title: HC011_N

description: Bulk RNA-seq normal thyorid


title: HC008_T

status: Public on Nov 13 2023

type: SRA

city: Boston

first: Russell

last: Jenkins

state: MA

address: 55 Fruit Street

country: USA

institute: Masschussetts General Hospital

description: Bulk RNA-seq Hürthle cell carcinoma

library_source: transcriptomic

data_processing:
STAR used to perform alignment and generate BAM files
featureCounts R package used to perform read quantification and generate counts matrix
Assembly: hg19
Supplementary files format and content: txt file containing raw counts

molecule: total RNA

organism: Homo sapiens

source_name: Human tissue

extract_protocol: none provided

tag: tissue

value: thyroid

tag: tissue type

value: tumor


title: HC009_N

description: Bulk RNA-seq normal thyorid

value: normal


title: Acute-stage-ODMLT  group 1

type: RNA

city: Hefei

first: Hui

last: Wang

address: 218 Jixi Road

country: China

institute: he First Affiliated Hospital of Anhui Medical University

description: Gene expression data from ODMLT patient at acute-stage

hyb_protocol: After purification the labeled RNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies)

data_processing:
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 14.8, Agilent Technologies) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were chosen for further data analysis. Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test.
 The threshold set for up- and down-regulated genes was a fold change >= 2.0 and a P value <= 0.05

source_name: ODMLT patient at acute-stage

label_protocol: total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP.

extract_protocol: Exosomes were isolated from serum samples using the exoEasy Maxi Kit (Qiagen, Hilden, Germany), in accordance with the manufacturer’s protocol.Total RNA was extracted from exosome pellet using the miRNeasy Serum Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol.Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity(RIN) was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The blood was collected into serum-separating tubes and allowed to sit for 30-60min at room temperature prior to centrifugation.

value: serum exosome

tag: develpomental stage

value: patient at acute-stage


title: HC008_N

description: Bulk RNA-seq normal thyorid


title: Y2: Oocytes, rep3

city: Ceske Budejovice

first: Lenka

last: Gahurova

address: Branisovska 1760

department: Department of molecular biology and genetics

country: Czech Republic

institute: University of South Bohemia

data_processing:
read trimming (Trim Galore! v0.6.1)
read mapping (Hisat2 v2.1.0)
data quantification (Seqmonk)
Assembly: HetGla2/HetGla_female_1.0; Cavpor3.0; degu sequences XM_023711114.1, XM_004630806.2 and XM_023716073.1
Supplementary files format and content: txt file with raw read counts of individual genes

organism: Heterocephalus glaber

source_name: oocytes

growth_protocol: Oocytes were isolated from freshly sacrificed females by manual disruption of the ovary in M2 media and washed in PBS.

extract_protocol:
Picopure RNA extraction kit (Arcturus)
Ribosomal RNA was depleted with NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) with sample purification beads (NEB, E7405) according to the manufacturer’s instructions, including DNase treatment by TURBO DNase (Thermo Fisher Scientific, AM2238) followed by library preparation using NEBNext Ultra II Directional RNA Library Prep with sample purification beads (NEB, E7765S) according to the manufacturer’s instructions.

tag: cell type

value: oocytes


title: D013.13

city: HOUSTON

first: Rui

last: Chen

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
The quality of raw sequencing data was first evaluated by FastQC (version 0.11.9)
Low quality reads and adapters were then trimmed by Trimmomatic (version 0.4.0)
Reads that passed quality control were aligned to GRCh38 using the 2-pass mode of STAR (version 2.7.7b)
Read counts were obtained by featureCount (version 1.22.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: nuclear RNA

source_name: macula retina

extract_protocol:
These samples came from 23 individuals aged 73-84 years old, who died of respiratory or heart failure, or from a myocardial infarction. The human donor eyes were obtained with the Utah Lions Eye Bank. We include samples within 6 hours post-mortem for this study. Dissections of donor’s eyes were carried out immediately according to a previously published protocol (Owen et. al., Investig. Ophtalmol. Vis. Sci., 2019). Specifically, the macula retina tissue was collected using a 6 mm disposable biopsy punch (Integra, Cat # 33–37) and flash frozen and stored at −80 °C. Donors with any history of retinal degeneration, diabetes, macular degeneration, or drusen were not used for this study; also each donor underwent an ophthalmology check to ensure the eye is in healthy condition. Matched samples with the snRNAseq were used for RNA isolation by applying TRIzol (Invitrogen) to the separated single-nuclei resuspension. cDNA were prepared from ∼1ng of total RNA by using the Smartseq v4 ultra low input RNA Kit according to the manufacturer’s directions (Takara).
Libraries were made using Nextera XT library prep (Illumina).

tag: sample condition

value: Normal

tag: ethnicity

value: Caucasian

tag: age

tag: gender

value: Male


title: Y1: Oocytes, rep2


title: D005.13


title: HC007_T

description: Bulk RNA-seq Hürthle cell carcinoma


title: Oocytes, rep1


title: HC007_N

description: Bulk RNA-seq normal thyorid


title: D019.19

value: Female


title: D011.19


title: GP: Oocytes, gp, rep1

organism: Cavia porcellus


title: 61L

city: London

first: Magdalena

last: Zak

address: 332 Grays Inn Road

country: United Kingdom

institute: UCL Ear Institute

data_processing:
Run data were demultiplexed and converted into fastq files using Illumina’s bcl2fastq Conversion Software v2.19
Kallisto package was used to map reads to a chicken reference genome (Gallus_gallus-GRCg6a) and to quantifying abundances of transcripts using default settings
Assembly: Gallus_gallus-GRCg6a

organism: Gallus gallus

source_name: otocyst

extract_protocol:
Total RNA was extracted from each individual otocysts using the RNAqueous™-Micro Total RNA Isolation Kit (Ambion) according to the manufacturers protocol. The quality of isolated RNA was tested using Agilent 2200 Tapestation and only samples with RIN of at least 9 were used for library
Libraries were made using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech): cDNA was generated using the SMART (Switching Mechanism at 5' End of RNA Template) technology during 10 cycles of PCR. cDNA integrity and quantity was checked on the Agilent Bioanalyser using the High Sensitivity DNA kit, and 200pg of cDNA was then converted to sequencing library using the Nextera XT DNA protocol (Illumina)
Samples were sequenced 43bp paired-end read and high output - 400 million reads per run on NextSeq 500 instrument (Illumina)

treatment_protocol: The E2 chicken right otic placodes were in ovo electroporated with T2-mCherry-T2A-3xHAtag-Bcat-LOF or control T2-mCherry (constructs described in https://doi.org/10.7554/eLife.59540). Both left untransfected and the right transfected otocysts were collected 24h later and cleaned from the surrounding mesenchyme.

value: otocyst

tag: strain

value: White Leghorn

value: embryonic day 3

tag: treatment

value: non-transfected

tag: duration of treatment


title: HC006_T

description: Bulk RNA-seq Hürthle cell carcinoma


title: a20_3

city: Birmingham

first: Daniel

middle: James

last: Gibbs

state: West Midlands

address: Edgbaston

department: School of Biosicences

institute: The University of Birmingham

data_processing:
Data cleaned with in-house Novogene perl scripts
Reference genome was built using Bowtie v2.2.3 a
Cleaned paired-end  reads were aligned to the reference genome using TopHat v2.0.12
Reads were mapped to each gene and counted using HTSeq v0.6.1
Differential expression analysis was performed using the DESeq R package (1.18.0)
Assembly: TAIR10
Supplementary files format and content: excel file showing read counts and log-fold changes

organism: Arabidopsis thaliana

source_name: 10-day old seedling

growth_protocol: 10 day old seedligns on vertical 1/2 MS plates

extract_protocol:
RNA was extracted from snap-frozen samples using an RNeasy minikit (QIAGEN)
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time RT-qPCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: no treatment

value: 10-day old seedling

tag: cell line

value: whole seedling

tag: genotype


title: 62L


title: a20_2


title: Control group 5

description: Gene expression data from age- and sex-matched healthy control subject

value: healthy control


title: D010.19


title: HC006_N

description: Bulk RNA-seq normal thyorid

value: thyroid


title: a20_1


title: 62R

value: mCherry


title: D009.13

value: Asian


title: Control group 1

source_name: age- and sex-matched healthy control subject

value: serum exosome


title: HC005_T

description: Bulk RNA-seq Hürthle cell carcinoma

value: tumor


title: 61R


title: a10_3


title: 60L


title: Control group 3


title: a10_2


title: D009.19

value: Hispanic


title: D006.19

value: Normal


title: D008.19


title: HC005_N

description: Bulk RNA-seq normal thyorid

value: normal


title: Control group 2


title: Control group 4


title: 60R


title: HC004_N

description: Bulk RNA-seq normal thyorid


title: a10_1


title: D005.19

value: Male


title: 52L


title: HC003_T

description: Bulk RNA-seq Hürthle cell carcinoma


title: D007.19

value: Caucasian


title: D10_3

value: doa10a/b RNAi 4-2


title: 51L

value: otocyst

value: White Leghorn


title: D10_2


title: 50L

value: embryonic day 3

value: non-transfected


title: D003.19


title: HC004_T

description: Bulk RNA-seq Hürthle cell carcinoma


title: D015.19


title: HC002_T

description: Bulk RNA-seq Hürthle cell carcinoma


title: D10_1

value: 10-day old seedling

value: whole seedling


title: 52R

value: Wnt-LOF


title: WT_3

value: WT


title: 51R


title: D014.19


title: WT_1


title: HC001_N

description: Bulk RNA-seq normal thyorid

value: thyroid


title: HC001_T

description: Bulk RNA-seq Hürthle cell carcinoma


title: 50R


title: WT_2


title: D013.19

value: Female


title: HC003_N

description: Bulk RNA-seq normal thyorid


title: HC002_N

description: Bulk RNA-seq normal thyorid


title: D016.19


title: Liver, Acsm3_KO3, 12 weeks

status: Public on Nov 12 2023

city: Beijing

first: Yibo

state: Beijin

address: 167 Beilishi Road, Xicheng District, Beijing

institute: Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Hisat2 (version:2.0.4)
Adaptor sequences contained in reads were removed using trimadap, bases with a mass Q below 20 at the 3 'end were removed by seqtk trimfq (version: 1.0), i.e., the base error rate was less than 0.01, (Q = -10 logerrorratio).
Reads less than 25 in length were removed using lengthsort.pl. Ribosome RNA reads of the species to which they belonged were removed by bowtie2 (version: 2.2.6).
Genome mapping of pre-processed reads was performed applying the spliced mapping algorithm of Hisat2 (version: 2.0.4).
Stringtie (version: 1.3.0) was applied to count the number of Fragments per gene after Hisat2 alignment, then the TMM (trimmed mean of M values) method was used to normalize, and finally the FPKM value of each gene was calculated using a perl script.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes FPKM values for all samples.
Supplementary files format and content: tab-delimited text files include counts for each sample.

organism: Mus musculus

source_name: Liver

growth_protocol: All animals were housed under a 12 h light/dark cycle at a temperature of 24 °C and relative humidity of (56 ± 10) %, with free access to water and normal diet

extract_protocol:
Total RNA was extracted using the MJzol Animal RNA Isolation Kit (Majorivd) and purified using RNAClean XP Kit (Beckman Coulter) and RNase-Free DNase Set (QIAGEN) according to standard operating procedures provided by the manufacturer. The mRNA was enriched using VAHTS® mRNA Capure Beads (Human/Mouse/Rat).
The mRNA sequencing libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme) according to standard operating procedures provided by the manufacturer.

value: Liver

value: 12 weeks

value: Acsm3 knockout

value: normal diet


title: adjacent normal tissue circRNA_2

city: Xi'an

first: shi

last: hongyang

address: 157 Xiwu Road, Xi'an City

department: Department of respiratory and critical care medicine

institute: The Second Affiliated Hospital of Xi'an Jiaotong University

description: circRNA expression data from Homo sapiens adjacent normal tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

source_name: adjacent normal tissue

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: lung adenocarcinomas and paired adjacent normal tissues

