title: Sam9l-Mut PIPC replicate 2

city: Memphis

first: Jeffery

last: Klco

state: Tennessee

address: 262 Danny Thomas Place, D4047B

department: Pathology

institute: St Jude Children's Research Hospital

data_processing:
200207_A00239_0357_BH5MJ5DSXY v3.4.4 and bcl2fastq 2.20.0 to make basecalling
200207_A00239_0359_BH5MJ5DSXY v3.4.4 and bcl2fastq 2.20.0 to make basecalling
RNA reads were mapped using our in house pipeline Strongarm, which utilizes bwa 0.7.15 and STAR 2.3.0e
Reads from aligned bam files were assigned to genes and counted using HTSeq (v0.11.2) with the GENCODE human release 19 gene annotation.  Log2 CPM (counts per million) values were used for differential gene expression analysis. A cut-off of 10 CPM was used as the threshold to define "expressed" genes. We first determined the number of samples in the smallest group among all groups being compared as N. For a gene to be considered as expressed, we required that at least N samples should have >=10 CPM.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix txt file for log2 CPM(counts per million) values for genes defined as "expressed".
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lin-cKit+ sorted BM cells

growth_protocol: The cells were isolated straight from mice and RNA was extracted

extract_protocol:
Total RNA was extracted using quick-RNA Microprep kit (Zymo Research, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment was performed.

tag: tissues

value: bone marrow

value: Lin-cKit+ hematopoietic cells

value: pIpC


title: Sam9l-Mut PIPC replicate 1

status: Public on Oct 08 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype

tag: cell type

tag: treatment


title: Sam9l-Mut Vehicle replicate 2

value: vehicle


title: Sam9l-WT PIPC replicate 2


title: Sam9l-WT PIPC replicate 1


title: Sam9l-WT Vehicle replicate 2


title: Sam9l-Mut Vehicle replicate 1


title: Sam9l-WT Vehicle replicate 1


title: BMDM_DKO-2

city: shanghai

first: shanshan

last: zhong

address: 320 Yueyang Rd

country: China

institute: Chinese Academy of Sciences (CAS)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: macrophages, Double KO (ALDH2/LDL)

growth_protocol: mice bone marrow derived macrophages are seperated from mice bone marrow and then culture 7days finally treat macrophages with oxLDL

extract_protocol:
cell total RNA was extracted by using Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: bone marrow derived macrophages

tag: age

tag: genotype/variation

value: Low Density Lipoprotein (LDL) receptor knockout

value: Acetaldehyde dehydrogenase 2 (ALDH2) knockout


title: BMDM_DKO-1


title: BMDM_LKO-1

source_name: macrophages, LDL KO

value: ow Density Lipoprotein (LDL) receptor knockout


title: BMDM_LKO-2


title: BMDM_LKO-3


title: BMDM_DKO-3


title: PyMT cell lines + Control CD4+ T cell Supernatant [Control-1]

city: Charleston

first: Heehwa

last: Son

state: MA

address: 149 13 street

institute: MASSACHUSETTS GENERAL HOSPITAL

data_processing:
RNA sequencing data were analyzed using the pipeline Version 5.0.
Sequences were aligned to the mouse reference genome (mm10) using Bowtie
Differentially expressed genes were screened using the Poisson distribution method, the Noiseq, or EBSeq packages
Assembly: mm10
Supplementary files format and content: FPKM values

source_name: breast

growth_protocol: PyMt cell line were plated in low adherence 48-wells plate in RPMI medium 1640 (Gibco), supplemented with 10% fetal bovine serum (Corning), 1% penicillin/streptavidin/glutamine (Thermo Fisher Scientific), 22 mM 2-mercaptoethanol (Gibco), and 5ug/ml insulin (medium) or in CD4+ T cell supernatants derived from Tslp-PyMttg (test), Tslp-PyMttg TslprKO and PyMttg (control) also supplemented with 5 μg/ml insulin (Sigma-Aldrich).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sorted CD4+ T cells were stimulated and rested ex vivo, and supernatants derived from these cultures were used for PyMt culture experiments

tag: tissue

value: breast

tag: cell line

value: PyMt cancer cell line

value: cancer


title: M20_VPA_rep2

city: Beijing

first: Zhongze

last: Yan

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, CAS

data_processing:
High-quality reads of RNA-seq were quantified using Salmon (v.1.1.0).
Assembly: GRCh38

organism: Homo sapiens

source_name: Human organoids from hESCs

growth_protocol: The human H9 (WA09) ESC line was obtained from Dr. Baoyang Hu at the Institute of Zoology, Chinese Academy of Sciences. H9 cells were cultured on Matrigel (BD, New Jersey, USA) using TeSR™-E8™ (STEMCELL Technologies, Vancouver, BC, Canada) and passaged with EDTA (100 μM). Organoid culture was used STEMdiff Cerebral Organoid Kit (STEMCELL Technologies, 08570) according to the manuscript. Briefly, hESCs were dissociated into single-cell suspension using accutase, and then 9,000 cells were plated into each well of 96-well plate for embryoid body (EB) formation. At day 7, EBs were embedded in Matrigel and cultured in the expansion medium for 3 days and then changed maturation medium renewed every 4 days.

extract_protocol: We isolated hESCs-derived neurons at day 40 in culture. Total RNAs were extracted using TRIzol reagent.

treatment_protocol: Total RNAs were extracted using TRIzol reagent, and sequenced on novaSeq 6000 system.

value: Human organoids from hESCs

value: VPA


title: M20_VPA_rep1


title: M8_KW_rep1


title: M8_VPA_rep2


title: M8_VPA_rep1


title: Peripheral Blood_ICM_rep5

type: RNA

city: Shanghai

first: Xiaohui

last: Zhou

address: No.150 Jimo Road,Pudong district

department: Shanghai Heart Failure Research Center

institute: Shanghai East Hospital, Tongji University School of Medicine, Shanghai

description: lncRNA and mRNA expressions in the plasma of patients with DCM and ICM

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

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 2 out of 20 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: Peripheral Blood, Ischemic cardiomyopathy, replicate 5

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was prepared with TRIzol Reagent (Thermo Fisher Scientific, catalog #15596026, Waltham, MA, USA) in according to the manufacturer’s instructions. The quality and quantity of extracted RNA were assessed by the NanoDrop ND1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) .

treatment_protocol: Peripheral blood was collected in Vaculatainer Plastic Blood Collection Tubes with spray-coated K2EDTA. Plasma samples were collected within 4 hours according to standard procedures and frozen at -80°C prior to the RNA extraction.

value: Plasma

tag: gendar

value: Female


title: Peripheral Blood_DCM_rep6

source_name: Peripheral Blood, dilated cardiomyopathy, replicate 6

value: Male


title: M20_KW_rep2


title: M8_KW_rep2


title: Peripheral Blood_DCM_rep11

source_name: Peripheral Blood, dilated cardiomyopathy, replicate 11


title: Peripheral Blood_DCM_rep7

source_name: Peripheral Blood, dilated cardiomyopathy, replicate 7


title: Peripheral Blood_ICM_rep6

source_name: Peripheral Blood, Ischemic cardiomyopathy, replicate 6


title: M20_DM_rep1

value: DMSO


title: Peripheral Blood_DCM_rep5

source_name: Peripheral Blood, dilated cardiomyopathy, replicate 5


title: Peripheral Blood_ICM_rep9

source_name: Peripheral Blood, Ischemic cardiomyopathy, replicate 9


title: M20_DM_rep2


title: Peripheral Blood_ICM_rep4

source_name: Peripheral Blood, Ischemic cardiomyopathy, replicate 4


title: Peripheral Blood_ICM_rep3

source_name: Peripheral Blood, Ischemic cardiomyopathy, replicate 3


title: Peripheral Blood_DCM_rep10

source_name: Peripheral Blood, dilated cardiomyopathy, replicate 10


title: Peripheral Blood_DCM_rep4

source_name: Peripheral Blood, dilated cardiomyopathy, replicate 4


title: Peripheral Blood_ICM_rep2

source_name: Peripheral Blood, Ischemic cardiomyopathy, replicate 2


title: Peripheral Blood_ICM_rep1

source_name: Peripheral Blood, Ischemic cardiomyopathy, replicate 1


title: Peripheral Blood_DCM_rep1

source_name: Peripheral Blood, dilated cardiomyopathy, replicate 1


title: Peripheral Blood_ICM_rep8

source_name: Peripheral Blood, Ischemic cardiomyopathy, replicate 8


title: Peripheral Blood_DCM_rep2

source_name: Peripheral Blood, dilated cardiomyopathy, replicate 2


title: Peripheral Blood_DCM_rep9

source_name: Peripheral Blood, dilated cardiomyopathy, replicate 9


title: M20_KW_rep1

source_name: Human organoids from hESCs


title: M8_DM_rep2


title: Control-sgRNA-3

city: Chongqing

first: Jun

last: Jiang

state: Chongqing

address: 10#, Changjiang Zhilu, Yuzhong District

department: Department of Urology

institute: Daping Hospital, Army Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

growth_protocol: 786-O cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 786-O cells were transfected with PHF8-sgRNA and Ctrl-sgRNA by using CRISPR-Cas9 methods.

value: clear cell renal cell cancer cells

value: PHF8 wildtype


title: Peripheral Blood_DCM_rep3

source_name: Peripheral Blood, dilated cardiomyopathy, replicate 3


title: Control-sgRNA-2


title: PX_DM_rep2

value: Wild type


title: Peripheral Blood_DCM_rep8

source_name: Peripheral Blood, dilated cardiomyopathy, replicate 8


title: Peripheral Blood_ICM_rep7

source_name: Peripheral Blood, Ischemic cardiomyopathy, replicate 7


title: Control-sgRNA-1


title: M8_DM_rep1


title: PHF8-sgRNA-1

value: PHF8 knockout


title: C72WLL4

city: Nanning

first: Liangfeng

last: Huang

state: Guangxi

address: No. 100, East University Road

department: Animal Reproduction Institute

institute: Guangxi University

data_processing:
The normalization of gene expression using TPM (transcripts per million) values
Genome_build: bGalGal1.mat.broiler.GRCg7b
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

organism: Gallus gallus

source_name: Liver

extract_protocol:
Total RNA was isolated from liver tissues by using RNAiso Plus reagent
RNA libraries were prepared for sequencing using standard mRNA enrichment protocols

value: Liver

value: post natal week 72

tag: laying performance

value: low


title: C72WLL3


title: PHF8-sgRNA-2


title: C72WLL2


title: C72WHL4

value: high


title: Crosslinked K562, EIF2S2 Input, rep2

city: La Jolla

first: Gene

middle: W

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Cellular & Molecular Medicine

institute: University of California San Diego

data_processing:
Data was processed using Skipper, available at: http://github.com/yeolab/skipper
Reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using skewer.
Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with fastp
Extracted reads were aligned using STAR: --alignEndsType EndToEnd --genomeDir {params.star_sjdb} --genomeLoad NoSharedMemory --outBAMcompression 10 --outFileNamePrefix {params.outprefix} --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outSAMmultNmax 1 --outMultimapperOrder Random --outFilterScoreMin 10 --outFilterType BySJout --limitOutSJcollapsed 5000000 --outReadsUnmapped None --outSAMattrRGline ID:{wildcards.replicate_label} --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped Within --readFilesCommand zcat --outStd Log --readFilesIn {input.fq} --runMode alignReads --runThreadN {threads}
Custom scripts called reproducible enriched windows and repetitive elements as part of Skipper
Assembly: GRCh38
Supplementary files format and content: reproducible enriched window files contain p values, q values, enrichment, and annotations for significantly bound transcriptome tiled windows
Supplementary files format and content: reproducible enriched re files contain p values, q values, enrichment, and annotations for significantly bound repetitive elements

extract_protocol:
Cells were lysed and and sonicated in eCLIP lysis buffer, and RNA was fragmented using RNase I (Ambion) and complexes were immunoprecipitated with protein-specific antibodies from Bethyl Laboratories
RNA was reverse transcripted with Superscript III, and adaptor was ligated with T4 RNA Ligase 1, then libraries were constructed with Q5 High-Fidelity 2x Master Mix (NEB)


