluating bisulfite conversion efficiency. After column-based purification, DNA was complemented with the random primer Preamp and Klenow polymerase (Enzymatics, P7010-HC-L). This random priming was repeated five times in total. Second strands were synthesized using another random primer, Adapter 2. Final libraries were generated after PCR amplification with the Illumina universal PCR primer and Illumina indexed primer, and were then purified using SPRI beads. Final libraries were subjected to paired-end 150 bp sequencing on a NovaSeq 6000 sequencer (Illumina) with PhiX spike-in control.

value: fibroblast

value: wild type

value: hybrd


title: Control fibroblast C38


title: w1118, 5.5-6h, H3K36me3, rep2


title: Blastocyst_WGBS_SCNT_rep2

description: this sample include sequencing reads from a different lanes

data_processing:
The raw sequencing reads were trimmed by fastp (version 0.23.2) with default parameters to remove low-quality bases and adapters in paired-end reads.
The remaining reads were aligned to the Macaca fascicularis genome (macFas5) by using Bismark (version 0.23.1) with parameters “--non_directional”.
The methylation level and coverage depth of each cytosine were extracted from the aligned reads with bismark_methylation_extractor.
HyperDMRs and hypoDMRs were identified using methpipe (version 3.4.3) and were further filtered requiring at least 25 CpG sites and at least 25% methylation difference.
Tiling window/region DNA methylation level was calculated by using methylKit package in the Bioconductor R program.
Assembly: macFas5
Supplementary files format and content: tab-delimited text files include CpG values for each Sample

source_name: embryo

extract_protocol:
ICSI and SCNT blastocysts were seeded into lysis buffer by mouth pipette and subjected to bisulfite conversion using the EZ DNA Methylation Direct Kit.
Each replicates containing 10~11 blastocysts were collected for the library construction. A small amount of unmethylated Lambda DNA (Promega, D152A) was added to each sample before bisulfite conversion to serve as spike-in controls for evaluating bisulfite conversion efficiency. After column-based purification, DNA was complemented with the random primer Preamp and Klenow polymerase (Enzymatics, P7010-HC-L). This random priming was repeated five times in total. Second strands were synthesized using another random primer, Adapter 2. Final libraries were generated after PCR amplification with the Illumina universal PCR primer and Illumina indexed primer, and were then purified using SPRI beads. Final libraries were subjected to paired-end 150 bp sequencing on a NovaSeq 6000 sequencer (Illumina) with PhiX spike-in control.

treatment_protocol:
ICSI: intracytoplasmic sperm injection
SCNT: somatic cell nuclear transfer

value: embryo

value: blastocyst

value: SCNT


title: HisC, 4.5-5h, H3K36me3, rep1


title: DLD-1 cells, shNAT10, bio rep2 [SL2A_DLD]

value: Human colorectal cancer cells

value: NAT10 knockdown

value: shNAT10 virus


title: DLD-1 cells, shNAT10, bio rep1 [SL1A_DLD]


title: M13-MEIS1-Cr-rep1


title: Control fibroblast C37_biological replicate

value: dermis

value: Skin fibroblasts

value: healthy donors

value: unaffected


title: Blastocyst_WGBS_SCNT_rep1


title: Control fibroblast C37


title: M13-SAFB-Cr-rep3

value: MLL-AF9 positive MOLM13

value: AML cell line

value: CRISPR-ko-SAFB


title: HisC, 5.5-6h, H3K27me3, rep2

value: whole embryo

value: Drosophila embryo 5.5-6h AEL

value: Df(2L)HisC, P{GAL4-twi.2xPE}/ Df(2L)HisC, P{UAS:eYFP}AH2

value: H3K27me3 (Active Motif, #39157)


title: Blastocyst_WGBS_ICSI_rep1

value: embryo

value: wild type

value: ICSI


title: Control fibroblast C36_biological replicate


title: Blastocyst_WGBS_ICSI_rep2

value: blastocyst


title: Control fibroblast C36


title: HisC, 5.5-6h, H3K27me3, rep1


title: w1118, 5.5-6h, H3K27ac, rep1

value: H3K27ac (Active Motif, #39134)


title: M13-SAFB-Cr-rep2


title: Fibroblast_WGBS_rep1

description: this sample contains sequencing data from 2 different lanes

value: fibroblast

value: hybrid


title: w1118, 5.5-6h, H3K27ac, rep2


title: Control fibroblast C35

value: dermis

value: Skin fibroblasts


title: w1118, 4.5-5h, H3K27ac, rep2

value: Drosophila embryo 4.5-5h AEL


title: M13-SAFB-Cr-rep1

value: MLL-AF9 positive MOLM13


title: Control fibroblast C35_biological replicate

value: healthy donors

value: unaffected


title: RNA-seq_Blastocyst_SCNT_rep2

data_processing:
The raw sequencing reads were trimmed by using fastp (v0.23.2) with default parameters to remove low-quality bases and adapters in paired-end reads.
The remaining reads were mapped to the Macaca fascicularis genome (macFas5) with Hisat2 (version 2.2.1) with parameters “--no-mixed”, “--no-discordant” and “--no-softclip”.
The sam files was converted to bam files using samtools (1.15.1), then the bam file were sorted and the index files were created.
Raw read counts were calculated by featureCounts (v2.0.1).
The indexed bam files were converted to bw files using the bamCoverage function of deeptools (version 3.5.1).
Allele-specific alignment was performed using the masked parental genome with bowtie2 (version 2.4.5).
Then, the allelic origin of reads that cover known SNP positions were identified by SNPsplit (version 0.5.0).
The bw files containing expression peaks of the paternal and maternal genomes were generated as described before.
Assembly: macFas5
Supplementary files format and content: a tab-delimited text file include count values for each Sample

extract_protocol:
ICSI and SCNT blastocyst were lysed in lysis buffer containing RNase inhibitor, and the cDNA was synthesed using SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Clontech, 634888) according to the user manual.
After amplification, the sequencing libraries were made with the fragmented cDNA using TruePrep DNA Library Prep Kit V2 for Illumina according to manufacturer’s instructions (Vazyme, TD503). Libraries were quantified using a Qubit dsDNA HS Assay Kit (Thermo Scientific, Q32854), quality-controlled using a Fragment Analyzer instrument (Agilent), and paired-end 150 bp sequencing was performed on a Novaseq 6000 sequencer (Illumina).

value: SCNT


title: M13-HOXA9-Cr-rep2

value: AML cell line


title: RNA-seq_Blastocyst_SCNT_rep1


title: RNA-seq_Blastocyst_ICSI_rep2


title: w1118, 4.5-5h, H3K27ac, rep1

value: whole embryo


title: M13-HOXA9-Cr-rep1


title: RNA-seq_Blastocyst_ICSI_rep1


title: HisC, 5.5-6h, H3K27ac, rep2

value: Drosophila embryo 5.5-6h AEL

value: Df(2L)HisC, P{GAL4-twi.2xPE}/ Df(2L)HisC, P{UAS:eYFP}AH2


title: M13-NT-Non-Targeting- rep3

value: CRISPR-ko nontargeting (NT)


title: Control fibroblast C34


title: M13-NT-Non-Targeting- rep2