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

treatment_protocol: Tissues from lung adenocarcinomas surgury and promptly frozen in liquid nitrogen.

value: adjacent normal tissue from lung adenocarcinomas


title: adjacent normal tissue circRNA_3


title: Liver, Acsm3_KO1, 12 weeks


title: Liver, Control1, 12 weeks


title: Liver, Control3, 12 weeks


title: Brown adipose tissue, Mcu fl/fl AKO mouse, replicate 3

city: Nanning

first: Lei

last: Zhou

state: Guangxi

address: Daxuedong Road, Xixiangtang District

department: College of Animal Science and Technology

institute: Guangxi University

data_processing:
Perl script was used to filter the original data: 1. Trim Smart-seq2 public primer sequence from the Reads; 2. Remove the contaminated reads for adapters; 3. Remove the low quality reads; 4. Remove the reads whose N base more than 5% for total bases.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

molecule: polyA RNA

source_name: Brown adipose tissue

extract_protocol:
Total RNA was isolated by standard TRIzol protocol.
A total amount of 1-3μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® (NR604-01/02) following the manufacturer’s recommendations.

value: Brown adipose tissue

value: Mcu fl/fl AKO mouse


title: Brown adipose tissue, Mcu fl/fl AKO mouse, replicate 2


title: Liver, Control2, 12 weeks


title: adjacent normal tissue circRNA_1


title: Brown adipose tissue, Mcu fl/fl mouse, replicate 2

value: Mcu fl/fl mouse


title: Brown adipose tissue, Mcu fl/fl AKO mouse, replicate 1


title: lung adenocarcinomas tissue circRNA_3

description: circRNA expression data from lung adenocarcinomas tissue

source_name: lung adenocarcinomas tissue

value: lung adenocarcinomas tissue


title: White adipose tissue, Mcu fl/fl mouse, replicate 3

source_name: Inguinal adipose tissue

value: Inguinal adipose tissue


title: White adipose tissue, Mcu fl/fl AKO mouse, replicate 1


title: Brown adipose tissue, Mcu fl/fl mouse, replicate 1


title: White adipose tissue, Mcu fl/fl AKO mouse, replicate 2


title: Brown adipose tissue, Mcu fl/fl mouse, replicate 3


title: White adipose tissue, Mcu fl/fl mouse, replicate 1


title: 60TM mice, scRNA-seq

city: Chuo

first: Kozo

last: Saito

address: 1110 Shimokato

department: Department of Neuropharmacology

country: Japan

institute: University of Yamanashi

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequenced samples were processed using the Cell Ranger 5.0.0 pipeline (10x Genomics) and mapped to the GRCm38 mouse reference genome.
Supplementary files format and content: Tab-separated values file and matrix files

source_name: hippocampus

extract_protocol:
All procedures were performed according to the manufacturer’s protocol. Briefly, hippocampi were removed and dissociated using a papain-based protocol. After mice were intra-cardially perfused with ice-cold HBSS, the hippocampi were dissected and then digested at 37°C using papain for 20 min. Following mechanical dissociation, the sample was suspended in cold DPBS. The cell suspension was centrifuged at 500×g for 7 min at 4°C. The supernatant was completely aspirated. The cell pellet was resuspended carefully with cold 0.5% BSA/DPBS buffer. After the removal of cell debris. The tube was filled with 0.5% BSA/DPBS buffer. The suspension was passed through a 30um cell filter. After centrifugation at 1000×g for 10 min at 4°C, the supernatant was completely aspirated. The cell pellet was resuspended carefully with cold 0.5% BSA/DPBS buffer.
Isolated cell samples were applied to a Chromium system (10x Genomics) according to the manufacturer's instructions. Single cells were captured in droplets with gel beads containing barcoded primers. Libraries were prepared with the Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics) and were sequenced with the NextSeq 6000 system (Illumina) at average sequence depths of 63,967 reads/cell (WT mice) and 54,044 reads/cell (60TM mice). The quality of cDNA libraries was assessed using 2100 Expert Bioanalyzer Software (Agilent). scRNA-seq was performed by the Life Science Data Research Center at the University of Tokyo Graduate School of Frontier Sciences.

value: hippocampus

value: GFAP-hGFAP (60TM) on C57BL6/J background

value: 7 weeks old


title: lung adenocarcinomas tissue circRNA_2


title: WT mice, scRNA-seq

description: 10x Genomics


title: White adipose tissue, Mcu fl/fl mouse, replicate 2


title: JS39_CBM13

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read. To assess read quality, FastQC was run and low quality reads were removed using sickle with default setting. BBDuk (version 36_49) was used to trim/filter low quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the human reference genome (GRCh38) was done using HISAT2 (version 2.1.0) applying --no-mixed and --no-discordant options. UMI specific workflow that was developed and distributed by NuGEN was used to extract reads that are free from PCR artifacts (i.e. deduplication). The resulting deduplicated reads were summarized to each gene using using HTseq-count (version 0.11.2) by supplementing Ensembl gene annotation (GRCh38.78) and ERCC spike-in genes.
Assembly: GRCm38
Supplementary files format and content: Raw read counts are provided in a JSsamples_rawcount.xlsx file.

source_name: PBMC

extract_protocol:
Two volumes of TRI Reagent® (Zymo Research) were added to the tube and samples were immediately vortexed. Samples were visually inspected to confirm the desired homogenization and then incubated at 37 °C for 5 min. Eight more volumes of TRI Reagent® were added and vortexed. Total RNA was extracted using Direct-zol™ RNA Miniprep Kit (Zymo Research). Optical density values of extracted RNA were measured using NanoDrop (Thermo Scientific) to confirm an A260:A280 ratio above 1.9. RNA integration number (RIN) was measured using BioAnalyzer (Agilent Technologies) RNA 6000 Nano Kit.
The cDNA libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TAKARA Bio) and Nextera XT DNA Library Prep Kit (Illumina) as per the manufacturer's instructions. The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). The libraries were pooled and diluted to 3 nM using 10 mM Tris-HCl, pH 8.5 and then denatured using the Illumina protocol. The denatured libraries were loaded onto an S1 flow cell on an Illumina NovaSeq 6000 (Illumina) and run for 2X50 cycles according to the manufacturer's instructions. De-multiplexed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read.
BBDuk was used to trim/filter low quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the mouse reference genome (GRCm38) was done using HISAT2 (version 2.1.0) applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq by supplementing Ensembl gene annotation (GRCh38.78). Gene expression values were calculated as counts per million (CPM). Genes with no detected CPM in all samples were filtered out.

treatment_protocol: CD1 mice recieved i.p. injections of 25% EtOH in PBS at 4.0 g/kg daily at E16 and E17 for PAE model. For OMD model, dams recieved i.p. injection of STZ at 150mg/kg in citrate buffer. Blood samples from PAE and OMD were collected at P35-40. Three subtypes (T cell, B cell and monocytes) of white blood cells were sorted by using Flow cytometer for RNA sequencing.

value: Monocyte

tag: Sex

value: Male

value: CBM

tag: batch


title: lung adenocarcinomas tissue circRNA_1


title: Liver, Acsm3_KO2, 12 weeks


title: JS38_CBM13

value: B cell


title: JS37_CBM13

value: T cell


title: JS36_CBM12


title: White adipose tissue, Mcu fl/fl AKO mouse, replicate 3


title: JS33_CBM11


title: JS32_CBM11


title: JS30_CBM10


title: JS29_CBM10


title: JS34_CBM12


title: JS28_CBM10


title: JS26_CBM9


title: JS22_CBM8

value: Female


title: JS27_CBM9


title: JS25_CBM9


title: JS19_CBM7


title: JS23_CBM8


title: JS15_CBM5


title: JS24_CBM8


title: JS17_CBM6


title: JS14_CBM5


title: JS20_CBM7


title: JS18_CBM6


title: JS12_CBM4


title: JS11_CBM4


title: JS16_CBM6


title: JS9_CBM3


title: JS8_CBM3


title: JS10_CBM4


title: JS6_CBM2


title: JS31_CBM11


title: JS7_CBM3


title: JS5_CBM2


title: JS35_CBM12


title: JS4_CBM2


title: JS3_CBM1


title: JS2_CBM1


title: JS1_CBM1


title: JS54_2

value: EtOH


title: JS21_CBM7


title: JS50_2


title: JS51_2


title: JS44_2


title: JS52_2


title: JS53_2


title: JS49_2


title: JS43_2


title: JS36_2


title: JS42_2


title: JS33_2


title: JS31_2


title: JS34_2


title: JS41_2


title: JS29_2


title: JS35_2


title: JS30_2


title: JS55_1


title: JS53_1


title: OC-2

first: Hanqiu

last: Zheng

address: Qinghuayuan Sub-District, Haidian District

department: School of Medicine

institute: Tsinghua University

data_processing:
Illumina adapter sequences have been trimmed off the reads, which were subsequently mapped against the mm10 mouse reference using STAR (version 2.6.0c).  The counts for each gene were obtained by using featureCounts (version 1.6.2), and the minimum mapping quality score were set to 30.
Assembly: mm10; hg19
Supplementary files format and content: Processed data provided as supplementary file

source_name: osteoclast induced by mouse bone derived macropahge

growth_protocol: MDA-MB-231 were cultured with 10% Fetal Bovine Serum (FBS), 1% penicillin/streptomycin culture medium; Macrophages were cultured with10% Fetal Bovine Serum (FBS), 1% penicillin/streptomycin, 50ng/ml M-CSF (Promega); Osteoclasts were cultured with10% Fetal Bovine Serum (FBS), 1% penicillin/streptomycin, 50ng/ml M-CSF (Promega) and RANKL.

extract_protocol:
RNA of DMSO-treated or Olaparib (40 μM) treated MDA-MB-231 cells were purified . NEBNextUltra II Directional RNA Library Prep Kit for Illumina  was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MDA-MB-231 were treated with either DMSO or 40 μM Olaparib for 3 days. Macrophages and osteoclasts without treatment.