title: Crosslinked K562, EIF2S2 Input, rep1


title: C72WLL1


title: Crosslinked K562, EIF3J Input, rep1


title: PX_DM_rep1


title: Crosslinked K562, EIF2D Input, rep1


title: Crosslinked K562, EIF2D Input, rep2


title: C72WHL2


title: C72WHL3


title: Crosslinked K562, EIF2B5 Input, rep2


title: C72WHL1


title: Crosslinked K562, EIF3J Input, rep2


title: Crosslinked K562, EIF2B5 Input, rep1


title: Crosslinked K562, RPS19 Input, rep2


title: C50WLL4

value: post natal week 50


title: Crosslinked K562, RPS19 Input, rep1


title: PHF8-sgRNA-3


title: C50WLL3


title: Crosslinked K562, RPL29 Input, rep1


title: C50WLL2


title: Crosslinked K562, RPS3A Input, rep2


title: C50WHL4


title: C50WLL1


title: Crosslinked K562, RPL35A Input, rep2


title: C50WHL2


title: Crosslinked K562, RPL35A Input, rep1


title: C50WHL3


title: C50WHL1


title: Crosslinked K562, RPS14 Input, rep1


title: Crosslinked K562, EIF3J IP, rep2


title: Crosslinked K562, EIF3J IP, rep1


title: C32WL2

value: post natal week 32


title: C32WL1


title: Crosslinked K562, EIF2S2 IP, rep2


title: Crosslinked K562, EIF2D IP, rep2


title: Crosslinked K562, EIF2S2 IP, rep1


title: C32WL3


title: Crosslinked K562, RPL29 Input, rep2


title: Crosslinked K562, EIF2D IP, rep1


title: Crosslinked K562, EIF2B5 IP, rep1


title: Crosslinked K562, RPS19 IP, rep2


title: Crosslinked K562, RPS3A Input, rep1


title: Crosslinked K562, EIF2B5 IP, rep2


title: TMEM100

city: St. Louis

first: Zhiyu

last: Dai

state: MO

address: 4960 Childrens Place

institute: Washington University in St. Louis

data_processing:
The original sequencing data were trimmed using HISAT2, The differential expression analysis was performed using Cuffdiff software
Supplementary files format and content: differential expression

source_name: HPMVEC

extract_protocol:
Total RNA was isolated from HPMVECs with Zymo RNA kit with DNase I digestion
RNA sequencing was carried out by Novogene corporation on Illumina Hiseq platform

value: HPMVEC

tag: agent


title: Crosslinked K562, RPS14 Input, rep2


title: C32WL4


title: Wild type MCF7, biological rep2

city: Bronx

first: Jihong

last: Cui

state: NY

address: 1301 Morris Park Avenue, Room 108/114

institute: Albert einstein college of medicine

description: Gene expression data from wild type MCF7 cells

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hours at 45°C on GeneChip human Gene 2.0ST. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000 7G.

data_processing:
The data were analyzed with Gene Expression Console with Affymetrix default setting.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: WT MCF7 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 800 ng total RNA.

growth_protocol: Cells were grown in DMEM  after supplementing with 10% FBS.

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

treatment_protocol: WT and Mll3-null cells were compared.

tag: tissue/cell type

value: Breast cancer cell


title: Crosslinked K562, RPS19 IP, rep1


title: Crosslinked K562, RPL29 IP, rep2


title: Mll3-null MCF7, biological rep3

description: Gene expression data from Mll3-null MCF7 cells

source_name: Mll3-null MCF7 cells

value: Mll3 knockout


title: YUMM1.1 IFNG 1

city: Sugar Land

first: Kumaraswamy Naidu

last: Chitrala

state: TX

address: 13850 University Blvd, SAB1 Room No: 214

department: Engineering Technology

institute: College of Technology, University of Houston

data_processing:
Rsubread algorithm
Preprocessed data files from the samples were subject to RNA sequencing data analysis using Rsubread package
Assembly: GRCm38
Supplementary files format and content: fastq files which include raw data files

growth_protocol: The murine melanoma cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: RNA libraries for RNA-seq were prepared using  manufacturer's protocols

treatment_protocol: Cells were exposed to IFNG (10 ng/ml) for 48 h (or untreated as controls) before harvesting

value: Murine Melanoma Cells

value: mouse IFNG (10 ng/ml)

tag: time


title: YUMM1.1 IFNG 3


title: Mll3-null MCF7, biological rep1


title: YUMM1.1 IFNG 2


title: YUMM1.1 Control 3


title: Crosslinked K562, RPL35A IP, rep2


title: Crosslinked K562, RPS14 IP, rep2


title: Crosslinked K562, RPL29 IP, rep1


title: Crosslinked K562, RPS3A IP, rep2


title: Crosslinked K562, RPS3A IP, rep1


title: Crosslinked K562, RPL35A IP, rep1


title: YUMM1.1 Control 1


title: YUMM1.1 Control 2


title: Crosslinked K562, RPS14 IP, rep1


title: B16 IFNG 2


title: B16 IFNG 3


title: Mll3-null MCF7, biological rep2


title: B16 IFNG 1


title: PDS5B-dTAG, DMSO, rep3

first: Guoyu

last: Chen

address: Xuhui District Yueyang Road 320

institute: PICB

data_processing:
Raw reads from RNA-seq were mapped to human genome (hg19) and GENECODE v38 using hisat2 v2.2.1
Quantification for each expressed gene was performed using featureCounts from Rsubread v2.0.1.
Differentially expressed genes were calculated by DESeq2 v1.32.0 with cutoffs as follows: padj < 0.05.
Functional annotations were done using enrichGO from clusterProfiler package
Assembly: hg19 and  GENECODE v38
Supplementary files format and content: tab-delimited text files include p-adjust values for each gene

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Total RNA was extracted from cells with Trizol reagent (Life Technologies). The RNA quality was assessed using the Agilent 2100 Bioanalyzer and mRNA was purified with VAHTS mRNA capture beads (Vazyme).
Strand-specific RNA libraries were prepared with VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme)

treatment_protocol: DMSO or dTAG-13 treated at a concentration of 200 nM for 24 hours

value: Hepatocarcinoma cells


title: PDS5B-dTAG, DMSO, rep2

value: DMSO


title: B16 Control 3


title: GFP

value: GFP


title: B16 Control 2


title: Wild type MCF7, biological rep3


title: Wild type MCF7, biological rep1


title: PDS5B-dTAG, DMSO, rep1


title: PDS5A-dTAG, DMSO, rep3


title: PDS5A-dTAG, DMSO, rep1


title: B16 Control 1


title: PDS5B-dTAG, dTAG, rep3

value: dTAG


title: PDS5A-dTAG, dTAG, rep3


title: alpha TC-1

city: Duarte

first: Guihua

last: Sun

address: 1500 East Duarte Rd.

department: Department of Neurodegenerative Diseases

institute: City of hope

description:
small RNA high throughput sequencing
Mouse cell line miRNA read count.xlsx

data_processing:
Basecalls performed using CASAVA version 1.8
cutadapt to remove three nucletide from 5' end
miRge
DEseq2

source_name: Alpha TC-1

extract_protocol:
Trizol extractd total RNA
Modified illumina v1.5 protocol, 3 random nucleotide added to the end of the 5' adaptor

value: Cell line

value: Pancreas


title: PDS5A-dTAG, dTAG, rep2


title: PDS5B-dTAG, dTAG, rep2


title: PDS5B-dTAG, dTAG, rep1


title: beta TC-6

source_name: Beta TC-6


title: MIN6


title: PDS5B-dTAG, DMSO, rep2_HiC

library_source: genomic

data_processing:
Raw sequencing reads were mapped to human genome hg19 and preprocessed with HiC-Pro v3.1.0.
The number of valid pairs for each condition was randomly sampled to the same.
Correlation between replicates was done using ‘hicCorrelate’ function from HiCExplorer (v2.2.1)
Valid read pairs were transferred to .hic file using hicpro2juicebox.sh
Interaction frequency as a function of genomic distance curve was ploted by ‘analyzeHiC’ from Homer.To segregate A and B compartments, we performed eigenvalue decomposition of the Hi-C matrix with ‘runHiCpca.pl’ from Homer.TADs were called using ‘hitad’ function from TADlib.Loops were called by ‘hiccups’ from juicer v1.22.01.
Assembly: hg19
Supplementary files format and content: .hic file
Supplementary files format and content: .bedpe file

molecule: genomic DNA

extract_protocol:
Cells were crosslinked using 1% formaldehyde, followed by quenching with 125 mM glycine for 5 min.Cells were penetrated and nuclei restriction reaction was performed overnight using DpnI digested DNA fragments were filled with biotin at 37°C for 1hr, and proximally ligated at RT for 4hr. Then DNA was de-crosslinked and purified with ethanol precipitation. After shearing to 300-700bp fragments,the biotin tagged DNA was captured by streptavidin T1 beads.
Hi-C libraries were prepared on streptavidin T1 beads using VAHTSTM Universal DNA Library Prep Kit for Illumina.After final PCR amplification, DNA could detach from beads.Size selection were perfromed with Agencourt AMPure XP beads from Beckman Coulter


title: BV2_HS_2

city: Guangzhou

first: Jie

last: Zhu

state: Guangdong

address: 111 Liuhua Road, Yuexiu District

institute: General Hospital of Southern Theater Command of PLA

data_processing:
The total RNA or purified sRNA fragment of the sample is extracted. The 3'-end and 5'-end junctions are ligated, reverse transcribed into cDNA, and then amplified by PCR.
Remove joints at the ends of reads, remove reads with fragment length <17nt and low-quality reads, etc., to complete the initial filtering of data and obtain high-quality data.
The clean reads are compared with the reference genome to obtain a genome-wide reads distribution map, and the clean reads are annotated with ncRNA classification.
The identified miRNAs are subjected to expression calculation, miRNA expression clustering and differentially expressed miRNA analysis between samples.
miRNA candidates with >2-fold up- or down-regulation and p<0.05 are considered as significantly altered miRNAs.
Assembly: not provided
Supplementary files format and content: tab-delimited text files include normalized RPKM values for each Sample

extract_protocol:
Exosomal RNA Extraction TRIzol reagent is used to extract the miRNA from exosomes.
The target fragment library is then recovered by gum cutting, and the libraries passed quality control. Libraries are sequenced on machine.

value: microglia

value: WT

value: heatstroke

value: HS 2h

tag: molecule type

value: microRNA


title: BV2_HS_1


title: BV2_NC_2

value: control

value: Control 2h


title: AHR KO-RNASeq-1

city: Stony Brook

first: Fei

state: New York

address: 100 Nicolls Road

institute: Stony Brook University

description:
bio rep 1 AHR KO-RNASeq
SRR21109350

data_processing:
RNA-seq:
The paired-end 42 bp sequencing reads (PE42) generated by Illumina  sequencing (using NextSeq 500) are mapped to the genome using the STAR algorithm with  default settings. Alignment information for each read is stored in the BAM format.
The number of fragments overlapping predefined genomic features  of interest (e.g. genes) are counted. Only read pairs that have both ends aligned are  counted. Read pairs that have their two ends mapping to different chromosomes or mapping  to same chromosome but on different strands are discarded. The gene annotations we use  were obtained from Subread package. These annotations were originally from NCBI RefSeq  database and then adapted by merging overlapping exons from the same gene to form a set  of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also  merged into one gene.
After obtaining the gene table containing the fragment counts of genes,  we perform differential analyses to identify statistically significant differential genes using  DESeq2. The following lists the pre-processing steps before differential calling
Using DESeq2 normalized gene counts, we perform  GSEA with default settings to determine whether members of a priori defined gene set  based on biological knowledge (e.g. genes sharing the same GO category) are enriched.
CHIP-seq:
Reads were aligned consecutively to the human genome (hg19) and to the Drosophila genome (dm3) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis.
The number of human alignments used in the analysis was adjusted according to the number of Drosophila alignments that were counted in the samples that were compared. Human alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library and assigned to 32-nt bins along the genome.
The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Assembly: hg19
Supplementary files format and content: excel file containing DESeq2-normalized gene counts and the results of a specific differential analysis
Supplementary files format and content: txt file show peak shapes in the form of a signal histogram and bed file contains the locations and names of all Intervals (shown as orange bars) and Merged Regions (green). It also contains the location and values of the Interval summits (purple).

source_name: Lung, bronchus

extract_protocol:
RNA-seq:
Total RNA was isolated from the cells using the Qiagen RNeasy Mini Kit (Qiagen, cat# 74104)
For each sample, 4 ug of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594).
ChIP-seq:
Cells were fixed with formaldehyde solution according to the protocol provided by Active Motif. Chromatin was then isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat# 53051).
An aliquot of chromatin (30 ug, spiked-in with 200 ng of Drosophila chromatin) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 10ul antibody against AhR (ENZO cat# BML-SA210). Antibody against H2Av (0.4 ug) was also present in the reaction to ensure efficient pull-down of the spike-in chromatin (Egan et al., 2016). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.    Quantitative PCR (QPCR) reactions were carried out in triplicate on specific genomic regions using SYBR Green Supermix (Bio-Rad).  The resulting signals were normalized for primer efficiency by carrying out QPCR for each primer pair using Input DNA

value: Lung, bronchus

value: epithelial cell

value: KO


title: AHR KO-RNASeq-2

description:
bio rep 2 AHR KO-RNASeq
SRR21109349


title: AHR KO-RNASeq-3

description:
bio rep 3 AHR KO-RNASeq
SRR21109348


title: AHR WT-RNASeq-2

description:
bio rep 2 AHR WT-RNASeq
SRR21109352


title: AHR WT-RNASeq-3

description:
bio rep 3 AHR WT-RNASeq
SRR21109351


title: AHR WT-RNASeq-1

description:
bio rep 1 AHR WT-RNASeq
SRR21109353


title: Input-ChIPSeq


title: PDS5B-dTAG, DMSO, rep1_HiC


title: PDS5A-dTAG, DMSO, rep2_HiC


title: PDS5B-dTAG, dTAG, rep2_HiC


title: PDS5B-dTAG, dTAG, rep1_HiC


title: PDS5A-dTAG, DMSO, rep1_HiC


title: PDS5A-dTAG, DMSO, rep2


title: BV2_NC_1


title: PDS5A-dTAG, dTAG, rep1


title: PDS5A-dTAG, dTAG, rep2_HiC


title: AHR-arsenic-ChIPSeq

value: Arsenic

tag: chip antibody

value: AhR (ENZO cat# BML-SA210 lot# 03011639)


title: MB002_IgG

city: Cincinnati

first: Zaili

last: Luo

state: OH

address: 3333 Burnet Ave.

institute: CCHMC

data_processing:
Bam files were calculated using Bowtie 2 and transform to Bigwig file using esATAC in R.
Assembly: hg38
Supplementary files format and content: BigWig
Library strategy: Cut&run

growth_protocol: hNSCs, MB002 and MB004 cells were cultured in complete NPC medium (Neurobasal medium containing B27 supplement, N2 supplement, 2 mM L-glutamine, 20 ng/ml EGF, 20 ng/ml bFGF, 2 mg/ml Heparin and 50 μg/ml BSA). hAstrocytes were cultured in DMEM with 10% FBS. Spheres were dissociated at a diameter of 100-200 μm and were changed with complete NPC medium every 3 days to maintain cell metabolic activity.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

value: IgG

value: Group3 MB tumor


title: MB004_IgG


title: MB3076_scRNA-seq

data_processing:
For scRNA-seq, According to the 10× CellRanger’s pipeline, the raw base call (BCL) files were demultiplexed into FASTQ files. The FASTQ files were aligned to the reference human genome GRCh38 (hg38) to generate raw gene-barcode count matrices. When clustering multiple samples together, we aggregated the multiple runs together to normalize on sequencing depth and re-computed the gene-barcode matrices.
For scATAC-seq, the data processing unit takes raw fastq files as input and outputs peak-by-cell count matrix, QC report and genome track files. It consists of the following modules: demultiplexing, adaptor trimming, read mapping, peak calling, cell calling, genome track file generation and quality control assessment. The downstream analysis unit consists of the following modules: dimension reduction, cell clustering, differential accessibility analysis, gene ontology analysis, TF motif enrichment analysis, TF footprinting analysis, linking regulatory DNA sequences with gene promoters, and integration of multiple datasets. We provide flexible options for most of analysis modules.
For Cut&run, Bam files were calculated using Bowtie 2 and transform to Bigwig file using esATAC in R.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: human MB tissue

growth_protocol: hNSCs and MB004 cells were cultured in complete NPC medium (Neurobasal medium containing B27 supplement, N2 supplement, 2 mM L-glutamine, 20 ng/ml EGF, 20 ng/ml bFGF, 2 mg/ml Heparin and 50 μg/ml BSA). Spheres were dissociated at a diameter of 100-200 μm and were changed with complete NPC medium every 3 days to maintain cell metabolic activity.

treatment_protocol: no treatment for the 2 cell lines


title: H3K36me2_Cal27_NSD1KO_EPZ

city: New York

first: Chao

last: Lu

address: 1130 Saint Nicholas Ave

department: Genetics & Development

institute: Columbia University Medical Center

data_processing:
Library strategy: CUT&Tag
Basecalls performed using Illumina CASAVA version 1.7
For RNA-seq samples, reads were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0). The mapped reads count of each gene was measured by featureCounts (v1.6.1).  For CUT&Tag samples, reads were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0). Potential PCR duplicates were removed by the function "MarkDuplicates" (parameter: REMOVE_DUPLICATES=true) of Picard (v2.23.1).
Genome_build: hg38
Supplementary_files_format_and_content: For RNA-seq samples, tab-delimited text files include reads count values for each gene in each sample. For CUT&Tag samples, bigwig files normalized to count per million reads.

source_name: Cell line

extract_protocol:
CUT&Tag was performed as described previously (nature communications, 2019).
CUT&Tag was performed as described previously (nature communications, 2019).

value: head and neck cancer cell line

value: Treated by EPZ-6438


title: PDS5A-dTAG, dTAG, rep1_HiC

value: Hepatocarcinoma cells

value: dTAG


title: MB002_H3K27ac


title: MB002_HNRNPH1


title: MB3271_scRNA-seq


title: H3K27me3_Cal27_NSD1KO_EPZ


title: H3K27me3_Cal27_NSD1KO_DMSO

value: Treated by DMSO


title: H3K27me3_Cal27

value: untreated


title: H3K36me2_Cal27_NSD1KO_DMSO


title: H3K36me2_Cal27


title: hAstrocyte_SOX11

source_name: Astrocyte

value: Astrocyte

value: human astrocyte


title: IgG_Cal27


title: hNSC_IgG

source_name: Neural stem cell

value: Neural stem cell

value: human NSC


title: Cal27_NSD1KO_EPZ_2

data_processing:
Basecalls performed using Illumina CASAVA version 1.7
For RNA-seq samples, reads were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0). The mapped reads count of each gene was measured by featureCounts (v1.6.1).  For CUT&Tag samples, reads were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0). Potential PCR duplicates were removed by the function "MarkDuplicates" (parameter: REMOVE_DUPLICATES=true) of Picard (v2.23.1).
Genome_build: hg38
Supplementary_files_format_and_content: For RNA-seq samples, tab-delimited text files include reads count values for each gene in each sample. For CUT&Tag samples, bigwig files normalized to count per million reads.

extract_protocol:
Total RNA was extracted in TRIzol (Invitrogen) and precipitated in ethanol (DECON Labs ).
Library preparation was performed with ribosomal RNA depletion according to instructions from the manufacturer (NEB) to achieve greater coverage of mRNA and other long non-coding transcripts.


title: Cal27_NSD1KO_EPZ_1


title: h_siTPRX2_d3_9c_smartseq

city: Peking

first: Zhuoning

last: Zou

address: 30 Shuangqing Rd

department: School of Life Sciences

institute: Tsinghua University

data_processing:
Illumina Casava1.8 software used for basecalling.
All RNA-seq data were trimmed by Trim Galore (v0.6.4) then mapped to transcriptome of mm9/hg19 by STAR (v2.5.3a). The gene expression level was calculated by Cufflinks (v2.2.1) based on the annotation of hg19 refFlat database from UCSC genome browser.
Ribo-lite data were trimmed with cutadapt (v1.14) with parameters: cutadapt --trim-n -a GATCGGAAGAGCACACGTCTG -a AGAGCACACGTCTG <input.file> | cutadapt -u 3 -a A{100} --no-indels -e 0.16666666666666666 - | cutadapt -O 8 --match-read-wildcards -g GTTCAGAGTTCTACAGTCCGACGATCSSS -m 18 - -o <output.file> , and the trimmed reads were sequentially mapped to human rRNAs sequences (hg19) using Bowtie2 (v2.2.2). Those aligned to rRNA were discarded, and the rest reads were mapped to transcriptome of hg19 using STAR (v2.5.3a). The gene expression level was then calculated by Cufflinks (v2.2.1) based on the annotation defined by hg19 refFlat database from the UCSC genome browser.
Assembly: hg19
Supplementary files format and content: The RNA FPKM tables including the FPKM of each gene for all the samples.

molecule: polyA RNA

source_name: Preimplantation embryo

extract_protocol:
Oocytes, embryos (after removing the zona pellucida) or cells extact preparation by detergent lysis, and RNA-Seq libraries were prepared using Smart-Seq2 protocol with slightly modification.
RNA libraries were prepared for sequencing using Smart-seq2 protocols as previously described (Picelli et al., 2014).

value: TPRX2 KD


title: hAstrocyte_HNRNPH1


title: hAstrocyte_H3K27ac


title: hAstrocyte_IgG


title: Cal27_NSD1KO_DMSO_2


title: h_siTPRX2_d3_8c_3_smartseq


title: AHR-control-ChIPSeq

value: Lung, bronchus

value: epithelial cell

value: Control


title: MB002_SOX11


title: Cal27_NSD1KO_DMSO_1


title: h_siTPRX2_d3_8c_2_smartseq


title: Cal27_DMSO_2


title: BICR78


title: h_siTPRX2_d3_7c_2_smartseq


title: Cal27_DMSO_1


title: MB002_H3K4me3


title: h_siTPRX2_d3_7c_1_smartseq


title: Cal27_NSD1KO


title: SKN3


title: h_siTPRX2_d3_4c_2_smartseq


title: h_siTPRX2_d3_4c_1_smartseq


title: h_siTPRX2_d3_11c_smartseq


title: h_siTPRX2_d3_10c_smartseq


title: h_siTPRX1_d3_8c_2_smartseq

value: TPRX1 KD


title: PDS5A;PDS5B-dTAG_dTAG_RAD21

data_processing:
Data quality of raw reads was qualified by FastQC v0.11.5
ChIP-seq reads were mapped to human genome hg19 with Bowtie v1.2.3.Duplicates were removed with samtools v1.9
Peaks were called using macs2 with threshold q-value < 0.01 (-q 0.01).
The spike-in strategy was used and scaleFactor was calculated. Normalized bigwig file was generated using ‘bamCompare’ from deepTools v3.3.0.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, Chromatin was sheared to an average length of 300-700 bp with a Qsonica sonicator.
ChIP-seq libraries were prepared using VAHTSTM Universal DNA Library Prep Kit for Illumina. After amplification and size selection with Agencourt AMPure XP beads from Beckman Coulter, the size distributions were determined with Agilent 2100 Bioanalyzer.