value: bone marrow

value: wild type

value: no treatment


title: JS54_1


title: JS55_2


title: JS52_1


title: OC-1


title: JS51_1


title: JS50_1


title: OC-3


title: NC-2

source_name: mouse bone derived macropahge


title: JS49_1


title: NC-3


title: NC-1


title: JS44_1


title: JS43_1


title: JS32_2


title: JS42_1


title: RAW-iKO HSV-1 4h-2 P65

city: beijing

first: yan

last: jiang

state: beijing

address: 东单三条5号 中国医学科学院基础医学研究所

institute: PUMC

library_source: genomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11, Chen et al., 2018) software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the  reference genome using BWA mem (v 0.7.12)
For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and present significant enrich. For single-end sequencing, the fragment size was estimated with MACS2 (Zhang et al.,   2008) predicted method with default parameters. MACS2 scan all the genome with a specific window size and calculate the reads enrichment level. A particular number of windows were used as samples to  build enrichment model and to predict fragment size. The following peak calling analysis was based on this predicted fragment size
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all  data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed
The interaction between transcript factor or chromatin histone modification and DNA were not random, while they show some specific sequence preference. Homer (Heinz et al., 2010) was used to detect the  denovo sequence motif and the matched known motifs
Assembly: mm10
Supplementary files format and content: narrowPeak

molecule: genomic DNA

growth_protocol: DMEM, 10% fetal bovine serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Cells were infected with HSV-1 for 4 hours before harvest

tag: chip antibody

value: HSV-1 4h


title: RAW-WT HSV-1 0h-1 P65

address: 东单三条5号 中国医学科学院基础医学研究所

value: HSV-1 0h


title: JS41_1


title: RAW-WT HSV-1 4h P65

address: 东单三条5号 中国医学科学院基础医学研究所


title: RAW-WT HSV-1 0h-2 P65

address: 东单三条5号 中国医学科学院基础医学研究所


title: RAW-iKO HSV-1 4h-1 P65

address: 东单三条5号 中国医学科学院基础医学研究所


title: RAW-iKO HSV-1 0h-2 P65

address: 东单三条5号 中国医学科学院基础医学研究所


title: JS38_1


title: JS39_1


title: JS37_1


title: RAW-WT, HSV-1-4h, H3K4me3

address: 东单三条5号 中国医学科学院基础医学研究所

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11, Chen et al., 2018)  software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads  containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the  reference genome using BWA mem (v 0.7.12)
For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and present significant enrich. For single-end sequencing, the fragment size was estimated with MACS2 (Zhang et al.,   2008) predicted method with default parameters. MACS2 scan all the genome with a specific window size and calculate the reads enrichment level. A particular number of windows were used as samples to  build enrichment model and to predict fragment size. The following peak calling analysis was based on this predicted fragment size
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all  data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed
Assembly: mm10
Supplementary files format and content: narrowPeak


title: JS36_1


title: RAW-iKO HSV-1 0h-1 P65

address: 东单三条5号 中国医学科学院基础医学研究所


title: JS35_1


title: JS34_1


title: RAW-WT, HSV-1-0h, H3K4me3

address: 东单三条5号 中国医学科学院基础医学研究所


title: RAW-iKO, HSV-1-4h, H3K4me3

address: 东单三条5号 中国医学科学院基础医学研究所


title: RAW-iKO, HSV-1-0h, H3K4me3

address: 东单三条5号 中国医学科学院基础医学研究所


title: JS32_1


title: JS33_1


title: RAW-WT HSV-1-0h, ATAC

address: 东单三条5号 中国医学科学院基础医学研究所

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated.
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2). These reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ ≥ 13), non mitochondrial chromosome, and properly paired reads (longer than 18 nt).
All peak calling was performed with macs2 using ‘macs2 callpeak --nomodel --keepdup all --call-summits’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
Assembly: mm10
Supplementary files format and content: narrowPeak

extract_protocol:
ATAC-seq was performed as previously reported (Buenrostro et al. 2013;Corces et al. 2017; Bajic M et al. 2018). Briefly, nuclei was extracted from samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min.
Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit

treatment_protocol: Cells were infected with or without HSV-1 for 4 hours before harvest


title: RAW-WT, HSV-1-4h-1, ATAC

address: 东单三条5号 中国医学科学院基础医学研究所


title: JS31_1


title: JS30_1


title: RAW-WT, HSV-1-4h-2, ATAC

address: 东单三条5号 中国医学科学院基础医学研究所


title: JS24_1


title: JS40_1


title: RAW-iKO, HSV-1-4h-1, ATAC

address: 东单三条5号 中国医学科学院基础医学研究所


title: RAW-iKO, HSV-1-4h-2, ATAC

address: 东单三条5号 中国医学科学院基础医学研究所


title: JS29_1


title: JS19_2

value: PBS


title: Fetal liver

city: Hyderabad

first: Rashna

last: Bhandari

state: Telangana

address: Bldg 7, Gruhakalpa, 5-4-399/B Nampally

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

data_processing:
To ensure the integrity, raw reads were subjected to quality assessment using FastQC
The adaptor sequences and low-quality bases were trimmed using TrimGalore
The optimized reads were then mapped to the human hg38 reference genome via the splice-aware aligner tool, STAR.
Curation and sorting of data into BAM format using samtools and then quantification of reads to specific genes was achieved with FeatureCounts.
Raw counts were normalised to TPM metrics using RNAnorm
Assembly: hg38
Supplementary files format and content: tab-separated values file includes raw counts
Supplementary files format and content: tab-separated values file includes TPM values

source_name: Liver (fetal)

extract_protocol:
Total RNA was isolated from liver tissue using Rneasy mini plus kit (Qiagen).
500 ng of total RNA with RIN ≥7 was used for mRNA library preparation using the MGIEasy RNA Library Prep Set (MGI).

value: Liver (fetal)

value: Hepatocytes

value: Homozygous nonsense variant in SERPINA11 gene, (NM_001080451.2;c.672C>A;p.Tyr224*)

tag: developmental stage

value: 19 week gestation


title: pFPCO S1

city: Minato Ku

first: kenta

last: takeuchi

state: Tokyo To

address: 4-6-1, Shirokanedai

institute: The Institute of Medical Science, The University of Tokyo

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values file and matrix files

source_name: Multicellular organoid derived PDAC cells, hiPSC-endothelial cells and hiPSC-mesenchymal cells

extract_protocol:
FPCOs were digested into single cell suspension with collagenase (Sigma-Aldrich) and Pronase (Roche) in reaction buffer(). The obtained cell suspension were filtered 70-μm cell straner (SPL), and re-suspended in PBS(-) to avoid cell-cell attachment.
Chromium NEXT GEM Single Cell 3' Kit v3.1 (PN-1000130, 10X Genomics), Chromium NEXT GEM Chip G Single Cell Kit (PN- 1000127) and Chromium NEXT GEM Single Cell 3' v3.1 Gel Beads (PN-1000129, 10X Genomics) were used to create the library according to Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) USER GUIDE. 5000 cells in FPCO-derived single cell suspension were loaded into the Chromium Controller to create single-cell Gel-Beads emulsions (GEMs). GEMs were subjected to reverse transcription in a T100 TM Thermal Cycler (Biolad). The resulting cDNA products were recovered from the GEMs using Recovery Agent and cleaned up using Dynabeads MyONE Saline (Beckman Coulter). The cDNA products were then subjected to amplification in a T100TM Thermal Cycler according to the manufacturer's protocol. The amplified cDNA products were cleaned up by SPRIselect (Beckman Coulter) and then their concentrations were measured using a high sensitivity D5000 ScreenTape (Agilent technology). The cDNA products were then fragmented by enzyme, end-repaired and poly A-tailed, and cleaned up again by SPRIselect. Next, adaptor ligation and subsequent cleanup by SPRIselect were performed, Only appropriately labeled samples were obtained by double-size selection using SPRIslect. Samples were quality-checked using a high sensitivity D5000 ScreenTape (Agilent technology) and sequenced on a NovaSeq6000 (Illumina) at pair-end 150 bp.


title: qFPCO S2

value: Multicellular organoid derived PDAC cells, hiPSC-endothelial cells and hiPSC-mesenchymal cells


title: JS18_2


title: A549, 16h Cort113 > 2h DEX+Cort113 rep1

city: Zürich

first: Katharina

last: Gapp

address: Winterthurerstrasse 190

department: Health Science and Technology

country: Switzerland

institute: Swiss Federal Institue of Technology

data_processing:
Gene expression was quantified from RNA-seq data using Salmon 1.7.0 with the --validateMappings option on the Ensembl 105 transcriptome.
Counts were aggregated to gene-level using the tximport package.
For differential expression analysis, all samples were considered together, and two surrogate variables were included in the model using the sva 3.44.0 package.
Differential expression analysis was performed with edgeR 3.38.1, filtering genes using filterByExpr with a minimum count of 20.
Assembly: GRCh38
Supplementary files format and content: geneCounts.tab  is a tab-delimited matrix of estimated read counts per gene and sample.
Supplementary files format and content: SE.processed.rds;  a R object of class SummarizedExperiment, containing raw and normalized gene expression, sample annotation, as well as the various differential expression results.

growth_protocol: A549 cells (CCL-185) were purchased from American Type Culture Collection (ATCC) and were maintained in F-12 medium with 10% FBS and 1% P/S. All cells were kept at 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Quick-RNA Microprep Kit (Zymoresearch, R1051), followed by cDNA synthesis. RNA concentration was measured by NanoDrop and integrity was checked on an agarose gel.
Next® Ultra RNA Library Prep Kit for Illumina

treatment_protocol: KH-95, KH-99, KH-102, KH-103, and dexamethasone  (Sigma) were used at 100nM except indicated otherwise. Mifepristone (Sigma-Aldrich), CORT113176 (courtesy from Corcept) were used at 1uM. MG-132 (MedChemExpress) was used at 20uM. All mentioned compounds were dissolved in DMSO.

value: 16h Cort113 >  2h DEX+Cort113


title: A549, 16h MIF  > 2h DEX+MIF rep1

value: 16h MIF  >  2h DEX+MIF


title: JS23_1


title: JS17_2

value: Monocyte

value: Male


title: JS16_2

value: B cell


title: A549, 16h KH-103 > 2h DEX+KH-103 rep1


title: A549, 16h DMSO > 2h DEX+DMSO rep1

value: 16h DMSO >  2h DEX+DMSO


title: JS15_2

value: T cell


title: JS14_2


title: A549, 2h DEX > 16h DEX+Cort113 rep4

value: 2h DEX >  16h DEX+Cort113


title: JS13_2


title: A549, 2h DEX > 16h DEX+MIF rep4

value: 2h DEX >  16h DEX+MIF


title: JS12_2


title: A549, 2h DEX > 16h DEX+KH-103 rep4

value: 2h DEX >  16h DEX+KH-103


title: JS11_2


title: A549, 18h Cort113 rep1

value: 18h Cort113


title: RAW-iKO, HSV-1-0h, ATAC

address: 东单三条5号 中国医学科学院基础医学研究所

value: HSV-1 0h


title: JS10_2

value: PBS


title: V0_L1

source_name: human breast cancer cell

tag: tissue

value: primary breast

value: DMSO


title: JS9_2

value: Female


title: JS8_2


title: JS20_2


title: CAF_10

data_processing:
The sequencing reads were aligned to hg19_AmpliSeq_Transcriptome_ERCC_v1 using Torrent Mapping Alignment Program. The data were analyzed on AmpliSeqRNA plug-in v5.2.0.3 of the Torrent Suite Software v5.2.2 (Thermo Fisher Scientific).
Assembly: hg19
Supplementary files format and content: Csv file include RPM value in each sample
Supplementary files format and content: Csv file include sample barcode and related sample information

source_name: Cancer associated fibroblast derived PDAC patient

extract_protocol:
RNA was harvested using PureLink RNA Micro Scale kit. RNA-Seq libraries were prepared using 100 ng and 50 ng of the total RNA from cancer cells and MCs, respectively.
RNA-seq library was prepared using Ion Ampliseq Transcriptome Human Gene Expression kit (Thermo Fisher Scientific, Carlsbad, CA), according to the manufacturer’s protocol.


title: A549, 16h MIF  > 2h DEX+MIF rep4


title: JS7_2


title: A549, 2h DEX > 16h DEX+DMSO rep4

value: 2h DEX >  16h DEX+DMSO


title: Bone marrow plasma cells

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Cell Ranger v5.0.0 was used to create raw read FASTQ files. Genewise reads counts were generated with Cell Ranger v7.0.0 using a custom reference made with the newly published human T2T-CHM13 reference assembly and a custom GTF file specific to human plasma cell usage.
Assembly: T2T-CHM13
Supplementary files format and content: Standard 10x output consisting of tab-separated text files and with read counts in matrix-market format.

source_name: bone marrow

extract_protocol:
Human plasma cells were sorted as CD138+CD38hi into ice-cold 0.5% bovine serum albumin (BSA) in PBS.
Cells were processed through the 10x Chromium Single Cell 3′ v2 Library Kit (10× Genomics), according to the manufacturer’s protocol. The channel was loaded with 10,000 cells yielding 6747 single cells for analysis. The cells were then partitioned into gel beads in emulsion in the instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, shearing, and 5′-adapter and sample index attachment.