value: RAD21 (Abcam, ab992)


title: h_siTPRX1_d3_8c_1_smartseq


title: h_siTPRX1_d3_7c_2_smartseq


title: PDS5A;PDS5B-dTAG_DMSO_CTCF

value: CTCF (Millipore, 07-729)

value: DMSO


title: PDS5A;PDS5B-dTAG_DMSO_input


title: PDS5A;PDS5B-dTAG_DMSO_RAD21


title: PDS5A;PDS5B-dTAG_dTAG_CTCF


title: PDS5B-dTAG_dTAG_RAD21

value: PDS5B -dTAG


title: h_siTPRX1_d3_7c_1_smartseq


title: PDS5A;PDS5B-dTAG_dTAG_input

value: Hepatocarcinoma cells


title: PDS5B-dTAG_dTAG_CTCF

value: dTAG


title: h_siTPRX1_d3_6c_smartseq


title: PDS5B-dTAG_dTAG_PDS5B

value: PDS5B (Bethyl, A300-537A)


title: h_siTPRX2_d3_8c_1_smartseq


title: h_siTPRX1_d3_11c_smartseq


title: h_siTPRX2_d3_6c_smartseq


title: PDS5B-dTAG_dTAG_PDS5A

value: PDS5A (Bethyl, A300-089A)


title: PDS5B-dTAG_dTAG_FLAG-PDS5B

value: FLAG (Sigma, F1804)


title: PDS5B-dTAG_dTAG_input


title: h_siTNCfor12_d3_8c_2_smartseq

value: Control siRNA


title: h_siTNCfor12_d3_9c_smartseq


title: Cal27

value: head and neck cancer cell line

value: untreated


title: h_siTPRX1_d3_7c_3_smartseq


title: h_siTNCfor12_d3_8c_1_smartseq


title: PDS5B-dTAG_DMSO_PDS5B


title: PDS5B-dTAG_DMSO_CTCF


title: h_siTNCfor12_d3_7c_1_smartseq


title: h_siTNCfor12_d3_7c_2_smartseq


title: PDS5B-dTAG_DMSO_PDS5A


title: h_siTNCfor12_d3_5c_smartseq


title: h_siTNCfor12_d3_12c_smartseq


title: PDS5B-dTAG_DMSO_input

value: Input


title: h_siTNCfor12_d3_10c_1_smartseq


title: UPN3550_HiC

data_processing:
Hi-C libraries were sequenced 2×150bp on a NovaSeq 6000 instrument (Illumina).
Reads were processed using Juicer, aligning to reference genome hg38 to generate Hi-C contact matrices (.hic files).
Contact matrices were visualized using Juicebox.
Assembly: Hg38

source_name: Brain

growth_protocol: UPN3550 cells were isolated from a group 4 MB patient's primary tumor tissue, in DMEM/F12 with 10% FBS, 2 mM L-glutamine and 1% penicillin/streptomycin. MB-004 cells were cultured in neurobasal medium (Sigma; SCM003) with 2% B-27, 1 mg/ml heparin, 2 mM L-glutamine and 1% penicillin/streptomycin, 25 ng/ml FGF and 25 ng/ml EGF at 37℃ in an atmosphere of 5% CO2.

extract_protocol:
Five million cells for each cell line were cross-linked with 1% formaldehyde for 10 mins at room temperature and then then quenched with 0.2M Glycine. Cell pellets were washed with cold PBS and lysed with lysis buffer to get nuclei pellets.
MB004 (G3 MB) and UPN3550 (G4 MB) cells were processed for Hi-C library construction using the Arima Hi-C Kit following the manual (Arima Genomics). Briefly,  nuclei were permeabilized and in situ digested. KAPA Hyper Prep kit was used for library amplification (KAPA, KK2802).

treatment_protocol: no treatment

value: Brain

value: medulloblastoma cells

value: wt

value: no


title: PDS5A-dTAG_dTAG_CTCF


title: PDS5A-dTAG_dTAG_RAD21

value: RAD21 (Abcam, ab992)


title: PDS5B-dTAG_DMSO_FLAG-PDS5B


title: h_siTNC_d4_morula_4_smartseq

data_processing:
Illumina Casava1.8 software used for basecalling.
All RNA-seq data were trimmed by Trim Galore (v0.6.4) then mapped to transcriptome of mm9/hg19 by STAR (v2.5.3a). The gene expression level was calculated by Cufflinks (v2.2.1) based on the annotation of hg19 refFlat database from UCSC genome browser.
Ribo-lite data were trimmed with cutadapt (v1.14) with parameters: cutadapt --trim-n -a GATCGGAAGAGCACACGTCTG -a AGAGCACACGTCTG <input.file> | cutadapt -u 3 -a A{100} --no-indels -e 0.16666666666666666 - | cutadapt -O 8 --match-read-wildcards -g GTTCAGAGTTCTACAGTCCGACGATCSSS -m 18 - -o <output.file> , and the trimmed reads were sequentially mapped to human rRNAs sequences (hg19) using Bowtie2 (v2.2.2). Those aligned to rRNA were discarded, and the rest reads were mapped to transcriptome of hg19 using STAR (v2.5.3a). The gene expression level was then calculated by Cufflinks (v2.2.1) based on the annotation defined by hg19 refFlat database from the UCSC genome browser.
The paired-end Stacc–seq reads were aligned with the parameters: -t -q -p 96 -N 1 -L 25 -X 2000 --no-unal -x by Bowtie2 (v 2.2.5). All reads were aligned to either the human (hg19) or the Drosophila (dm6) (spike-in) reference genome.
Genome_build: hg19
Supplementary_files_format_and_content: The RNA FPKM tables including the FPKM of each gene for all the samples.
Supplementary_files_format_and_content: The BedGraph for Stacc-seq samples.

value: Preimplantation embryo

value: morula

value: Control siRNA and morpholino


title: h_siTPRX1_d3_10c_smartseq

value: TPRX1 KD


title: PDS5A-dTAG_dTAG_PDS5A

value: Hepatocarcinoma cells

value: dTAG


title: PDS5A-dTAG_dTAG_PDS5B

value: PDS5B (Bethyl, A300-537A)


title: MB004_HiC


title: PDS5B-dTAG_DMSO_RAD21

value: PDS5B -dTAG

value: DMSO


title: h_siTNC_d4_morula_1_smartseq


title: PDS5A-dTAG_DMSO_CTCF

value: CTCF (Millipore, 07-729)


title: h_siTNC_d4_9C_2_smartseq


title: PDS5A-dTAG_dTAG_FLAG-PDS5A

value: FLAG (Sigma, F1804)


title: PDS5A-dTAG_DMSO_RAD21


title: h_siTNC_d4_morula_3_smartseq


title: PDS5A-dTAG_DMSO_PDS5B


title: h_siTNC_d4_9C_1_smartseq


title: h_siTNC_d4_8C_2_smartseq


title: PDS5A-dTAG_DMSO_PDS5A

value: PDS5A (Bethyl, A300-089A)


title: PDS5A-dTAG_DMSO_input


title: h_siTNCfor12_d3_10c_2_smartseq

value: Control siRNA


title: h_siTNC_d4_6C_smartseq


title: PDS5A-dTAG_DMSO_FLAG-PDS5A


title: h_siTNC_d4_5C_2_smartseq


title: h_siTNC_d4_10C_smartseq


title: h_siTNC_d4_5C_1_smartseq


title: h_siTPRX12L_d4_morula_2_smartseq

value: TPRX12L KD


title: h_siTPRX12L_d4_morula_1_smartseq


title: h_siTNC_d4_morula_2_smartseq


title: PDS5A-dTAG_dTAG_input


title: Wild type - sample 4

city: Richmond

first: Janina

middle: P

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

description:
Pgr analysis - WT iron replete
Wild Type vs Pgr Mutant - all data

data_processing:
Base calls were done using CLC Genomic Workbench
Reads were aligned to the genome of Porphyromonas gingivalisW83 using Genomic Workbench
Reads per gene were determined using Genomic Workbench
Statistical analysis was done using Genomic Workbench

organism: Porphyromonas gingivalis

source_name: Bacterial cell

growth_protocol: Samples of wildtype and V3130 Pgr mutant P. gingivalis were grown in an overnight culture of BHI media. The overnight cultures served to inoculate cultures of BHI media starting at an OD660 of approximately 0.05. Cultures were grown with and without dipyridyl to mid-log phase, centrifuged, and stored at -20 °C.

extract_protocol:
RNA isolation was carried out using the RNeasy mini-kit (Qiagen) following manufacturers protocol. Residual DNA was removed using the DNA-free DNase kit (Ambion) following manufacturers protocol.
For RNA-seq library generation, the Ovation complete Prokaryotic RNA-Seq DR multiplex kit (Nugen) was used. The library was generated following the manufacturers protocol and fragment sizes from sonication during library generation was confirmed using a bioanalyzer (Agilent Technologies). Libraries were sequenced by VCU nucleic acid sequencing core using Miseq Illumina sequencing.

treatment_protocol: Dipyridyl (Fe Chelator) - 150uM

tag: phase of growth

value: logarithmic phase of growth

tag: dp treatment

value: iron replete


title: Wild type + DP - sample 3

description:
Pgr analysis - WT iron deplete
Wild Type + DP vs Pgr Mutant + DP - all data

value: iron deplete


title: Wild type - sample 3


title: Wild type + DP - sample 4


title: h_siTPRX12L_d4_9C_smartseq

value: Preimplantation embryo

tag: genotype


title: Wild type - sample 2


title: Wild type + DP - sample 1


title: Wild type + DP - sample 2


title: h_siTPRX12L_d4_8C_2_smartseq

tag: cell type


title: h_siTNC_d4_8C_1_smartseq


title: h_siTPRX12L_d4_8C_1_smartseq


title: Wild type - sample 1


title: Pgr mutant + DP - sample 4

description:
Pgr analysis - mutant iron deplete
Wild Type + DP vs Pgr Mutant + DP - all data


title: h_siTPRX12L_d4_7C_2_smartseq


title: h_siTPRX12L_d4_7C_4_smartseq


title: Pgr mutant - sample 4

description:
Pgr analysis - mutant iron replete
Wild Type vs Pgr Mutant - all data


title: h_siTPRX12L_d4_7C_3_smartseq


title: Pgr mutant + DP - sample 3


title: Pgr mutant + DP - sample 2


title: h_siTPRX12L_d4_7C_1_smartseq


title: h_siTPRX12L_d4_6C_smartseq


title: Pgr mutant - sample 3


title: Pgr mutant + DP - sample 1


title: Pgr mutant - sample 2


title: h_siLNC_d3_9C_smartseq


title: h_siLNC_d3_8C_5_smartseq


title: h_siLNC_d3_8C_4_smartseq


title: Pgr mutant - sample 1


title: h_siLNC_d3_8C_3_smartseq


title: h_siLNC_d3_8C_2_smartseq


title: h_siLNC_d3_8C_1_smartseq


title: h_siLNC_d3_10C_3_smartseq


title: h_siLNC_d3_5C_smartseq


title: TaSEP3-7B

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

data_processing:
library strategy: DAP-seq
Sequencing reads were cleaned with the fastp(version 0.20.0) and Trim Galore (version 0.4.4), which eliminated bases with low quality scores(< 25) and irregular GC contents, sequencing adapters, and short reads.
The remaining clean reads were mapped to the Chinese Spring (T. aestivum) genome with the Burrows–Wheeler Aligner(version 0.7.17-r1188).
The MACS(version 2.2.6) program was used to identify the read-enriched regions(peaks) based on the criteria: P < 1e−10. The peaks detected from samples introduced with Halo tag only were considered as non-specific bindings, and TF peaks overlapping with peaks detected from Halo samples were removed for subsequent analysis.
Assembly: IWGSC RefSeq v1.1
Supplementary files format and content: peak files and bigwig files

organism: Triticum aestivum

source_name: Triticum aestivum seedling

growth_protocol: 16h light, 8h dark, 22°C

extract_protocol:
Genomic DNA was extracted from leaves using Plant DNAzol Reagent(invitrogen). RNA was extracted using TRIzol.
Genomic DNA was fragmented. And then end repaired using the End-It kit(Lucigen) and A-tailed using Klenow(3′–5′ exo-; NEB). Truncated Illumina Y-adapter was ligated to DNA using T4 DNA Ligase(Promega). Full length TF was cloned into pIX-Halo vector. Halo-tagged TF was expressed in vitro using TNT SP6 Coupled Wheat Germ Extract System(Promega). Halo-TF was immobilized by Magne HaloTag Beads(Promega) and then incubated with the DNA library. TF specific binding DNA was eluted for 10 min at 98°C and amplified with indexed Illumina primer using Phanta Max Super-Fidelity DNA Polymerase(Vazyme). Meanwhile, to capture background DNA which captured by Halo, pIX-Halo vector without TF cloned was expressed and incubated with the DNA library as well. The PCR product was purified using VAHTS DNA Clean Beads(Vazyme).

tag: dap antibody

value: Halo

tag: antibody manufacturer

value: Promega

tag: antibody catalog #

tag: cultivar

value: Chinese Spring


title: TaSEP3-7D


title: TaSEP3-7A


title: TdDof-3A


title: TaVRT2-7D


title: Tamyb10-3D


title: h_siLNC_d3_10C_1_smartseq

tag: tissue


title: h_siLEUTX_d3_9C_4_smartseq

value: LEUTX KD


title: Tamyb10-3B


title: h_siLNC_d3_10C_2_smartseq


title: h_siLEUTX_d3_9C_3_smartseq


title: TaMOR-4B


title: h_siLEUTX_d3_9C_2_smartseq


title: GNI-U


title: h_siLEUTX_d3_8C_2_smartseq


title: GNI-2D


title: h_siLEUTX_d3_8C_1_smartseq


title: WRKY-6A-1

data_processing:
Library strategy: DAP-seq
Sequencing reads were cleaned with the fastp(version 0.20.0) and Trim Galore (version 0.4.4), which eliminated bases with low quality scores(< 25) and irregular GC contents, sequencing adapters, and short reads.
The remaining clean reads were mapped to the Chinese Spring (T. aestivum) genome with the Burrows–Wheeler Aligner(version 0.7.17-r1188).
The MACS(version 2.2.6) program was used to identify the read-enriched regions(peaks) based on the criteria: P < 1e−10. The peaks detected from samples introduced with Halo tag only were considered as non-specific bindings, and TF peaks overlapping with peaks detected from Halo samples were removed for subsequent analysis.
Genome_build: IWGSC RefSeq v1.1
Supplementary_files_format_and_content: peak files and bigwig files

extract_protocol:
Genomic DNA was extracted from leaves using Plant DNAzol Reagent(invitrogen). RNA was extracted using TRIzol.
Genomic DNA was fragmented. And then end repaired using the End-It kit(Lucigen) and A-tailed using Klenow(3'-5' exo-; NEB). Truncated Illumina Y-adapter was ligated to DNA using T4 DNA Ligase(Promega). Full length TF was cloned into pIX-Halo vector. Halo-tagged TF was expressed in vitro using TNT SP6 Coupled Wheat Germ Extract System(Promega). Halo-TF was immobilized by Magne HaloTag Beads(Promega) and then incubated with the DNA library. TF specific binding DNA was eluted for 10 min at 98°C and amplified with indexed Illumina primer using Phanta Max Super-Fidelity DNA Polymerase(Vazyme). Meanwhile, to capture background DNA which captured by Halo, pIX-Halo vector without TF cloned was expressed and incubated with the DNA library as well. The PCR product was purified using VAHTS DNA Clean Beads(Vazyme).


title: WRKY-1D-2


title: h_siLEUTX_d3_7C_2_smartseq


title: TUB-3A-1


title: WRKY-1D-1


title: h_siLEUTX_d3_7C_1_smartseq


title: Vrn1-5D-1


title: TUB-1B-1


title: Trihelix-2B-1


title: h_siLEUTX_d3_3C_smartseq


title: Trihelix-2A-1


title: h_siLEUTX_d3_12C_2_smartseq


title: h_siLEUTX_d3_5C_2_smartseq


title: TaMOR-4D


title: h_siLEUTX_d3_9C_1_smartseq


title: h_siLEUTX_d3_12C_1_smartseq


title: Tify-6B-1


title: h_siLEUTX_d3_10C_smartseq


title: SBP-7B-2


title: h_siLEUTX_d3_5C_1_smartseq


title: h_siTNC_d3_8C_2_smartseq

value: Control siRNA and morpholino


title: Tify-5A-1


title: SPL16-gw8-7D-1


title: h_siTNC_d3_9C_2_smartseq


title: SPL16-gw8-7B-1


title: RWP-RK-2D-1


title: h_siTNC_d3_8C_1_smartseq


title: h_siTNC_d3_8C_3_smartseq


title: h_siTNC_d3_9C_1_smartseq


title: Rht-4D-1


title: h_siTNC_d3_7C_5_smartseq


title: Rht-4B-1


title: h_siTNC_d3_7C_3_smartseq


title: h_siTNC_d3_7C_4_smartseq


title: REF6-3D-1


title: Tify-5B-1


title: h_siTNC_d3_7C_2_smartseq


title: Q-5A-1


title: PLATZ-D


title: h_siTNC_d3_6C_smartseq


title: PLATZ-B


title: h_siTNC_d3_7C_1_smartseq


title: h_siTNC_d3_5C_4_smartseq


title: PLATZ-A


title: h_siTNC_d3_5C_3_smartseq


title: PIF-5D-1


title: h_siTNC_d3_5C_2_smartseq


title: PIF-5B-1


title: NF-YB-1B-1


title: NAM-B1-6D-1


title: h_siTNC_d3_4C_5_smartseq


title: NAC-7D-2


title: Q-5B-1


title: F8

city: Orange

first: Patricia

middle: C

last: Lopes

address: 450 N Center St

department: Biological Sciences

institute: Chapman University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Data filtering: reads containing adapters, reads containing N > 10% and low quality reads were filtered out
Mapping was done using HISAT2
Normalized abundance counts were generated using the DESeq2 R package
Genome_build: GCA_001577835.1 Coturnix_japonica_2.0
Supplementary_files_format_and_content: tab-delimited text file includes raw (not normalized) readcount values for each sample

organism: Coturnix japonica

source_name: control F exposed to saline M

extract_protocol:
An aliquot of blood was placed in Qiazol lysis reagent and homogeneized; Total RNA was extracted from the aqueous layer formed after chloroform precipitation, using the RNA Clean & Concentrator Kit-5 (Zymo Research, item # R1013) following manufacturer’s instructions and including the DNase I in-column treatment step.
RNA libraries were prepared for sequencing using NEBNext® UltraTM RNA Library Prep Kit, following standard protocols

value: blood

tag: treatments

tag: female injection

value: SAL

tag: male treatment


title: F79

source_name: control F exposed to LPS M

value: LPS


title: F100

source_name: LPS F exposed to saline M


title: h_siTNC_d3_4C_4_smartseq


title: NAC-7B-2


title: F2


title: NAC-7A-2


title: NAC-6D-1


title: NAC-7A-1


title: h_siTNC_d3_4C_3_smartseq


title: NAC-6B-1


title: F72


title: h_siTNC_d3_4C_2_smartseq


title: NAC-6A-1


title: h_siTNC_d3_5C_1_smartseq


title: F76


title: h_siTNC_d3_4C_1_smartseq


title: F77


title: NAM-B1-6A-1


title: NAC-3D-1


title: NAC-2D-6


title: h_siTNC_d3_12C_2_smartseq


title: NAC-2A-4


title: F74


title: NAC-2A-1


title: F37


title: NAC-3A-1


title: h_siTNC_d3_12C_1_smartseq


title: NAC-1D-1


title: F35


title: MYB-7A-5


title: h_siTNC_d3_10C_7_smartseq


title: h_siTNC_d3_10C_5_smartseq


title: MYB-5A-1


title: MYB-4A-2


title: h_siTNC_d3_10C_4_smartseq


title: F52


title: MYB-5B-1


title: MYB-4A-1


title: F55


title: MYB-7A-3


title: MYB-3D-1


title: h_siTNC_d3_10C_3_smartseq


title: F57


title: MYB-3A-1


title: NAC-2A-3


title: h_siTNC_d3_10C_2_smartseq


title: MYB-2A-1


title: MYB-2A-2


title: h_siTNC_d3_10C_1_smartseq


title: h_siTNC_d3_10C_6_smartseq


title: MYB-1A-2


title: F99


title: F95


title: MYB-6D-1


title: h_siTPRX12L_d3_8C_3_smartseq


title: MADS-MIKC-5A-1


title: MADS-MIKC-7A-1


title: F96


title: F53


title: h_siTPRX12L_d3_8C_2_smartseq


title: MADS-M-4D-1


title: F60


title: F51YY


title: MADS1-lgy3-4D-1


title: MADS1-lgy3-4B-1


title: LOB-3D-1


title: LOB-3D-2


title: h_siTPRX12L_d3_7C_5_smartseq


title: LOB-3A-1


title: F62


title: LOB-1A-1


title: MYB-1A-1


title: h_siTPRX12L_d3_7C_4_smartseq


title: LOB-3B-1


title: F63


title: h_siTPRX12L_d3_7C_3_smartseq


title: F67


title: F69


title: LIM-7B-1


title: LIM-7D-1


title: h_siTPRX12L_d3_7C_2_smartseq


title: F26


title: IPA1-7B-1


title: h_siTPRX12L_d3_7C_1_smartseq


title: HSF-U


title: HB-WOX-D


title: h_siTPRX12L_d3_8C_1_smartseq


title: MADS1-lgy3-4A-1


title: HB-WOX-B


title: HB-WOX-A


title: h_siTPRX12L_d3_7C_6_smartseq


title: h_siTPRX12L_d3_6C_7_smartseq


title: HB-PHD-6A-1


title: HB-HD-ZIP-6B-2


title: F90Y


title: HB-HD-ZIP-6A-2


title: h_siTPRX12L_d3_6C_6_smartseq


title: HB-HD-ZIP-6A-1


title: F46


title: h_siTPRX12L_d3_6C_5_smartseq


title: HB-HD-ZIP-2B-1


title: F88


title: HB-HD-ZIP-2A-1


title: h_siTPRX12L_d3_6C_4_smartseq


title: Halo-merge


title: h_siTPRX12L_d3_6C_3_smartseq


title: HB-BELL-4B-1


title: h_siTPRX12L_d3_6C_2_smartseq


title: GRF4-2D-1


title: HB-BELL-5D-1


title: h_siTPRX12L_d3_6C_1_smartseq


title: GRF4-2B-1


title: F51Y


title: h_siTPRX12L_d3_5C_3_smartseq


title: ATAC-Seq MAP cells, Rosi3D 2

city: Indianapolis

first: Jisun

last: So

state: IN

address: 635 Barnhill Drive

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

description: paired-end

data_processing:
Raw sequencing reads were trimmed and filtered using fastp.
The filtered reads were aligned to GrCM38/mm10 using Bowtie2.
Mitochondrial reads and PCR duplicates were removed using SAMtools and Picard.
Peaks were called uing MACS2, merged from all samples using BEDOPS, and then quantified using featureCounts.
bigWig files were generated using the deepTools. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: mm10
Supplementary files format and content: txt (a master matrix of raw counts from all samples), bigWig

source_name: Immortalized mouse adipocyte progenitor (MAP) cells

growth_protocol:
MAP cells were maintained in DMEM supplemented with 10% fetal bovine serm (FBS) and antibiotics.
Upon cell confluency (designated day 0, D0),  adipogenic differentation was induced with 5mg/ml insulin,  500uM isobutylmethylxanthine,  1uM dexamethasone, and  1uM rosiglitazone for 2 days.
MAP cells were then treatwed with 5mg/ml insulin and 1uM rosiglitazone for another 2 days for full differentiation.

extract_protocol:
MAP cell nuclei were isolated by homogenization and sorted using Hoechst 33342.
ATAC-seq libraries were prepared using the Nextera DNA Libarary Preparation Kit (Illumina). 10,000 adipocyte nuclei were used as starting material.
Libraries were amplified using 12 cycles on the thermocycler and size-selected using AMPure XP beads (Beckman Coulter). The resulting libraries were quantified by Qubit and analyzed for Agilent Bioanalyzer for size distribution.

treatment_protocol: Adipocyte browning was induced by treating fully differentiated adipocytes (at day 7-8) with forskolin for 4 hours, 1 day, or 3 days or with rosiglitazone for 3 days.