value: plasma cells

value: bone marrow


title: CAF_8

value: Cancer associated fibroblast derived PDAC patient


title: CAF_6


title: CAF_7


title: A549, 16h KH-103 > 2h DEX+KH-103 rep4


title: CAF_9


title: JS6_2

value: Monocyte


title: JS5_2

value: B cell


title: CAF_4


title: A549, 18h Cort113 rep4


title: CAF_5


title: V40_L1

value: 40 microM Olaparib


title: CAF_3


title: CAF_2


title: A549, 18h MIF rep4

value: 18h MIF


title: CAF_1


title: A549, 16h Cort113 > 2h DEX+Cort113 rep4

value: 16h Cort113 >  2h DEX+Cort113


title: hBMMSC_replicate3

source_name: Bone Marrow Mesenchymal Stem Cells

value: Bone Marrow Mesenchymal Stem Cells


title: JS3_2

value: Male


title: A549, 18h KH-103 rep4


title: hBMMSC_replicate2


title: JS2_2


title: A549, 18h MIF rep1


title: qFPCO-CAF_replicate3

value: Mesenchymal cells cocultured with PCOs and hiPSC-EC


title: A549, 18h DMSO rep3

value: 18h DMSO


title: qFPCO-CAF_replicate2


title: hBMMSC_replicate1


title: qFPCO-CAF_replicate1


title: JS1_2

value: T cell

value: PBS


title: JS22_1


title: pFPCO-CAF_replicate3


title: A549, 18h untreated rep4

value: 18h untreated


title: pFPCO-CAF_replicate2


title: pFPCO-CAF_replicate1


title: A549, 16h DMSO > 2h DEX+DMSO rep4

value: 16h DMSO >  2h DEX+DMSO


title: A549, 2h DEX > 16h DEX+Cort113 rep3

value: 2h DEX >  16h DEX+Cort113


title: hiPSC-MC_replicate2

value: Mesenchymal cell derived hiPSC


title: JS21_1

value: Female


title: JS4_2


title: A549, 2h DEX > 16h DEX+MIF rep3

value: 2h DEX >  16h DEX+MIF


title: hiPSC-MC_replicate3


title: JS20_1


title: JS19_1

value: Monocyte


title: hiPSC-MC_replicate1


title: qFPCO-cancer_cell_replicate2

source_name: Cancer cells cocultured with hiPSC-EC and MC


title: A549, 2h DEX > 16h DEX+KH-103 rep3

value: 2h DEX >  16h DEX+KH-103


title: qFPCO-cancer_cell_replicate3

value: Cancer cells cocultured with hiPSC-EC and MC


title: JS18_1

value: B cell


title: qFPCO-cancer_cell_replicate1


title: A549, 2h DEX > 16h DEX+DMSO rep3

value: 2h DEX >  16h DEX+DMSO


title: pFPCO-cancer_cell_replicate3


title: JS17_1


title: pFPCO-cancer_cell_replicate1


title: JS16_1


title: pFPCO-cancer_cell_replicate2


title: A549, 16h MIF  > 2h DEX+MIF rep3

value: 16h MIF  >  2h DEX+MIF


title: PCO_replicate2

source_name: Cancer cells derived PDAC patient

value: Cancer cells derived PDAC patient


title: PCO_replicate1


title: A549, 16h DMSO > 2h DEX+DMSO rep3


title: A549, 16h Cort113 > 2h DEX+Cort113 rep3

value: 16h Cort113 >  2h DEX+Cort113


title: A549, 16h KH-103 > 2h DEX+KH-103 rep3


title: RNAseq_WT_testes_BamGAL4_rep2

city: Stanford

first: Neuza

last: Reis Matias

state: CA

address: 279 Campus Drive

department: Developmental Biology

institute: Stanford University

data_processing:
Adapters and low-quality bases were trimmed with trimGalore: trim_galore –quality 20 –stringency 1 –length 30 –paired_end –clip_R1 3 $Input1 $Input2 –output_dir trim_PE/
Reads were mapped to the Drosophila melanogaster genome build dm6 using STAR. Reads that fell within gene regions were counted with STAR using Ensembl annotation BDGP6.84. star_pass1: STAR –runThreadN 4 –runMode alignReads –genomeDir $star_index –alignSJoverhangMin 10 –alignIntronMax 100000 –alignMatesGapMax 100000 –outFilterMismatchNoverLmax 0.04 –readFilesIn $Input1_trimmed $Input2_trimmed –outFileNamePrefix $pass1_prefix –outSAMtype None. star_pass2: STAR –runThreadN 4 –runMode alignReads –quantMode GeneCounts –genomeDir $star_index –alignIntronMax 100000 –alignMatesGapMax 100000 –outFilterMismatchNoverLmax 0.04 –sjdbFileChr- StartEnd $junction –readFilesIn $Input1_trimmed $Input2_trimmed –out- SAMtype BAM SortedByCoordinate –limitBAMsortRAM 10000000000 –outFileNamePrefix $pass2_prefix.
Samtools was used to create .bw files for visualization: bamCoverage -b $Input -o $Output –binSize 1 –normalizeUsing CPM -p 4
Assembly: Ensembl annotation BDGP6.84
Supplementary files format and content: STAR output: ReadsPerGene
Supplementary files format and content: bamCoverage output: bw files for visualization

organism: Drosophila melanogaster

source_name: Testes

growth_protocol: Crosses were maintained for 3 days at 25C, the adult flies removed and the progeny moved to 29C until dissection time.

extract_protocol:
total RNA was extracted using the kit: RNeasy Plus Mini Kit from QIAGEN
Library was constructed using the kit: NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (#E7760S) using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (#E7490S).

treatment_protocol: 150 pairs of testes per sample were dissected in PBS in a glass cyclops dish in batches of 50 pairs. Testes were transferred to a 1.7 ml tube with PBS using forceps. PBS was removed and the sample snap-frozen in liquid nitrogen. Samples were kept at −80°C until the next step.

value: Testes


title: JS14_1

value: Male


title: A549, 18h KH-103 rep1


title: RNAseq_WT_testes_BamGAL4_rep1


title: A549, 18h Cort113 rep3

value: 18h Cort113


title: A549, 18h MIF rep3

value: 18h MIF


title: JS12_1

value: T cell

value: PBS


title: L5-Bsh-Dam, rep3

city: Eugene

first: Chris

last: Doe

address: 1440 Franklin Blvd

institute: University of Oregon

data_processing:
each fastq file was assessed for quality using FastQC (v0.11.9)
The damidseq pipeline was run to generate bedgraph files
Supplementary files format and content: bedgraph: it contains Dam-only and Log2 ratio (Bsh-Dam/Dam-only)
Library strategy: Targeted DamID

source_name: Lamina neuron 5

extract_protocol:
DNA was extracted using a QIAamp DNA Micro Kit (Qiagen), digested with DpnI (NEB) overnight, and cleaned up using Qiagen PCR purification columns. DamID adaptors were ligated using T4 DNA ligase (NEB) followed by DpnII (NEB) digestion for 2 h and PCR amplification using MyTaq HS DNA polymerase (Bioline).
DamID-adaptors removed by AlwI-digestion, end-repaired, A-tailed, followed by ligation of Sequencing-adaptors and PCR-amplification (Marshall, O et al., 2016, Nat Protoc)

value: Lamina neuron 5


title: L5-Bsh-Dam, rep1


title: L5-Bsh-Dam, rep2


title: JS11_1


title: easyCLIP_NoEpitope_2

description: easyCLIP

library_source: other

data_processing:
cutadapt was used to trim the reads and move the UMI to the read name: cutadapt -ACTGTCTCTTATACACATCTGACGCTGCCGACGANNNNNNNNNNGTGTAGATCTCGGTGGTCGCCGTATCATT -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG –pair-filter=any -u 13 -U 10 -j 1 –rename=“{id}__{r1.cut_prefix}-{r2.cut_prefix}” –minimum-length 14 -o $Output1 -p $Output2 $Input1 $Input2
Reads were mapped to the Drosophila melanogaster genome build dm6 using STAR. Reads that fell within gene regions were counted with STAR using Ensembl annotation BDGP6.84. star_pass1: STAR –runThreadN 4 –runMode alignReads –genomeDir $star_index –alignSJoverhangMin 10 –alignIntronMax 100000 –alignMatesGapMax 100000 –outFilterMismatchNoverLmax 0.04 –readFilesIn $Input1_trimmed $Input2_trimmed –outFileNamePrefix $pass1_prefix –outSAMtype None. star_pass2: STAR –runThreadN 4 –runMode alignReads –quantMode GeneCounts –genomeDir $star_index –alignIntronMax 100000 –alignMatesGapMax 100000 –outFilterMismatchNoverLmax 0.04 –sjdbFileChr- StartEnd $junction –readFilesIn $Input1_trimmed $Input2_trimmed –out- SAMtype BAM SortedByCoordinate –limitBAMsortRAM 10000000000 –outFileNamePrefix $pass2_prefix
Duplicates were removed using samtools followed by umi_tools: samtools view –bam -h -F 256 -f 64 -F 4 -q 10 -o $Output1 $Input; samtools index $Output1; umi_tools dedup –stdin=$Output1 –stdout= $Output2 –umi-separator=“__” –extract-umi-method=read_id
Samtools was used to create .bw files for visualization: bamCoverage -b $Input -o $Output –binSize 1 –normalizeUsing CPM -p 4
Reads that fell within gene regions were counted with featureCounts using Ensembl annotation BDGP6.84: featureCounts -t exon -g gene_id -p -a $gtf_file -o $Output $Input
Assembly: Ensembl annotation BDGP6.84
Supplementary files format and content: bamCoverage output: bw files for visualization
Supplementary files format and content: featureCounts output: ReadsPerGene

molecule: other

growth_protocol: Flies were raised at 25C

extract_protocol: Due to complexity of protocol, please check methods on this publication for details: Cell-type-specific interacting proteins collaborate to regulate the timing of Cyclin B protein expression in male meiotic prophase. Baker CC, Gallicchio L, Matias NR, Porter DF, Parsanian L, Taing E, Tam C, Fuller MT. Development. 2023 Oct 27:dev.201709. doi: 10.1242/dev.201709

tag: rip antibody

value: anti-GFP (mouse, Millipore Sigma #11814460001)


title: easyCLIP_SYP_1

description: easyCLIP

treatment_protocol: Due to complexity of protocol, please check methods on this publication for details: Cell-type-specific interacting proteins collaborate to regulate the timing of Cyclin B protein expression in male meiotic prophase. Baker CC, Gallicchio L, Matias NR, Porter DF, Parsanian L, Taing E, Tam C, Fuller MT. Development. 2023 Oct 27:dev.201709. doi: 10.1242/dev.201709

value: eYFP-Syp


title: easyCLIP_SYP_2

description: easyCLIP


title: JS10_1


title: L5-Dam-only, rep3


title: A549, 18h KH-103 rep3


title: PCO_replicate3


title: JS15_1


title: L5-Dam-only, rep2


title: JS9_1

value: Monocyte

value: Female


title: A549, 18h DMSO rep2

value: 18h DMSO


title: JS13_1

value: B cell


title: L5-Dam-only, rep1


title: JS8_1


title: easyCLIP_NoEpitope_1

description: easyCLIP


title: JS6_1


title: A549, 2h DEX > 16h DEX+Cort113 rep2

value: 2h DEX >  16h DEX+Cort113


title: A549, 2h DEX > 16h DEX+MIF rep2

value: 2h DEX >  16h DEX+MIF


title: JS5_1


title: Peyer’s patches plasmablasts, biol rep 2

data_processing:
Sequencing was undertaken on an Illumina NextSeq 500 to produce 86bp single-end reads.
Read alignment was performed with the align function of the Rsubread package.
Genewise read counts were obtained with the featureCounts function of the Rsubread package and Rsubread's inbuilt mm10 annotation.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files with columns for Entrez Gene ID, gene length (number of bases in union of all exons), and the number of reads. The supplementary file GenewiseCounts.txt.gz gives read counts for all samples in one file.