tag: cell line

value: adipocyte progenitor cells


title: ATAC-Seq MAP cells, Rosi3D 1

description: paired-end

value: Immortalized mouse adipocyte progenitor (MAP) cells


title: ATAC-Seq MAP cells, FSK3D 2

description: paired-end


title: ATAC-Seq MAP cells, FSK3D 1

description: paired-end


title: F60Y


title: ER00573 sarZ::tet, 5 hours, Replicate 3 [MRSA-42]

first: Harm

middle: van

last: Bakel

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

data_processing:
Raw reads were first trimmed by removing Illumina adapter sequences from 3’ ends using cutadapt, and by removing 3′ read sequences if more than 20 bases with Q≥20 were present. Paired-end reads were then mapped to the FPR3757 (NC_007793) reference genome using Bowtie2, and htseq-count was used to produce strand-specific transcript count summaries. Raw fragment (i.e., paired-end read) counts were then combined into a numeric matrix, with genes in rows and samples in columns.
Differential gene expression analysis was performed with the limma R package in Bioconductor. Normalization factors were computed on the data matrix using the weighted trimmed mean of M-values (TMM) method, followed by voom 65 mean-variance transformation in preparation for Limma linear modeling. Only genes with expression levels ≥1 FPKM (fragments per kb per million reads) in at least 50% of samples, and a length ≥200 bp, were retained for further analysis. Filtered data were fitted to a design matrix containing all sample groups, and pairwise comparisons were performed between the groups of interest. Finally, eBayes adjusted P-values were corrected for multiple testing using the Holm method and used to select genes with significant expression differences (q ≤ 0.05).
Genome_build: FPR3757 (NC_007793)
Supplementary_files_format_and_content: Tab-delimited text file with normalized log (counts per million)

organism: Staphylococcus aureus

source_name: ER00573 sarZ::tet_5 hours

growth_protocol: Each strain was cultured for 3h (logarithmic growth) and 5h (stationary phase) in 5mL tryptic soy broth (TSB), spun down, and resuspended in 1mL RNA STAT-60TM (Amsbio).

extract_protocol:
Samples were bead beated using FastPrep and spun down. Upper phase was collected and 200µL chloroform was added. 0.5mL isopropanol was added to aqueous phase to precipitate RNA. RNA was washed with 70% ethanol, air dried, and resuspended in RNase free water. 2500ng of RNA was DNase treated (TURBO DNA-freeTM kit, Invitrogen Ambion).
For each sample, 250ng of RNA was first depleted of bacterial rRNAs using enzymatic ribodepletion with the Illumina Ribo-Zero Plus rRNA Depletion Kit (Illumina, Catalog no. 20037135) according to the manufacturers protocol. RNA-Seq libraries were then prepared using the Illumina TruSeq Stranded Total RNA Library Prep kit using the depleted rRNA material as input and following the manufacturer’s protocol.

tag: strain

value: 5 hours


title: GRAS-4B-2


title: ER00573 sarZ::tet, 5 hours, Replicate 2 [MRSA-41]

tag: time


title: HB-HD-ZIP-2A-2


title: h_siTPRX12L_d3_5C_2_smartseq


title: GRF-6A-1


title: GRF4-2A-1


title: ER00573 sarZ::tet, 5 hours, Replicate 1 [MRSA-40]


title: h_siTPRX12L_d3_5C_1_smartseq


title: ATAC-Seq MAP cells, FSK1D 2

description: paired-end


title: ATAC-Seq MAP cells, FSK1D 1

description: paired-end


title: GARP-G2-5B-3


title: GARP-G2-4D-2


title: ATAC-Seq MAP cells, FSK4h 2

description: paired-end


title: h_siTPRXL_d3_morula_smartseq

value: morula

value: TPRXL KD


title: GARP-G2-4A-1


title: ATAC-Seq MAP cells, FSK4h 1

description: paired-end


title: ER00573, 5 hours, Replicate 1 [MRSA-37]

source_name: ER00573_5 hours

value: WT sarZ


title: ER00573, 5 hours, Replicate 2 [MRSA-38]


title: GARP-G2-3B-1


title: ER00594 + WT sarZ, 5 hours, Replicate 2 [MRSA-35]

source_name: ER00594 + WT sarZ_5 hours

value: FS1 + WT sarZ


title: GRAS-2A-1


title: GARP-G2-2B-1


title: h_siTPRXL_d3_9C_smartseq


title: ATAC-Seq MAP cells, Control 2

description: paired-end


title: h_siTPRXL_d3_8c_1_smartseq


title: h_siTPRXL_d3_8c_2_smartseq


title: GARP-ARR-7A-3


title: ER00573, 5 hours, Replicate 3 [MRSA-39]


title: GARP-G2-2A-1


title: h_siTPRXL_d3_7c_2_smartseq


title: ER00594 + WT sarZ, 5 hours, Replicate 3 [MRSA-36]


title: h_siTPRX12L_d3_3C_smartseq

value: TPRX12L KD


title: ATAC-Seq MAP cells, Control 1

description: paired-end


title: iWAT, female, infected, rep3

city: Manchester

first: Matthew

middle: Christopher

last: Sinton

state: Greater Manchester

address: Core Technology Facility

department: Division of Immunology, Immunity to Infection and Respiratory Medicine

country: United Kingdom

institute: University of Manchester

data_processing:
Clustering of the index-coded samples was performed on a cBot Cluster Generation System using a TruSeq PE Cluster Kit v3-cBot-HS (Illumina, California, USA) according to the manufacturer’s instructions. After cluster generation, libraries were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw reads in fastq format were processed through proprietary Perl scripts developed by Novogene (Cambridge, UK). Clean reads were obtained by removing reads containing adapters, poly-N, or low-quality reads from raw data. Concurrently, the Q20, Q30 and GC content of the clean data was calculated.
Genome and genome annotation files (Genome Reference Consortium Mouse Build; GRCm39) were downloaded. An index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The featureCounts (v. 1.5.0-p3) package was used to count read numbers mapped to each gene, before calculating the Fragments Per Kilobase of transcript sequence per Millions base pairs (FPKM) of each gene using the length of the gene and reads count mapped to this gene.
Assembly: Genome Reference Consortium Mouse Build; GRCm39
Supplementary files format and content: The csv file reports Normalised readcounts, counts,fpkms.

source_name: Inguinal white adipose tissue

growth_protocol: All mice were fed ad libitum and kept on a 12 h light–dark cycle

extract_protocol:
iWAT was harvested from mice and stored in TRIzol (Cat. #15596026, Invitrogen, Massachusetts, USA). Total RNA was then purified from iWAT using an RNeasy Kit (Cat. #74004, Qiagen, Dusseldorf, Germany) as per the manufacturer’s recommendations. The RNA was purified in 30 µL of nuclease-free water (Cat. #129112, Qiagen, Dusseldorf, Germany), and RNA concentration measured on a NanoDrop 2000 (Cat. #ND2000, Thermo Fisher Scientific, Massachusetts, USA). Samples were shipped to Novogene (Cambridge, UK) to undergo quality control, library preparation and sequencing.
Library preparation was performed by Novogene (Cambridge, UK). Messenger RNA (mRNA) was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in a First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was then performed using DNA Polymerase I and RNase H. Remaining overhangs were converted to blunt ends via exonuclease/polymerase activity. Following adenylation of 3’ ends of DNA fragments, adaptors with hairpin loop structures were ligated. To select cDNA fragments of 370~420 bp in length, library fragments were purified using AMPure XP beads (Beckman Coulter, Beverly, USA), as per the manufacturer’s instructions. PCR was then performed using Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) primers. Finally, PCR products were purified (AMPure XP system) using AMPure XP beads (Beckman Coulter, Beverly, USA), as per the manufacturer’s instructions, and library quality was assessed using a Bioanalyzer 2100 (Agilent Technologies, CA, USA).

treatment_protocol: Mice were infected with ~2,000 Trypanosoma brucei brucei Antat1.1E parasites by intraperitoneal injection, and housed for 25 days. Naïve mice did not undergo any treatment

value: Wild type

tag: Sex

value: female

tag: infection

value: T. brucei

value: Inguinal white adipose tissue


title: GARP-ARR-7A-1

value: Halo

value: Promega

value: Chinese Spring


title: iWAT, female, infected, rep4


title: ER00594, 5 hours, Replicate 3 [MRSA-33]

source_name: ER00594_5 hours


title: h_siTPRX12L_d3_10C_smartseq

value: Preimplantation embryo


title: ER00594 + WT sarZ, 5 hours, Replicate 1 [MRSA-34]


title: ER00594, 5 hours, Replicate 2 [MRSA-32]


title: GARP-ARR-6A-1


title: iWAT, female, infected, rep2


title: ER00594, 5 hours, Replicate 1 [MRSA-31]


title: iWAT, female, infected, rep1


title: h_siTPRXL_d3_6c_2_smartseq


title: AH LAC sarZ::bursa + WT sarZ, 5 hours, Replicate 3 [MRSA-30]

source_name: AH LAC sarZ::bursa + WT sarZ_5 hours

value: AH LAC

value: sarZ::bursa + WT sarZ


title: EIL-4D-1


title: h_siTPRXL_d3_6c_1_smartseq


title: h_siTPRXL_d3_3C_2_smartseq


title: AH LAC sarZ::bursa + WT sarZ, 5 hours, Replicate 2 [MRSA-29]


title: DBP-1B-1


title: DBP-1D-1


title: AH LAC sarZ::bursa + WT sarZ, 5 hours, Replicate 1 [MRSA-28]


title: h_siTPRXL_d3_3C_1_smartseq


title: DBB-7A-1


title: AH LAC sarZ::bursa + empty vector, 5 hours, Replicate 3 [MRSA-27]

source_name: AH LAC sarZ::bursa + empty vector_5 hours

value: sarZ::bursa + empty vector


title: h_siTPRXL_d3_10C_smartseq


title: h_siTPRXL_d3_7c_1_smartseq


title: h_siTPRX12_d3_9C_3_smartseq

value: TPRX12 KD


title: iWAT, female, naïve, rep1

value: naive


title: AH LAC sarZ::bursa + empty vector, 5 hours, Replicate 2 [MRSA-26]

value: 5 hours


title: C3H-3A-2


title: h_siTPRX12_d3_9C_2_smartseq


title: iWAT, male, infected, rep3

value: male


title: AH LAC sarZ::bursa + empty vector, 5 hours, Replicate 1 [MRSA-25]


title: iWAT, female, naïve, rep4


title: iWAT, male, infected, rep2


title: h_siTPRX12_d3_9C_1_smartseq


title: iWAT, female, naïve, rep2


title: iWAT, male, infected, rep1


title: AH LAC + empty vector, 5 hours, Replicate 2 [MRSA-23]

source_name: AH LAC + empty vector_5 hours

value: empty vector


title: iWAT, male, infected, rep4


title: h_siTPRX12_d3_8C_smartseq


title: iWAT, male, naïve, rep4


title: AH LAC + empty vector, 5 hours, Replicate 3 [MRSA-24]


title: iWAT, female, naïve, rep3


title: C3H-1D-2


title: AH LAC + empty vector, 5 hours, Replicate 1 [MRSA-22]


title: h_siTPRX12_d3_7C_smartseq


title: iWAT, male, naïve, rep3


title: C3H-7B-1


title: C2H2-6D-2


title: ER00573 sarZ::tet, 3 hours, Replicate 3 [MRSA-21]

source_name: ER00573 sarZ::tet_3 hours

value: 3 hours


title: C2H2-6B-1


title: iWAT, male, naïve, rep2

value: Wild type


title: C3H-3A-1


title: h_siTPRX12_d3_4C_smartseq

source_name: Preimplantation embryo


title: ER00573 sarZ::tet, 3 hours, Replicate 2 [MRSA-20]


title: iWAT, male, naïve, rep1


title: C2H2-6A-1


title: h_siTPRX12_d3_3C_smartseq


title: C2H2-5B-1


title: h_siTPRX12_d3_12C_smartseq


title: ER00573, 3 hours, Replicate 3 [MRSA-18]

source_name: ER00573_3 hours

value: WT sarZ


title: FGD5_cko_P4

city: Beijing

first: Tingting

last: Zhang

address: 1 Xian Nong Tan Street

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software and Seurat 3.0(R package) were used for basecalling.Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K-means algorithm and graph-based algorithm, respectively.
GO enrichment, KEGG enrichment, Reactome enrichment and Disease enrichment (human only) of cluster markers were performed using KOBAS software with Benjamini-Hochberg multiple testing adjustment, using top 20 markers gene of cluster. The results were visualized using R package.
Protein-protein interaction was obtained from STRING database with combine_score >=400. For each cluster, the interaction of top 20 marker genes was extracted from the database and the results were visualized using Cytoscape software, respectively.
Transcription Factors were predicted within 2000 bp upstream and 500 bp downstream of TSS for top 20 marker genes of each cluster using TFBSTools and JASPAR database. The gene and TF network for each cluster was visualized using Cytoscape software.
GSEA was performed by using GSEA software version 2.2.2.4, which uses predefined gene sets from the Molecular Signatures Database (MSigDB v6.2).All genes detected in all cells of one sample were used. Gene expression data was calculated by mean umi count of gene in one cluster and the rest cluster, respectively. The minimum and maximum criteria for selection of gene sets from the collection were 0 and 500 genes, respectively.
Assembly: mm9
Supplementary files format and content: matrix table with raw gene count for every gene and every cell

source_name: Mammary gland

extract_protocol:
Using single cell 3 'Library and Gel Bead Kit V3 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200 (performed by CapitalBio Technology, Beijing).
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3.