source_name: Peyer’s patches

extract_protocol:
RNeasy Plus Mini kit (Qiagen).
TruSeq RNA Sample preparation kit (Illumina)

value: Peyer’s patches

value: Plasmablasts

value: female


title: Peyer’s patches plasma cells, biol rep 1

value: Plasma cells


title: Spleen plasma cells, biol rep 1

source_name: Spleen

value: Spleen


title: JS4_1


title: Spleen plasmablasts, biol rep 1


title: Small intestine plasma cells, biol rep 3

source_name: Small intestine (lamina propria)

value: Small intestine (lamina propria)


title: Peyer’s patches plasmablasts, biol rep 1


title: Peyer’s patches plasma cells, biol rep 2


title: Spleen plasma cells, biol rep 2


title: A549, 2h DEX > 16h DEX+KH-103 rep2

value: 2h DEX >  16h DEX+KH-103


title: A549, 16h Cort113 > 2h DEX+Cort113 rep2

value: 16h Cort113 >  2h DEX+Cort113


title: Colon plasma cells, biol rep 3

source_name: Colon

value: Colon


title: SD rat, Myocardial infraction induced, ETA53 75mpk (2)

city: Suwon-si

first: Uisuk

last: Jeong

state: Gyeonggi-do

address: 206, World cup-ro

department: Molecular Science and Engineering

country: South Korea

institute: Ajou university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to rn6 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Rattus norvegicus

source_name: left ventricle

growth_protocol: after the sacrifice of the rat, the left ventricle tissue was kept in RNAlater™ Stabilization Solution.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: left ventricle

value: male

value: 7 weeks

value: WT

tag: disease state

value: Left Anterior Descending Coronary Artery Ligation


title: A549, 18h untreated rep3

value: 18h untreated


title: JS2_1

source_name: PBMC

tag: cell type

value: B cell

value: Male

value: PBS


title: SD rat, Myocardial infraction induced, ETA53 75mpk (3)


title: Spleen plasmablasts, biol rep 2

value: Plasmablasts


title: Mammary gland plasma cells, biol rep 2

source_name: Mammary gland (day 18 postpartum)

value: Mammary gland (day 18 postpartum)

value: female


title: A549, 18h DMSO rep1

value: 18h DMSO


title: JS7_1

value: T cell

value: Female


title: JS1_1


title: JS3_1

value: Monocyte


title: SD rat, Myocardial infraction induced, ETA53 20mpk (3)


title: Mammary gland plasma cells, biol rep 1

value: Plasma cells


title: A549, 2h DEX > 16h DEX+DMSO rep2

value: 2h DEX >  16h DEX+DMSO


title: RAW-WT, HSV-1-4h-3

address: 东单三条5号 中国医学科学院基础医学研究所

data_processing:
Base calling was performed using the BGISeq500 platform.
The sequencing data was filtered with SOAPnuke (v1.5.2), by removing adaptor sequences, contamination and low-quality reads.
lean 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)
differential expression analysis was performed using the PossionDis with False Dicovery Rate (FDR)<= 0.001 and │log2Ratio│>=1.
Assembly: mm10
Supplementary files format and content: Excel table with FPKM values for each gene in each sample
Supplementary files format and content: Excel table with raw read counts for each gene and each sample

extract_protocol:
Total RNA were extracted using trizol reagent. Oligo(dT)-attached magnetic beads were used to purified mRNA.
Library was constructed by BGI using library construction methods underlying the BGISEQ-500 platform.

value: HSV-1 4h


title: A549, 16h KH-103 > 2h DEX+KH-103 rep2


title: A549, 16h DMSO > 2h DEX+DMSO rep2

value: 16h DMSO >  2h DEX+DMSO


title: RAW-WT, HSV-1-4h-1

address: 东单三条5号 中国医学科学院基础医学研究所


title: Small intestine plasma cells, biol rep 1

value: Small intestine (lamina propria)

value: male


title: SD rat, Myocardial infraction induced, ETA53 20mpk (1)

value: left ventricle

value: 7 weeks

value: WT

value: Left Anterior Descending Coronary Artery Ligation


title: Small intestine plasma cells, biol rep 2

value: pooled male and female


title: SD rat, Myocardial infraction induced, ETA53 20mpk (2)


title: RAW-WT, HSV-1-4h-2

address: 东单三条5号 中国医学科学院基础医学研究所


title: SD rat, Myocardial infraction induced (3)


title: RAW-WT, HSV-1-0h-3

address: 东单三条5号 中国医学科学院基础医学研究所

value: HSV-1 0h


title: Mammary gland plasma cells, biol rep 3

value: Mammary gland (day 18 postpartum)

value: female


title: A549, 18h MIF rep2

value: 18h MIF


title: SD rat, Myocardial infraction induced (2)


title: SD rat, Myocardial infraction induced, ETA53 75mpk (1)


title: Colon plasma cells, biol rep 1

value: Colon


title: SD rat, Myocardial infraction induced (1)


title: A549, 18h KH-103 rep2


title: Bone marrow plasma cells, biol rep 1

source_name: Bone marrow

value: Bone marrow


title: RAW-WT, HSV-1-0h-1

address: 东单三条5号 中国医学科学院基础医学研究所


title: SD rat, sham  surgery (3)


title: A549, 16h MIF  > 2h DEX+MIF rep2

value: 16h MIF  >  2h DEX+MIF


title: Bone marrow non-IgA plasma cells, biol rep 3

value: Plasma cells (non-IgA)


title: RAW-iKO, HSV-1-4h-3

address: 东单三条5号 中国医学科学院基础医学研究所

value: HSV-1 4h


title: SD rat, sham  surgery (2)


title: Bone marrow IgA plasma cells, biol rep 3

value: Plasma cells (IgA)


title: Colon plasma cells, biol rep 2

value: Plasma cells


title: A549, 18h Cort113 rep2

value: 18h Cort113


title: RAW-iKO, HSV-1-4h-2

address: 东单三条5号 中国医学科学院基础医学研究所


title: A549, 2h DEX > 16h DEX+Cort113 rep1

value: 2h DEX >  16h DEX+Cort113


title: SD rat, sham  surgery (1)

value: left ventricle

value: male

value: 7 weeks


title: RAW-iKO, HSV-1-0h-3

address: 东单三条5号 中国医学科学院基础医学研究所


title: A549, 18h untreated rep1

value: 18h untreated


title: EMO, 20%O2, day7 2

city: Sendai

first: Shun

last: Shibata

address: 2-1 Seiryo-chou

department: Graduate School of Medicine

institute: Tohoku University

data_processing:
The sequenced data were first trimmed for quality control using the TrimGalore software (v0.6.7).
The reads were then aligned to the reference genome (UCSC hg38) using STAR (v2.7.10a)
The expression levels (transcript per million) of the Refseq genes were calculated using RSEM(v1.3.1)
Assembly: UCSC hg38
Supplementary files format and content: comma-separated values file includes raw counts for each sample
Supplementary files format and content: comma-separated values file include TPM values for each sample

source_name: human decidua

extract_protocol:
Total RNA was extracted using the RNeasy Mini or Micro Kit (QIAGEN), and genomic DNA was removed by digestion with RNase-free DNase I (QIAGEN).
RNA libraries were prepared using the NEBNext UltraII Directional RNA Library Prep Kit (New England Biolabs)

value: human decidua

value: endometrial epithelial cells

tag: lot


title: A549, 2h DEX > 16h DEX+KH-103 rep1

value: 2h DEX >  16h DEX+KH-103


title: RAW-WT, HSV-1-0h-2

address: 东单三条5号 中国医学科学院基础医学研究所

value: HSV-1 0h


title: EMO, 20%O2, day7 1


title: RAW-iKO, HSV-1-4h-1

address: 东单三条5号 中国医学科学院基础医学研究所


title: A549, 2h DEX > 16h DEX+MIF rep1

value: 2h DEX >  16h DEX+MIF


title: EMO, 5%O2, day7 2


title: A549, 2h DEX > 16h DEX+DMSO rep1

value: 2h DEX >  16h DEX+DMSO


title: RAW-iKO, HSV-1-0h-2

address: 东单三条5号 中国医学科学院基础医学研究所


title: Bone marrow IgA plasma cells, biol rep 1

value: Bone marrow

value: female


title: Bone marrow IgA plasma cells, biol rep 2


title: A549, 18h untreated rep2


title: Bone marrow non-IgA plasma cells, biol rep 2

value: Plasma cells (non-IgA)


title: IgG-CR-OCIAML2

status: Public on Nov 11 2023

first: Aliaksandra

last: Radzisheuskaya

address: 237 Fulham road

department: Cancer Biology

institute: The Institute of Cancer Research

data_processing:
The sequencing reads were 3’ trimmed and filtered for quality and adapter content using TrimGalore (v0.4.5), with a quality setting of 15, and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Reads were aligned to human assembly hg38 with version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and were deduplicated using MarkDuplicates in Picard Tools (v2.16.0).
Subsequent Cut&Run data visualization and analysis were performed using EaSeq software.
Assembly: GRCh38/hg38
Supplementary files format and content: bigwig files
Library strategy: CUT&RUN

source_name: blood

growth_protocol: RPMI 1640, GlutaMAX supplement, sodium pyruvate medium containing 10% heat-inactivated FBS and 1x Penicillin/Streptomycin; 20% FBS for U937 and OCI-AML2 cells.

extract_protocol:
Cut&Run was performed using the CUTANA™ ChIC/CUT&RUN Assay kit (EpiCypher) according to the manufacturer’s instructions or the homemade reagents according to EpiCypher CUTANA protocol.
NEBNext Ultra II

treatment_protocol: Where indicated, the cells were transduced with the lentiviruses driving the corresponding sgRNA expression and collected for Cut&Run 4 days post-transduction.

value: blood

value: myeloid

value: wild type

value: no treatment


title: RAW-iKO, HSV-1-0h-1

address: 东单三条5号 中国医学科学院基础医学研究所


title: SMARCA5-CR-OCIAML2


title: EMO, 5%O2, day7 1


title: culture_eTIP_WT_500uM_ETOP_Input_1

city: St. Louis

first: Harrison

last: Gabel

state: MO

address: 4523 Clayton Ave

department: Neuroscience

institute: Washington University in St. Louis

description: mixed (males and females)

data_processing:
Sequenced reads were mapped to the mm9 genome using bowtie2 alignment and reads were extended based on library sizes and deduplicated. Bedtools coverage -counts parameter was used to quantify eTIP signal at promoter associated region, defined as 1kb upstream to 3kb downstream of the transcription start site (TSS), and at the gene body, defined as 3kb downstream of the TSS to the transcription end site (TES). edgeR was then used to determine differential eTIP-signal across conditions. Bigwig files were generated using bedtools genomecov to convert reads to bedgraph format. Bedgraphs were normalized to counts per million (cpm) and then converted to bigWigs.
Assembly: mm9
Supplementary files format and content: bigwig
Library strategy: eTIP-Seq

source_name: primary neuron cultures

growth_protocol: Primary neurons were cultured in neurobasal medium with 5% fetal bovine serum, GlutaMAX, B27 Supplement and Antibiotic-Antimycotic and maintained at 37oC with 5% CO2. Neurons were grown in vitro for 3 days. At DIV3 and DIV9, cells were fed with neurobasal medium with 4.84 ug/mL uridine 5’-triphosphate, 2.46 ug/mL 5-fluoro-2’-deoxyuridine, GlutaMAX, B27 Supplement and Antibiotic-Antimycotic.

extract_protocol:
Acute cortical slices were treated with 0.5mM etoposide (VP-16) for 15 minutes at 37oC. To fragment DNA, the lysates were sonicated with Covaris E220 sonicator (5% Duty Factory, 140 Peak Incidence Power, 200 cycles per burst, milliTUBE 1mL AFA Fiber). eTIP was performed with TOP2B (Fortis Life Sciences, A300-950A) or TOP2B (Santa Cruz, sc-13059).
At 12 days in vitro (DIV12), primary neuron cultures were treated with etoposide (VP-16) and incubated at 37oC. To fragment DNA, the lysates were sonicated with Covaris E220 sonicator (5% Duty Factory, 140 Peak Incidence Power, 200 cycles per burst, milliTUBE 1mL AFA Fiber). eTIP was performed with TOP2B (Fortis Life Sciences, A300-950A) or TOP2B (Santa Cruz, sc-13059).
eTIP libraries were generated using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences).
Libraries were pooled to a final concentration of 4-10nM and reads were generated on the Illumina HiSeq 3000 with the Genome Technology Access Center or generated on the Illumina Nextseq 500 with the Center for Genome Science at Washington University in St. Louis, typically yielding 15-40 million single-end reads per sample.

treatment_protocol: Primary neuron cultures were transduced with lentivirus at an MOI of 3 on days in vitro (DIV3).

value: primary neuron cultures

value: wildtype

value: Embryonic day (E) 14.5

value: etoposide

tag: viral treatment

tag: antibody


title: culture_eTIP_WT_500uM_ETOP_Input_2

description: mixed (males and females)

tag: age


title: culture_eTIP_WT_500uM_ETOP_TOP2B_A300-950A_1

description: mixed (males and females)

value: Topo II b (Fortis Life Sciences, A300-950A)


title: BPTF-CR-OCIAML2

city: London


title: ETd8_rep2

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Koyto Univ.

data_processing:
Illumina Real-Time Analysis (RTA) software used for basecalling.
The raw reads were trimmed and quality-filtered using the Trim Galore! (ver. 0.6.5), Trimmomatic (ver. 0.39) and cutadapt (ver. 2.7) software. Clean reads were aligned versus the N2 Caenorhabditis elegans reference genome ce11 (WBcel235.98) using STAR (ver. 2.7.2b).
The read count of gene features was performed with the featureCounts tool (ver. 1.6.4)
Supplementary files format and content: ce11
Supplementary files format and content: tab-delimited text files include featureCount values for each sample

organism: Caenorhabditis elegans

source_name: Whole

extract_protocol:
Approximately 200 worms in each group were collected and soaked in RNAlater solution (Qiagen). Total RNA was isolated using the RNeasy Lipid Tissue kit (Qiagen).
mRNAs were purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit (Clontech)

treatment_protocol: Three-day-old worms were cultured for five days on mNGM plates covered with OP50 (control group) or ETEC.

value: Whole

tag: strain

value: Bristol N2

value: hermaphrodite

value: wild-type

value: feeding ETEC

value: three-day-old


title: Bone marrow non-IgA plasma cells, biol rep 1

value: Bone marrow

value: female


title: ETd8_rep1

tag: treatment


title: CTCF-CR-OCIAML2

value: blood


title: OPd8_rep2

value: feeding OP50


title: IgG-CR-U937

value: monocyte

value: wild type


title: SMARCA5-CR-U937

value: no treatment


title: HA835_5_Adult_Apos_MET

city: Montreal

first: Alyson

last: Fournier

state: QC

address: 3801 Rue University

department: Department of Neurology and Neurosurgery

country: Canada

institute: McGill University

data_processing:
The GenPipes workflow
Raw FastQ files were aligned to the GRCh38 genome reference using STAR aligner with default parameter
Raw reads were quantified using HTseq count
Raw read counts were normalized, variance-stabilized, and transformed using the DESeq2 package in R
Instead of comparing differentially expressed genes (DEGs) between populations of samples using DESeq2, we took advantage of having paired samples (treated versus untreated) for each patient. We performed paired t-test analysis to account for the effect of metformin treatment within each pair samples. This approach allowed us to address the substantial heterogeneity between different samples, which vary in terms of age and sex.
Assembly: GRCh38 human genome

source_name: Brain

growth_protocol: Total dissociated cell sample was cultured overnight in DMEM/F12 medium (Sigma, Oakville, ON) containing N1 supplementary media (Sigma, Oakville, ON), 0.01% bovine serum albumin (Sigma, Oakville, ON)

extract_protocol: RNA was extracted from dissociated cultures of A2B5+ or A2B5- cells after two days in culture under control conditions or with addition of metformin. Bulk sequencing studies were conducted on 3 or 4 samples from each of the age groups

treatment_protocol: Metformin (10µM (Sigma, Oakville, ON)) was added to selected nanofiber or dissociated cell cultures every other day. H2O was used as vehicle control for metformin experiments.

value: Brain

value: Oligodendrocyte lineage

value: Metformin


title: BPTF-CR-U937


title: HA834_5_Adult_Aneg_MET


title: HA847_8_Adult_Aneg_MET


title: HA847_3_Adult_Apos_MET


title: HA843_3_Ped_Apos_MET


title: gcn4, vehicle, rep 10

city: Tempe

first: Blaise

middle: L

last: Mariner

state: AZ

address: 427 E Tyler Mall, LSC 356

department: School of Life Sciences and Center for Evolution and Medicine

institute: Arizona State University

data_processing:
fastqc
fastp
HISAT2
featurecounts
Assembly: R68
Supplementary files format and content: gene, counts

organism: Saccharomyces cerevisiae

source_name: Vehicle

extract_protocol: Zymo RNA extraction

value: yeast cells

value: Vehicle


title: gcn4, vehicle, rep 12


title: HA843_6_Ped_Aneg_MET


title: gcn4, vehicle, rep 9


title: gcn4, vehicle, rep 11


title: HA842_6_Adult_Aneg_MET


title: CTCF-CR-U937


title: gcn4, vehicle, rep 8


title: HA842_2_Adult_Apos_MET


title: CTCF-CR_experiment2_NegCtrl_rep2

value: lentiviral transduction


title: HA841_8_Ped_Aneg_MET


title: HA841_2_Ped_Apos_MET


title: HA834_2_Adult_Apos_MET


title: gcn4, vehicle, rep 7


title: CTCF-CR_experiment2_BPTF-KO_rep2

value: BPTF KO


title: OPd8_rep1

value: Whole

value: Bristol N2

value: hermaphrodite

value: wild-type


title: gcn4, vehicle, rep 6


title: HA838_2_Ped_Apos_MET


title: CTCF-CR_experiment2_SMARCA5-KO_rep1

value: SMARCA5 KO


title: HA838_6_Ped_Aneg_MET


title: HA836_10_Ped_Aneg_MET


title: HA836_5_Ped_Apos_MET


title: CTCF-CR_experiment2_SMARCA5-KO_rep2

value: blood


title: HA847_7_Adult_Aneg_N1

value: Control


title: HA847_1_Adult_Apos_N1


title: gcn4, vehicle, rep 4


title: HA843_1_Ped_Apos_N1


title: gcn4, vehicle, rep 5


title: CTCF-CR_experiment1_SMARCA5-KO

value: monocyte


title: gcn4, vehicle, rep 3


title: HA842_5_Adult_Aneg_N1


title: CTCF-CR_experiment1_NegCtrl

value: wild type


title: HA842_1_Adult_Apos_N1


title: gcn4, vehicle, rep 2


title: HA841_7_Ped_Aneg_N1


title: gcn4, vehicle, rep 1


title: HA841_1_Ped_Apos_N1


title: CTCF-CR_experiment1_BPTF-KO


title: wild type, vehicle, rep 12


title: HA838_1_Ped_Apos_N1


title: HA838_5_Ped_Aneg_N1


title: HA836_6_Ped_Aneg_N1


title: HA836_1_Ped_Apos_N1


title: wild type, vehicle, rep 11


title: ATAC_SA5KI_dTAGV1_4hrs_rep1

description: Illumina Nextseq 1000/2000

data_processing:
The sequencing reads were 3’ trimmed and filtered for quality and adapter content using TrimGalore (v0.4.5), with a quality setting of 15, and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Reads were aligned to human assembly hg38 with version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and were deduplicated using MarkDuplicates in Picard Tools (v2.16.0).
The BEDTools suite (http://bedtools.readthedocs.io) was used to create normalized read density profiles, using a read extension of 0 bps.
A global peak atlas was created by first removing blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz), then merging all peaks within 500 bp, and counting reads with version 1.6.1 of featureCounts (http://subread.sourceforge.net). Comparison of intra vs inter-group clustering in principle component analysis was used to determine normalization strategy, using either the median ratio method of DESeq2 or a sequencing depth-based factor normalized to ten million uniquely mapped fragments.
Differential enrichment was scored using DESeq2 for all pairwise group contrasts. Peak-gene associations were created using linear genomic distance to the transcription start site.
Assembly: GRCh38/hg38
Supplementary files format and content: DESEq2 output table

growth_protocol: RPMI 1640, GlutaMAX supplement, sodium pyruvate medium containing 10% heat-inactivated FBS and 1x Penicillin/Streptomycin

extract_protocol: Corces MR, Trevino AE, Hamilton EG, et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods. 2017;14(10):959-962. doi:10.1038/nmeth.4396

treatment_protocol: The cells were treated with either DMSO or dTAG-V1

value: SMARCA5-dTAG knockin

value: dTAG-V1 4hrs


title: wild type, vehicle, rep 10


title: HA834_4_Adult_Aneg_N1

value: Brain

value: Oligodendrocyte lineage


title: CTCF-CR_experiment2_NegCtrl_rep1


title: HA843_4_Ped_Aneg_N1


title: ATAC_SA5KI_DMSO_rep2

description: Illumina Nextseq 1000/2000

value: DMSO


title: HA835_1_Adult_Apos_N1


title: CTCF-CR_experiment2_BPTF-KO_rep1


title: ATAC_SA5KI_DMSO_rep1

description: Illumina Nextseq 1000/2000


title: wild type, vehicle, rep 9

value: yeast cells

value: Vehicle


title: A549 cells, shCtrl [ICAA]

city: nanjing

first: Zhang

last: Jun

state: jiangsu

address: longmiandadao

institute: China Pharmaceutical University

description: ICAA

data_processing:
Cutadapt (v.2.8) was used to trim the adapters and low quality sequences with parameter (--match-read-wildcards -a NNNNNNNNNNAGATCGGAAGAGCAC -q 20 -e 0.1 -O 3 -m 20 -U 10 -A AGATCGGAAGAGCGT -A AGATCGGAAGAGCGTC -A AGATCGGAAGAGCGTCG -A AGATCGGAAGAGCGTCGT -A AGATCGGAAGAGCGTCGTG -A AGATCGGAAGAGCGTCGTGT).
Reads were aligned to rRNA and tRNA sequences so as to remove rRNA and tRNA reads using bowtie2 (v2.2.5) software.
Then the clean reads were aligned to human genome (GRCh38) using STAR aligner (v2.7.5c) and gencode genes (gencode.v38.annotation.gtf) transcriptome annotation with parameter (--outFilterMultimapNmax 10 --alignEndsType EndToEnd --outFilterMismatchNmax 2 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 --outFilterIntronMotifs RemoveNoncanonicalUnannotated). The mapped reads were quantified using featureCounts (v2.0.1) with -t exon parameter.
Differential expression analysis was performed using edgeR (v3.40.2) and genes with |log2Fold change (FC) | > =1 and p value < 0.05 were regarded as differentially expressed genes.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: lung

growth_protocol: A549 was cultured in DMEM (KeyGen Biotech, KGM12800N-500) supplemented with 10% FBS (Viva Cell, C04001-500) and 1% Penicillin-Streptomycin (Life,15140122) at 37℃ with 5% CO2.