value: mammary gland

tag: cell marker


title: WT_P4

value: WT


title: ER00573, 3 hours, Replicate 2 [MRSA-17]


title: h_siTPRX12_d3_11C_smartseq


title: C2H2-4A-1

source_name: Triticum aestivum seedling

value: Halo


title: C2H2-3D-2

value: Promega


title: C3H-1A-1

value: Chinese Spring


title: ER00573, 3 hours, Replicate 1 [MRSA-16]


title: h_siTPRX12_d3_10c_smartseq

value: Preimplantation embryo


title: h_siTPRX12_d3_5C_smartseq


title: ER00594 + WT sarZ, 3 hours, Replicate 3 [MRSA-15]

source_name: ER00594 + WT sarZ_3 hours

value: FS1 + WT sarZ


title: h_4C_DMSO_control_blast_smartseq

value: blastocyst

value: DMSO treatment


title: C2H2-2A-1


title: WT+CXCL14-1

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates.
The GO (Gene Ontology, http://geneontology.org/) enrichment of DEGs was implemented by the hypergeometric test, in which p-value is calculated and adjusted as q-value, and data background is genes in the whole genome.
KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) is a database resource containing a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
Mammary gland were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mammary gland

tag: age

value: Post natal day 45

tag: treatment

value: Recombinant mouse CXCL14 protein


title: WT+CXCL14-2

tag: genotype


title: ER00594 + WT sarZ, 3 hours, Replicate 2 [MRSA-14]


title: C2H2-3A-1

tag: dap antibody


title: ER00573 sarZ::tet, 3 hours, Replicate 1 [MRSA-19]


title: C2-D

tag: antibody manufacturer


title: WT-3

value: untreated


title: h_4C_DMSO_control_blast_2_smartseq

tag: cell type


title: ER00594 + WT sarZ, 3 hours, Replicate 1 [MRSA-13]


title: h_4C_DMSO_control_10C_smartseq


title: C2C2-Dof-4D-1

tag: antibody catalog #

tag: cultivar


title: ER00594, 3 hours, Replicate 3 [MRSA-12]

source_name: ER00594_3 hours


title: WT-2

tag: tissue


title: h_4C_DMSO_control_10C_2_smartseq


title: WT-1


title: h_4C_CHX_9C_smartseq

value: cycloheximide treatment


title: C2C2-Dof-4A-1


title: ER00594, 3 hours, Replicate 2 [MRSA-11]

value: 3 hours


title: ER00594, 3 hours, Replicate 1 [MRSA-10]


title: WT+CXCL14-3


title: C2C2-Dof-2D-1


title: Samd9l-Mut (Vehicle)_LK

city: Memphis

first: Jeffery

last: Klco

address: 262 Danny Thomas Place, D4047B

institute: St Jude Children's Research Hospital

data_processing:
fastq files were aligned and quantified via cellranger -v (2.1.1). All files used for analysis resulted from the cellranger program run.
CellRanger command was: cellranger count --id=sample_name --fastqs=fastq_dir --sample=sample_name --transcriptome=path_to_cellranger_installation_mm10_genome_build --expect-cells=5000"
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx files contain genewise read counts for all cells in a space-efficient matrix market format; features[genes].tsv files contain Ensembl IDs and gene symbols as tab-delimited text; barcode.tsv files contain the 10X barcodes used to identify cells.

source_name: LK cells from Samd9l-Mut mouse treated with vehicle

extract_protocol:
mice were euthanized as previously reported (Abdelhamed et al, EMBO reports, 2019).
4000 cells were isolated for single-cell barcoding of and 5’ GEX library preparation using 10x Genomics® Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 following the manufacturer’s protocol
Libraries were pooled and sequenced on a Novaseq 6000 using a Novaseq 6000 SP Reagent Kit v1.5 (100 cycles, Illumina Cat#20028401)

treatment_protocol: Mice were treatd with vehicle or pI:pC twice a week for 4 weeks. This treatment protocol was adapted from previous reports (Walter et al, Nature, 2015).

value: Bone Marrow

tag: cells

value: lineage- cKit+ (LK)

value: Vehicle


title: Samd9l-Mut (Vehicle)_WBM

source_name: WBM cells from Samd9l-Mut mouse treated with vehicle

value: WBM


title: h_4C_CHX_6C_smartseq


title: h_4C_CHX_7C_smartseq


title: C2-B

value: Halo


title: C2C2-Dof-2A-1

value: Promega


title: AH LAC sarZ::bursa + WT sarZ, 3 hours, Replicate 2 [MRSA-08]

source_name: AH LAC sarZ::bursa + WT sarZ_3 hours

value: AH LAC

value: sarZ::bursa + WT sarZ


title: AH LAC sarZ::bursa + WT sarZ, 3 hours, Replicate 3 [MRSA-09]


title: Samd9l-Mut (pI:pC)_LK_2

source_name: LK cells from Samd9l-Mut mouse treated with pI:pC


title: Samd9l-Mut (pI:pC)_LK_1


title: AH LAC sarZ::bursa + WT sarZ, 3 hours, Replicate 1 [MRSA-07]


title: h_1C_DMSO_control_morula_4_smartseq

value: Preimplantation embryo

value: morula


title: C2-A

value: Chinese Spring


title: h_1C_DMSO_control_morula_2_smartseq

value: DMSO treatment


title: h_1C_DMSO_control_morula_3_smartseq


title: bZIP-D


title: Samd9l-Mut (pI:pC)_WBM

source_name: WBM cells from Samd9l-Mut mouse treated with pI:pC


title: AH LAC sarZ::bursa + empty vector, 3 hours, Replicate 2 [MRSA-05]

source_name: AH LAC sarZ::bursa + empty vector_3 hours

value: sarZ::bursa + empty vector


title: Samd9l-WT (pI:pC)_LK

source_name: LK cells from Samd9l-WT mouse treated with pI:pC


title: bZIP-A


title: h_1C_DMSO_control_morula_1_smartseq


title: AH LAC sarZ::bursa + empty vector, 3 hours, Replicate 3 [MRSA-06]


title: AH LAC sarZ::bursa + empty vector, 3 hours, Replicate 1 [MRSA-04]


title: h_1C_DMSO_control_5C_smartseq


title: Samd9l-WT (pI:pC)_WBM

source_name: WBM cells from Samd9l-WT mouse treated with pI:pC


title: bZIP-7A-1


title: AH LAC + empty vector, 3 hours, Replicate 3 [MRSA-03]

source_name: AH LAC + empty vector_3 hours

value: empty vector


title: h_1C_DMSO_control_12C_smartseq


title: bZIP-6A-1


title: Samd9l-WT (Vehicle)_LK

source_name: LK cells from Samd9l-WT mouse treated with vehicle


title: Samd9l-WT (Vehicle)_WBM

source_name: WBM cells from Samd9l-WT mouse treated with vehicle


title: AH LAC + empty vector, 3 hours, Replicate 2 [MRSA-02]


title: h_1C_CHX_4C_smartseq

source_name: Preimplantation embryo


title: bZIP-5B-3


title: AH LAC + empty vector, 3 hours, Replicate 1 [MRSA-01]


title: h_1C_CHX_3C_2_smartseq


title: bZIP-B


title: bZIP-5A-1


title: Samd9l-KO

source_name: WBM cells from Samd9l-KO mouse

value: no


title: bZIP-3A-2


title: Samd9l-Mut

source_name: WBM cells from Samd9l-Mut mouse


title: h_1C_CHX_2C_smartseq

value: cycloheximide treatment


title: bZIP-3A-1

source_name: Triticum aestivum seedling


title: INS1

description:
small RNA high throughput sequencing
Rat cell line miRNA read count.xlsx

data_processing:
Basecalls performed using CASAVA version 1.8
cutadapt to remove three nucletide from 5' end
miRge
DEseq2

organism: Rattus rattus

extract_protocol:
Trizol extractd total RNA
Modified illumina v1.5 protocol, 3 random nucleotide added to the end of the 5' adaptor

value: Cell line

value: Pancreas


title: h_1C_CHX_1C_3_smartseq


title: bZIP-2A-3


title: h_1C_CHX_1C_2_smartseq


title: RNA-seq suvhsuvh9_sdlg_2

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

data_processing:
FASTQ reads were analyzed using the plant sequencing analysis pipeline pRNASeqTools (https://github.com/grubbybio/pRNASeqTools).
raw reads were treated using cutadapt v3.4 to remove the adapters
remaining reads were mapped to TAIR10 using STAR v2.7.9a with parameters “--alignIntronMax 5000 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outFilterMismatchNoverLmax 0.1”.
DE genes and TEs (fold change ≥ 2 and P value< 0.01) were identified by the R package DESeq2 v1.30.1 based on the gene expression matrix quantified by featureCounts v2.0.0.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files containing raw read counts on genes and TEs with annotated length

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: All the plants were grown in a greenhouse at 20°C under long-day cycle (16 h light/8 h dark, humidity 75%).

extract_protocol:
For meiocyte, 1 U/μL Recombinant RNase Inhibitor (Takara, 2313A) was added to the collection buffer. 300-400 meiocyte masses were used to extract ~400-1000 ng RNA for a biological replicate. The RNA was extracted using Trizol (ThermoFisher, 15596026). For seedling, 4-5 plants were ground in liquid nitrogen and the total RNA was also extracted using Trizol.
RNA-seq libraries were constructed with the TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer’s instructions

value: 20-day-old seedlings


title: bZIP-2A-2


title: RNA-seq suvhsuvh9_sdlg_1


title: chr18KO-rep23

city: Tsukuba

first: Inoue

last: Kimiko

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

country: Japan

institute: RIKEN

description:
RLTR45-int putative non-null embryos
SMART-Seq HT kit
Raw.read.counts_KO.embryos.txt

data_processing:
Sequence reads were trimmed for adaptor sequence using trimmomatic.
Trimmed sequence reads were mapped to the mouse genome build mm10 using STAR.
Read count extraction and normalization were performed using featureCounts and R, respectively.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw read counts for genes and transposal elements in each sample.

source_name: Embryo

growth_protocol: C57BL/6N female mice at 4–20 weeks of age were superovulated by injection of 7.5 IU equine chorionic gonadotropin or anti-inhibin serum, followed 46–52 h later by injection of 7.5 IU human chorionic gonadotropin. Female mice were euthanized by cervical dislocation 16 h after the hCG injection, and then cumulus–oocyte complexes were collected from the ampullae of excised oviducts 16 h after the hCG injection, and placed in 100-μL droplets of human tubal fluid medium. For in vitro fertilization, spermatozoa were collected from the cauda epididymidis of adult DBA2 male mice and preincubated for at least 30 min in a 400-μL droplet of HTF. After preincubation, 3–5 μL of the sperm suspension was added to the oocyte cultures. At 3 h post-insemination, morphologically normal fertilized embryos were collected and cultured in potassium simplex optimized medium. For somatic cell nuclear transfer, cumulus cells used as nuclear donors were collected from wild-type and Xist heterozygous knockout female mice with a BDF1 (C57BL/6N ×DBA2) genetic background. Recipient oocytes were collected from BDF1 female mice following superovulation as above, and placed in KSOM droplets containing 0.1% bovine testicular hyaluronidase to remove cumulus cells. The cumulus-free oocytes were enucleated in Hepes-buffered KSOM containing 7.5 μg/mL cytochalasin B using a Piezo-driven pipette. After being cultured in fresh KSOM for 1 h, the enucleated oocytes were injected with cumulus cell nuclei in Hepes-buffered KSOM at room temperature. After 1 h culture, the injected oocytes were activated by culture in a Ca2+-free KSOM containing 3 mM strontium chloride and 5 μg/mL cytochalasin B for 1 h. The reconstructed oocytes were cultured in KSOM containing 5 μg/mL cytochalasin B for 5 h. After being washed thoroughly, SCNT-derived embryos were injected with 10 pL of 1500 ng/μL mouse Kdm4d mRNA at 5–6 h post-activation.