extract_protocol:
total RNA was isolated by Trizol (Invitrogen)
Samples were deep sequenced on an Illumina Novaseq platform at Novogene

treatment_protocol: A549 lung cancer cells were treated with complete medium or starvation medium for 2 h

value: lung

value: lung cancer

value: WT

value: amino acid starvation


title: A549 cells, shM16 [IKD16AA]

value: METTL16 knockdown


title: CR_exp3_deltaBROMO-BPTF_aBPTF_rep2

data_processing:
The sequencing reads were 3’ trimmed and filtered for quality and adapter content using TrimGalore (v0.4.5), with a quality setting of 15, and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Reads were aligned to human assembly hg38 with version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and were deduplicated using MarkDuplicates in Picard Tools (v2.16.0).
The BEDTools suite (http://bedtools.readthedocs.io) was used to create normalized read density profiles, using a read extension of 200 bp
Subsequent Cut&Run data visualization and analysis were performed using EaSeq software. For BPTF and HA-SMARCA5 Cut&Run analysis, to call peaks, the ALT tool within the Easeq software was used with default parameters and using BPTF KO or dTAG-treated cells as background controls, respectively.
Assembly: GRCh38/hg38
Supplementary files format and content: bigwig files and an excel spreadsheet with the called peaks
Library strategy: CUT&RUN

extract_protocol:
Cut&Run was performed using the CUTANA™ ChIC/CUT&RUN Assay kit (EpiCypher) according to the manufacturer’s instructions.
NEBNext Ultra II

treatment_protocol: Experiment 1: The cells were transduced with the lentiviruses driving the corresponding sgRNA expression and collected for Cut&Run 4 days post-transduction. Experiment 2: The cells were treated with either DMSO or dTAG-V1 for 24hr before collecting for Cut&Run. Experiment 3: No treatment of the established cell lines was performed.

value: BPTF truncation

value: lentiviral transduction


title: A549 cells, shCtrl [ICN]

description: ICN

value: normal culture


title: wild type, vehicle, rep 8


title: A549 cells, shM16 [IKD16N]


title: wild type, vehicle, rep 7


title: CR_exp3_deltaBROMO-BPTF_aBPTF_rep1

value: blood

value: monocyte


title: ATAC_SA5KI_dTAGV1_4hrs_rep2

description: Illumina Nextseq 1000/2000

value: SMARCA5-dTAG knockin


title: wild type, vehicle, rep 6

value: wild type


title: Pre1_con

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
RNA velocity were calculated using Velocyto (v0.17.17) and generated loom files. The loom files were merged with Loompy (v3.0.7).
Quality check and filtering were performed using R and Seurat package (v4.3.0). We filtered out cells that express less than 1,000 or more than 6,000 genes, along with cells with a proportion of mitochondrial RNA larger than 1% and UMI counts inferior than 3,200 from the downstream analysis. Cell cycling was also considered and along with mitochondrial content were regressed out during normalization process conduct using SCTransform (v0.3.5)
Trajectory analysis was performed with scVelo (v0.2.5) using “dynamical model” mode, and the UMAP coordinates were imported from the Seurat object using the package SeuratDisk (v0.0.0.9020)
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: 10X filtered files: Tab-separated values files and matrix files
Supplementary files format and content: ari_org_annotated.rds: processed samples and filtered cells including normalized counts, clustering, UMAP coordinates, and cluster annotations.
Supplementary files format and content: ari_org.annotated.h5ad: imported object from R that includes all features and integrates RNA velocities for trajectory analysis.
Supplementary files format and content: ari.merged.loom: includes splicing and unsplicingratios for RNA velocity calculations.

source_name: Endometrium

extract_protocol:
AO-EMO with eSC and HUVEC were collected into a LoBind 1.5 ml tube and subjected to two PBS washes. Afterward, 1 ml Nuclei EZ lysis buffer (Sigma) was added and the AO-EMO were homogenized using a plastic pestle with 10–20 strokes. The solution was then transferred to a 15 ml tube (BD Falcon) using a wide-bore pipette, 2 ml Nuclei EZ lysis buffer was added, and the mixture was incubated on ice for 5 min with gentle mixing using a pipette. The solution was passed through a 35 µm filter, and the resulting supernatant was obtained through centrifugation at 500 × g for 5 min at 4°C. Afterward, the pellet was gently resuspended in 1.5 ml Nuclei EZ lysis buffer and incubated on ice for 5 min before being subjected to another centrifugation step, as described above. The final pellet was washed and resuspended in 1 ml Nuclei Wash and Resuspension buffer (Sigma) and passed through a 35 µm filter. Then 1 µl DAPI solution (10 μg/ml) was added, and the nuclei were visually inspected on a hemocytometer. A 10 µl aliquot of the suspension was added to a C-chip (VWR), and nuclei were counted using Image J software. DAPI+ nuclei were sorted using a FACS Aria II cell sorter (BD Biosciences) and collected in low-cell adsorption tubes (STEMFULL™, Sumitomo Bakelite). The sample was centrifuged at 500 × g for 5 minutes at 4°C, and the supernatant was meticulously removed. Subsequently, 1 ml Nuclei Wash and Resuspension Buffer was added, and the sample was again centrifuged at 500 × g for 5 min at 4°C. The resulting supernatant was discarded, and 300 µl Nuclei Wash and Resuspension Buffer was added to the sample. The nuclei were then quantified, and the sample was once more centrifuged at 500 × g for 5 min at 4°C. The nuclei concentration was adjusted to 1000 nuclei/µl, and 10,000 single nuclei were subsequently loaded onto a Chromium Controller (10x Genomics) for further analysis
Library was performed according to the manufacter’s instructions (single cell v3.1 protocol, 10x Genomics).

value: Endometrium

value: AO-EMO, eSC, HUVEC

value: Epithelial, stromal, endothelial cells


title: CR_exp3_deltaPHDBROMO-BPTF_aBPTF_rep2


title: ATAC-shCTR-Rep-2

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

institute: Zhejiang University

description:
shCTR-ATAC-Rep.bw
shCTR-ATAC-Rep_peaks.narrowPeak

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the human genome (hg38) using Bowtie2 (v2.2.5) with options: --no-unal --no-mixed --no-discordant -X 2000 --local
For peak calling, parameters used were macs2 (v2.1.2) callpeak: -p 1e-5 -f BAMPE --keep-dup all -g hs.
The bigwig files were generated with bamCoverage function in deepTools (v3.4.3) with default parameter settings.
Assembly: hg38
Supplementary files format and content: bigwig, peakfile text file

source_name: OTF cells

growth_protocol: hESCs were cultured in hESC medium: DMEM/F12 (Life Technologies), 20% KnockOut Serum Replacement (KSR) (Life Technologies), 1× Non-Essential Amino Acids (NEAA) (Life Technologies), 0.055 mM 2-mercaptoethanol (Sigma), 1× Penicillin/Streptomycin, and 10 ng ml-1 bFGF (Peprotech). OTF cells were cultured in DMEM, 10% Fetal Bovine Serum, 1× penicillin-streptomycin, and 250 μM vitamin C.OTF cells were reprogrammed using hRep medium: Basic DMEM (Gibco), 10% KSR, 10% FBS, 1× Non-Essential Amino Acids, 1× Penicillin/Streptomycin, 0.055 mM 2-Mercaptoethanol, 10 ng mL-1 bFGF, 0.5 mM VPA, 10 μM 616452, 0.5 μM AM580, 5 μM EPZ004777, 5 μM Forskolin, 0.2 μM PD0325901, and 2 μM Doxycycline.

extract_protocol:
Cells were lysed by lysis buffer (10 mM NaCl, 3 mM MgCl2, 10 mM Tris pH 7.4, and 0.1% NP-40).
Sequencing libraries were generated using Hyperactive ATAC-seq Library Prep Kit for Illumina (Vazyme) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: We performed shCTR or shANP32B lentivirus transfection in hESCs and in OTF cells.

value: OTF cells

value: Human fibroblasts

value: Control

value: Lentiviral particles coding for control shRNA


title: EMO6_hor

source_name: Decidua

value: Decidua


title: wild type, vehicle, rep 5

value: yeast cells

value: Vehicle


title: ATAC-shCTR-Rep-1


title: ATAC-shA32B-Rep-2

description:
shA32B-ATAC-Rep.bw
shA32B-ATAC-Rep_peaks.narrowPeak

value: Knockdown of ANP32B

value: Lentiviral particles coding for shANP32B


title: CR_exp3_deltaPHDBROMO-BPTF_aBPTF_rep1

value: BPTF truncation

value: lentiviral transduction


title: ATAC-shCTR-ESC-1

description:
ATAC-shCTR.bw
ATAC-shCTR_peaks.narrowPeak

source_name: MEL1 hESC line

value: MEL1 hESC line

value: Human embryonic stem cells


title: CR_exp3_wtBPTF_aBPTF_rep2

value: blood

value: monocyte

value: wild type


title: wild type, vehicle, rep 4


title: ATAC-shA32B-ESC-2

description:
ATAC-shA32B.bw
ATAC-shA32B_peaks.narrowPeak


title: ATAC-shCTR-ESC-2


title: wild type, vehicle, rep 3


title: CR_exp3_wtBPTF_aBPTF_rep1


title: ATAC-shA32B-Rep-1


title: Pre1_hor

value: Endometrium

value: AO-EMO, eSC, HUVEC

value: Epithelial, stromal, endothelial cells


title: wild type, vehicle, rep 1


title: CR_exp2_SA5KI_aHA_dTAG_rep2

value: SMARCA5-dTAG KI

value: dTAG-v1 treatment


title: ATAC-shA32B-ESC-1


title: wild type, vehicle, rep 2


title: CR_exp2_SA5KI_aHA_dTAG_rep1


title: gcn4, borrelidin, rep 24

source_name: Borrelidin

value: Borrelidin


title: gcn4, borrelidin, rep 23

value: yeast cells


title: CR_exp2_SA5KI_aHA_DMSO_rep2

value: DMSO treatment


title: ESC-shA32B-1

description: ESC-gene-expression.txt

data_processing:
Raw RNA-seq data were trimmed by fastp (v0.20.1) to remove adapter sequence and reads with low sequencing quality, paired-end sequencing was carried out with the Illumina HiSeq 2500 with paired-end 150-bp read length.
Clean reads were aligned to the human genome (hg38) using HISAT2 software (v2.1.0) with the default parameter settings.
Transcript assembly was performed by stringtie software (v2.0) and expression of transcripts sharing each gene_id was quantified as transcripts Per Million (TPM).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each sample

growth_protocol: hESCs were cultured in hESC medium: DMEM/F12 (Life Technologies), 20% KnockOut Serum Replacement (KSR) (Life Technologies), 1× Non-Essential Amino Acids (NEAA) (Life Technologies), 0.055 mM 2-mercaptoethanol (Sigma), 1× Penicillin/Streptomycin, and 10 ng ml-1 bFGF (Peprotech).  OTF cells were cultured in DMEM, 10% Fetal Bovine Serum, 1× penicillin-streptomycin, and 250 μM vitamin C.OTF cells were reprogrammed using hRep medium: Basic DMEM (Gibco), 10% KSR, 10% FBS, 1× Non-Essential Amino Acids, 1× Penicillin/Streptomycin, 0.055 mM 2-Mercaptoethanol, 10 ng mL-1 bFGF, 0.5 mM VPA, 10 μM 616452, 0.5 μM AM580, 5 μM EPZ004777, 5 μM Forskolin, 0.2 μM PD0325901, and 2 μM Doxycycline.

extract_protocol:
Cells were havested and total RNA was isolated using Fast Pure Cell Total RNA Isolation Kit (Vazyme)
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Knockdown of ANP32B


title: ESC-shCTR-2

description: ESC-gene-expression.txt

value: Control

value: Lentiviral particles coding for control shRNA


title: Rep-shA32B-1

description: Rep-gene-expression.txt

value: OTF cells

value: Human fibroblasts

value: Lentiviral particles coding for shANP32B


title: ESC-shCTR-1

description: ESC-gene-expression.txt

value: MEL1 hESC line

value: Human embryonic stem cells


title: Rep-shCTR-1

description: Rep-gene-expression.txt


title: ESC-shA32B-2

description: ESC-gene-expression.txt


title: Rep-shCTR-2

description: Rep-gene-expression.txt


title: Rep-shA32B-2

description: Rep-gene-expression.txt


title: gcn4, borrelidin, rep 22


title: CR_exp1_sgBPTF_aBPTF_rep2

value: blood

value: monocyte

value: BPTF KO

value: lentiviral transduction


title: Pre2_EPCP_in

source_name: human endometrium

treatment_protocol: We cultured human endometrial organoids in collagen-based gels (70% type-I collagen and 30% matrigel) for 7-10 days with ECSY medium. The composition of the ECSY medium was as follows: DMEM/F-12  supplemented with 1% ITS-X supplement, 0.15% BSA, 1% Knockout Serum Replacement, 200 mM L-ascorbic acid, 50 ng/ml EGF, 2 μM CHIR99021, 2 μM SB202190, and 10 μM Y27632. Following the ECSY culture, we sequentially introduced 17β-estradiol 172 (E2), medroxyprogesterone acetate (MPA), 8-bromoadenosine 3′,5′-cyclic monophosphate 173 (8-Br-cAMP), and prolactin. The treatment durations were as follows: 2 days for E2 and 4 days for the combined treatment of E2, MPA, 8-Br-cAMP, and prolactin (EPCP).  As a control, we prepared AO-EMO without any hormone treatment as well as AO-EMO treated exclusively with E2. To isolate the outer and inner cells of AO-EMO, the culture medium was aspirated, and PBS was added to wash. Subsequently, TrypLE Express was added to the culture dish, and plates were incubated at 37℃ for 30 min. Following the incubation, TrypLE was removed and AO-EMO were washed with PBS. The outer cells were detached by pipetting PBS onto the surface of the AO-EMOeveral times using a manual pipette. We used 4 independent organoids from 4 donors.

value: human endometrium

value: endometrial organoids

value: endometrial epithelial cells

tag: position

value: In


title: gcn4, borrelidin, rep 21

value: yeast cells

value: Borrelidin


title: Pre2_EPCP_out

tag: cell line

value: Out


title: Pre2_con_out


title: CR_exp1_sgBPTF_aBPTF_rep1

tag: genotype


title: Pre1_EPCP_in


title: gcn4, borrelidin, rep 20


title: CR_exp1_sgNegCtrl_aBPTF_rep2

value: wild type


title: gcn4, borrelidin, rep 19


title: Pre1_E2_in


title: Pre1_E2_out


title: CR_exp1_sgNegCtrl_aBPTF_rep1


title: gcn4, borrelidin, rep 18


title: CR_exp2_SA5KI_aHA_DMSO_rep1

value: SMARCA5-dTAG KI

value: DMSO treatment


title: Pre1_con_in


title: ATAC_exp2_sgSMARCA5_rep2

treatment_protocol: The cells were transduced with the lentiviruses driving the corresponding sgRNA expression and collected for sequencing 4 days post-transduction

value: SMARCA5 KO


title: gcn4, borrelidin, rep 17


title: Pre1_EPCP_out


title: Pre1_con_out


title: EMO9_EPCP_out

value: human decidua


title: ATAC_exp2_sgNegCtrl_rep2


title: gcn4, borrelidin, rep 15


title: EMO9_E2_in


title: EMO9_EPCP_in


title: ATAC_exp2_sgNegCtrl_rep1


title: ATAC_exp2_sgSMARCA5_rep1


title: EMO9_E2_out


title: EMO9_con_out


title: EMO9_con_in


title: Pre2_con_in


title: gcn4, borrelidin, rep 14


title: EMO6_EPCP_in


title: ATAC_exp1_sgBPTF-2_rep2


title: gcn4, borrelidin, rep 13


title: EMO6_EPCP_out


title: EMO6_E2_out


title: wild type, borrelidin, rep 24


title: ATAC_exp1_sgBPTF-1_rep2


title: EMO6_con_in


title: ATAC_exp1_sgNegCtrl_rep2


title: ATAC_exp1_sgNegCtrl_rep1


title: H1-CFS_EUdiff

city: Hong Kong

first: Xinyi

last: Lin

state: NY

address: 562-570, Queen's Road West， Hong Kong Island

institute: The University of Hong Kong

data_processing:
Single-cell 10X RNA-seq data were processed using Cellranger (v6.1.2) with default parameters and raw sequencing reads were aligned to the GRCh38 human genome.
Assembly: GRCh38 human genome
Supplementary files format and content: CFS_filtered_feature_bc_matrix.h5


title: notochord 8 weeks

data_processing:
Single-cell 10X RNA-seq data were processed using Cellranger (v6.1.2) with default parameters and raw sequencing reads were aligned to the GRCh38 human genome
Assembly: GRCh38 human genome
Supplementary files format and content: The filtered_feature_bc_matrix.h5 was generated as an output from the Cell Ranger pipeline that contains information on the filtered and aligned reads, the detected features (genes) and the barcodes associated with each feature.

source_name: notochord

extract_protocol:
The fetal notochord (NCC) was dissected out, cut into ~1mm pieces, and digested with 10mL pre-warmed digestion buffer containing 0.5% dispase (5mg/mL), 0.5% collagenase type II (5mg/mL), 0.25mg/ml collagenase P in FBS-free DMEM for 1hr at 37⁰C on a rocking platform. The digest was gently triturated every 30 min to further aid in the release of cells from the tissue. After digestion, the cells were collected, filtered through a 40µm sieve, and resuspended in 0.04% BSA in phosphate buffered saline (PBS). Cells were centrifuged (300g, 3 min) at RT, resuspended in 0.04% BSA in PBS and adjusted to a concentration of 1000 cells/µL.
20,000 cells in suspension were prepared and loaded into individual wells of 10X Chromium Single Cell chip. Single cells were then encapsulated into Gel Beads-in-emulsion (GEM) by 10X Chromium Single Cell Controller. The Single Cell 3’ Reagent Kit v3 was used to perform downstream steps. In brief, reverse transcription was performed on GEMs, followed by cDNA cleanup and amplification. The double-stranded cDNA underwent enzymatic fragmentation, adapter ligation, index PCR and SPRIselect size selection as per manufacturer’s protocol. Library size and concentration were determined by Qubit, quantitative PCR and Bioanalyzer assays. The libraries were then sequenced using paired-end sequencing (151 bp) using the Illumina NovaSeq 6000. Using software from Illumina (bcl2fastq), sequencing reads were assigned to the individual sample and subsequently converted to fastq format.

value: notochord


title: wild type, borrelidin, rep 22


title: ATAC_exp1_sgBPTF-1_rep1

value: blood


title: wild type, borrelidin, rep 23


title: EMO6_con_out


title: hiPSC ThermoF, day 7 NOTO transfected

description:
CellPlex 10x Genomics
ThermoF D7 NOTO

data_processing:
CellRanger mkfastq function was used to generate FASTQ files, and FASTQ alignment to the human reference genome (CRCh38-2020-A), filtering, barcode and UMI counting were performed with CellRanger multi. Resulting UMI count tables were further analyzed using Seurat v4 (Hao et al 2021.)
Assembly: CRCh38-2020-A
Supplementary files format and content: per sample BAM file that are demultiplexed and contain all the sample-specific information, and matrix file

source_name: Gibco Episomal hiPSC Line

growth_protocol: Described in STAR Methods

extract_protocol:
Cell were gently dissociated using TryplE for 7min at 37°C and then labelled using 10X CellPlex protocol for tag assignment (CG000388, 10X Genomics)
40,000 freshly collected cells were loaded into a Chromium Controller (10X Genomics), containing 5,000 untransfected cells, 10,000 cells NOTO transfected, 5,000 cells NOTO transfected and supplemented with 5µM SB431542 from day 2, repeated for two independant experiments with hiPSC lines a and b. In brief, single cells were encapsulated into Gel Beads-in-emulsion (GEM) by 10X Chromium Single Cell Controller. Single Cell 3’ Reagent Kit was used to perform reverse transcription, cDNA cleanup and amplification. The double-stranded cDNA underwent enzymatic fragmentation, adapter ligation, index PCR and SPRIselect size selection as per manufacturer’s protocol. All libraries were sequenced using paired-end sequencing using the Illumina NovaSeq 6000 following manufacturer’s instructions.

treatment_protocol: Described in STAR Methods

value: Gibco Episomal hiPSC Line

value: Notochordal-like cells

value: day 7 NOTO transfected


title: gcn4, borrelidin, rep 16


title: WT-A32B-CUT_Tag_2

description:
WT-A32B-CUT_Tag_2
WT-A32B-CUT_Tag-peaks.bed
WT-A32B-CUT_Tag.bw

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the human genome (hg38) using Bowtie2 (v2.2.5) with options: --no-unal --no-mixed –nodiscordant --local --very-sensitive-local --phred33 -I 10 -X 700.
For peak calling, parameters used were macs2 (v2.1.2) callpeak: -p 1e-5 -f BAMPE --keep-dup all -g hs. For peak calling of histone modifications, --broad should be added.
The bigwig files were generated with bamCoverage function in deepTools (v3.4.3) with default parameter settings.
assembly: hg38
Supplementary files format and content:bigwig, peakfile text file
Library strategy: CUT&Tag

growth_protocol: hESCs were cultured in hESC medium: DMEM/F12 (Life Technologies), 20% KnockOut Serum Replacement (KSR) (Life Technologies), 1× Non-Essential Amino Acids (NEAA) (Life Technologies), 0.055 mM 2-mercaptoethanol (Sigma), 1× Penicillin/Streptomycin, and 10 ng ml-1 bFGF (Peprotech). hESCs were maintained on CF1 feeder cells at 37°C and 5% CO2.

extract_protocol:
CUT&Tag assay was performed using NovoNGS_ CUT&Tag High- Sensitivity Kit (Novoprotein) according to the manufacturer’s recommendation.
We used TruePrep DNA Library Prep Kit V2 for library construction.

treatment_protocol: We performed shCTR or shNAT10 lentivirus transfection in hESCs.

value: MEL1 hESC line

value: Human embryonic stem cells

value: WT

value: ANP32B (ProteinTech, 10843-1-AP)


title: hiPSC 190 PBMC 4F SeV, day 7 NOTO transfected with 5µM SB431542 from day 2

description:
CellPlex 10x Genomics
190 PBMC D7 NOTO + SB from Day 2

source_name: 190 PBMC 4F SeV

value: 190 PBMC 4F SeV


title: hiPSC 190 PBMC 4F SeV, day 7 NOTO transfected

description:
CellPlex 10x Genomics
190 PBMC D7 NOTO


title: hiPSC ThermoF, day 7 untransfected

description:
CellPlex 10x Genomics
ThermoF D7 NT

value: day 7 untransfected


title: KD-A32B-CUT_Tag-2

description:
KD-A32B-CUT_Tag-2
KD-A32B-CUT_Tag-peaks.bed
KD-A32B-CUT_Tag.bw

value: NAT10 KD


title: wild type, borrelidin, rep 21

value: yeast cells

value: wild type

value: Borrelidin


title: hiPSC ThermoF, day 7 NOTO transfected with 5µM SB431542 from day 2

description:
CellPlex 10x Genomics
ThermoF D7 NOTO + SB from Day 2


title: EMO6_E2_in

value: endometrial organoids

value: endometrial epithelial cells

value: In


title: wild type, borrelidin, rep 18


title: WT-A32B-CUT_Tag_1

description:
WT-A32B-CUT_Tag_1
WT-A32B-CUT_Tag-peaks.bed
WT-A32B-CUT_Tag.bw


title: wild type, borrelidin, rep 19


title: wild type, borrelidin, rep 20


title: hiPSC 190 PBMC 4F SeV, day 7 untransfected

description:
CellPlex 10x Genomics
190 PBMC D7 NT