extract_protocol:
IVF- and SCNT-derived embryos were collected at 69–70 h post-insemination/activation, and washed twice in 0.05% bovine serum albumin in phosphate-buffered saline.
RNA-seq libraries were constructed by using SMART-Seq v4 kits or SMART-Seq HT kits.

value: Embryo

tag: developmental stage

value: Morula

value: Transfection of Cas9/gRNA targetting RLTR45-int on chr18

value: IVF


title: chr18KO-rep24


title: RNA-seq pol2a-suvhsuvh9_sdlg_2


title: RNA-seq pol2a-suvhsuvh9_sdlg_1


title: h_1C_CHX_1C_1_smartseq


title: chr18KO-rep22


title: bHLH-U

value: Halo

value: Promega


title: h_1C_CHX_3C_1_smartseq

value: Preimplantation embryo


title: RNA-seq pol2a-2_sdlg_2


title: Samd9l-WT

source_name: WBM cells from Samd9l-WT mouse

value: Bone Marrow

value: WBM


title: H9_TPRX2_OE48h_staccseq

data_processing:
Library strategy: Stacc-seq
Illumina Casava1.8 software used for basecalling.
All RNA-seq data were trimmed by Trim Galore (v0.6.4) then mapped to transcriptome of mm9/hg19 by STAR (v2.5.3a). The gene expression level was calculated by Cufflinks (v2.2.1) based on the annotation of hg19 refFlat database from UCSC genome browser.
Ribo-lite data were trimmed with cutadapt (v1.14) with parameters: cutadapt --trim-n -a GATCGGAAGAGCACACGTCTG -a AGAGCACACGTCTG <input.file> | cutadapt -u 3 -a A{100} --no-indels -e 0.16666666666666666 - | cutadapt -O 8 --match-read-wildcards -g GTTCAGAGTTCTACAGTCCGACGATCSSS -m 18 - -o <output.file> , and the trimmed reads were sequentially mapped to human rRNAs sequences (hg19) using Bowtie2 (v2.2.2). Those aligned to rRNA were discarded, and the rest reads were mapped to transcriptome of hg19 using STAR (v2.5.3a). The gene expression level was then calculated by Cufflinks (v2.2.1) based on the annotation defined by hg19 refFlat database from the UCSC genome browser.
The paired-end Stacc–seq reads were aligned with the parameters: -t -q -p 96 -N 1 -L 25 -X 2000 --no-unal -x by Bowtie2 (v 2.2.5). All reads were aligned to either the human (hg19) or the Drosophila (dm6) (spike-in) reference genome.
Genome_build: hg19
Supplementary_files_format_and_content: The RNA FPKM tables including the FPKM of each gene for all the samples.
Supplementary_files_format_and_content: The BedGraph for Stacc-seq samples.

source_name: Embryonic stem cell

extract_protocol:
Stacc–seq was was performed as previously described with the wash version (Liu et al., 2020). Briefly, the collected cells were incubated with concanavalin-coated magnetic beads and antibody and pG–Tn5 mixture. Beads were washed twice and resuspended for Tn5 digestion, which was stopped by SDS. Then DNA was purified by SPRI beads for library amplification and next-generation sequencing.
Stacc-seq libraries were prepared using Stacc-seq as previously described (Liu et al., Nature, 2020).

value: Embryonic stem cell


title: chr18KO-rep21


title: H9_TPRX1_OE48h_staccseq


title: bHLH-7A-3

value: Chinese Spring


title: chr18KO-rep20


title: RNA-seq pol2a-1_sdlg_2


title: RNA-seq pol2a-1_sdlg_1


title: bHLH-7A-2


title: RNA-seq WT_sdlg_2

value: WT


title: H9_TPRXL_OE48h_smartseq_rep3

extract_protocol:
Oocytes, embryos (after removing the zona pellucida) or cells extact preparation by detergent lysis, and RNA-Seq libraries were prepared using Smart-Seq2 protocol with slightly modification.
RNA libraries were prepared for sequencing using Smart-seq2 protocols as previously described (Picelli et al., 2014).


title: bHLH-6A-1


title: chr18KO-rep18


title: chr18KO-rep19


title: RNA-seq pol2a-2_sdlg_1


title: RNA-seq WT_sdlg_1


title: H9_TPRXL_OE48h_smartseq_rep1


title: chr18KO-rep17


title: chr18KO-rep16


title: RNA-seq pol2a-suvhsuvh9_meiocyte_1

source_name: Meiocyte

value: Meiocytes isolated from stage 9-10 floral buds


title: bHLH-5A-1


title: H9_TPRX2_OE48h_smartseq_rep3


title: bHLH-7D-2


title: H9_TPRX2_OE48h_smartseq_rep2


title: bHLH-5A-4


title: RNA-seq suvhsuvh9_meiocyte_2


title: bHLH-4B-1


title: H9_TPRXL_OE48h_smartseq_rep4


title: RNA-seq pol2a-suvhsuvh9_meiocyte_2


title: bHLH-3A-2


title: RNA-seq suvhsuvh9_meiocyte_1


title: RNA-seq pol2a-2_meiocyte_2


title: H9_TPRX1_OE48h_smartseq_rep3


title: chr18KO-rep14


title: chr18KO-rep13


title: bHLH-1A-1


title: H9_TPRX2_OE48h_smartseq_rep1


title: BES1-D


title: chr18KO-rep12

description:
RLTR45-int putative null embryos
SMART-Seq HT kit
Raw.read.counts_KO.embryos.txt


title: RNA-seq pol2a-2_meiocyte_1


title: chr18KO-rep11


title: H9_TPRXL_OE48h_smartseq_rep2


title: RNA-seq pol2a-1_meiocyte_2


title: BES1-B


title: H9_TPRX1_OE48h_smartseq_rep1


title: chr18KO-rep10


title: BES1-A


title: H9_naive_TPRXL_plusDOX48h_smartseq_rep3


title: BES1-6A-1


title: RNA-seq pol2a-1_meiocyte_1


title: chr18KO-rep9


title: RNA-seq WT_meiocyte_2


title: chr18KO-rep15


title: B3-ARF-3B-2


title: chr18KO-rep8


title: RNA-seq WT_meiocyte_1


title: H9_naive_TPRXL_plusDox48h_smartseq_rep1


title: B3-ARF-3A-1


title: H9_naive_TPRXL_minusDOX48h_smartseq_rep3


title: chr18KO-rep7


title: chr18KO-rep6


title: hNSC_SOX11

data_processing:
Library strategy: Cut&run
For scRNA-seq, According to the 10× CellRanger’s pipeline, the raw base call (BCL) files were demultiplexed into FASTQ files. The FASTQ files were aligned to the reference human genome GRCh38 (hg38) to generate raw gene-barcode count matrices. When clustering multiple samples together, we aggregated the multiple runs together to normalize on sequencing depth and re-computed the gene-barcode matrices.
For scATAC-seq, the data processing unit takes raw fastq files as input and outputs peak-by-cell count matrix, QC report and genome track files. It consists of the following modules: demultiplexing, adaptor trimming, read mapping, peak calling, cell calling, genome track file generation and quality control assessment. The downstream analysis unit consists of the following modules: dimension reduction, cell clustering, differential accessibility analysis, gene ontology analysis, TF motif enrichment analysis, TF footprinting analysis, linking regulatory DNA sequences with gene promoters, and integration of multiple datasets. We provide flexible options for most of analysis modules.
For Cut&run, Bam files were calculated using Bowtie 2 and transform to Bigwig file using esATAC in R.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Neural progenitor cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

tag: chip antibody

value: Neural progenitor cells


title: H9_naive_TPRXL_minusDox48h_smartseq_rep2


title: H9_TPRX1_OE48h_smartseq_rep2


title: chr18KO-rep5


title: B3-7D-1


title: H9_naive_TPRXL_minusDox48h_smartseq_rep1


title: hNSC_HNRNPH1


title: H9_EGFP_OE48h_smartseq_rep3


title: B3-7B-1


title: chr18KO-rep4


title: H9_naive_TPRXL_plusDox48h_smartseq_rep2


title: B3-6D-2


title: hNSC_H3K4me3


title: H9_EGFP_OE48h_smartseq_rep2


title: B3-6D-1


title: chr18KO-rep3


title: MB004_SOX11

source_name: human MB cell lines


title: B3-5D-2


title: chr18KO-rep1


title: H9_EGFP_OE48h_smartseq_rep4


title: B3-ARF-2D-1


title: B3-5B-1


title: chr4KO-rep24

value: Transfection of Cas9/gRNA targetting RLTR45-int on chr4


title: chr4KO-rep23


title: h_zygote_3PN_25_Ribo_rep2

data_processing:
Library strategy: Ribo-seq
Illumina Casava1.8 software used for basecalling.
All RNA-seq data were trimmed by Trim Galore (v0.6.4) then mapped to transcriptome of mm9/hg19 by STAR (v2.5.3a). The gene expression level was calculated by Cufflinks (v2.2.1) based on the annotation of hg19 refFlat database from UCSC genome browser.
Ribo-lite data were trimmed with cutadapt (v1.14) with parameters: cutadapt --trim-n -a GATCGGAAGAGCACACGTCTG -a AGAGCACACGTCTG <input.file> | cutadapt -u 3 -a A{100} --no-indels -e 0.16666666666666666 - | cutadapt -O 8 --match-read-wildcards -g GTTCAGAGTTCTACAGTCCGACGATCSSS -m 18 - -o <output.file> , and the trimmed reads were sequentially mapped to human rRNAs sequences (hg19) using Bowtie2 (v2.2.2). Those aligned to rRNA were discarded, and the rest reads were mapped to transcriptome of hg19 using STAR (v2.5.3a). The gene expression level was then calculated by Cufflinks (v2.2.1) based on the annotation defined by hg19 refFlat database from the UCSC genome browser.
The paired-end Stacc–seq reads were aligned with the parameters: -t -q -p 96 -N 1 -L 25 -X 2000 --no-unal -x by Bowtie2 (v 2.2.5). All reads were aligned to either the human (hg19) or the Drosophila (dm6) (spike-in) reference genome.
Genome_build: hg19
Supplementary_files_format_and_content: The RNA FPKM tables including the FPKM of each gene for all the samples.
Supplementary_files_format_and_content: The BedGraph for Stacc-seq samples.

extract_protocol:
Ribo-lite was performed as previously described (Xiong et al., NCB, accepted), after removing the zona pellucida, oocytes or embryos extact preparation by detergent lysis, RNase I digestion, ultracentrifugation and size selection through polyacrylamide gel, RPFs were subjected to a small RNA-seq library preparation method (CATS, Diagenode).
Ribo-lite libraries were prepared using Ribo-lite developed in-house (accepted by NCB in principle), RPFs were subjected to a small RNA-seq library preparation method (CATS, Diagenode).


title: MB004_H3K27ac


title: MB004_H3K4me3


title: h_zygote_2PN_21_Ribo_rep1


title: B3-5A-1


title: hNSC_H3K27ac


title: B3-4B-2


title: chr4KO-rep22


title: UPN3550_scRNA-seq

data_processing:
For scRNA-seq, According to the 10× CellRanger’s pipeline, the raw base call (BCL) files were demultiplexed into FASTQ files. The FASTQ files were aligned to the reference human genome GRCh38 (hg38) to generate raw gene-barcode count matrices. When clustering multiple samples together, we aggregated the multiple runs together to normalize on sequencing depth and re-computed the gene-barcode matrices.
For scATAC-seq, the data processing unit takes raw fastq files as input and outputs peak-by-cell count matrix, QC report and genome track files. It consists of the following modules: demultiplexing, adaptor trimming, read mapping, peak calling, cell calling, genome track file generation and quality control assessment. The downstream analysis unit consists of the following modules: dimension reduction, cell clustering, differential accessibility analysis, gene ontology analysis, TF motif enrichment analysis, TF footprinting analysis, linking regulatory DNA sequences with gene promoters, and integration of multiple datasets. We provide flexible options for most of analysis modules.
For Cut&run, Bam files were calculated using Bowtie 2 and transform to Bigwig file using esATAC in R.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: human MB tissue


title: h_MII_9_Ribo_rep1

source_name: Oocyte

value: Oocyte

value: MII oocyte


title: chr18KO-rep2

value: Embryo