title: Pb120

city: Changchun

first: Zhu

last: Rining

address: Xi'an Road No.5333

institute: Jilin University

data_processing:
The raw data (raw reads) were first processed through  quality control (QC), including removing the raw  reads with an adapter or poly-N sequences and the low  quality reads, in order to obtain clean data (clean  reads).
The Q20 parameters (the proportion of reading  bases whose error was \ 1%), the GC contents,  sequencing randomness, etc. were evaluated after the  first QC.
we used the SOAPaligner/SOAP2  tool to count the clean reads mapped to  each gene. The reads per kb per million reads (RPKM)  were used to calculate the expression level for each  gene
Furthermore, hypothesis  testing was performed based on the binomial distribution , the pre-set false  discovery rate (FDR) cannot exceed 0.05, and the DEGs between the two  samples were screened out.
In our analysis, the DEGs  were defined as an FDR B 0.001 and an RPKM ratio  of more than 2 times
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited text files for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: PBMCs

extract_protocol:
Peripheral blood samples were collected from the anterior vena cava of piglets at different infection stages. These piglets came from control group (Pb0:0 h), from 3 piglets at the stage where they were showing slight symptoms of infection (Pb24:24 h post-infection), and from another 3 piglets at the severe infection symptom stage (Pb120:120 h postinfection). PBMCs from the three groups of peripheral  blood were extracted using the PBMC separation kit (TBDscience Biotech Co., Tianjin, China) according to the manufacturer’s instructions. Three duplicate samples of each group (0/24/120 h) were mixed in equal amounts. Then, the total RNA of the PBMCs was extracted and was treated with DNase I (Takara Bio., Dalian, China) to remove DNA. More than 20 lg of qualified total RNA from each sample (0/24/120 h) was used for RNA sequencing using an Illumina HiSeqTM 4000 platform (QL Bio., Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: domestic pig

value: APP infected

tag: time post infection

value: PBMCs


title: Developing mouse embryo sections F06A04_S66

status: Public on Jul 01 2021

type: SRA

city: Seattle

first: Sanjay

middle: R

last: Srivatsan

state: WA

address: 3720 15TH Ave NE Genome Sciences S Foefe Bldg

department: Genome Sciences

country: USA

institute: University of Washington

description:
Developing mouse embryo sections
sci-Space Slides 7-14
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell

library_source: transcriptomic

data_processing:
Basecalls performed using bcl2fastq version 2.20
Poly-dT adapters were trimmed using Trimmomatic and aligned to mm10 using STAR. Mapped reads were then deduplicated and assigned to a gene (GENCODE vM15 - mouse). UMIs were enumerated for each cell/gene combination and finally a count matrix was made.
Count matrix was loaded into Monocle3 for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: Count Matrix (matrix marker file- .mtx), Cell Metadata (tab separated values- .tsv), Gene Metadata (tab separated values- .tsv)

molecule: polyA RNA

organism: Mus musculus

source_name: E14 saggital sections 8-10um thick

extract_protocol:
Nuclei were extracted with a permeabilization buffer, sonicated and fixed. cDNA molecules within nuclei are extracted after tagmentation through the use of denaturants.
3' end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis, tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it, a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.

tag: genotype

tag: tissue

value: E14 Mouse Embryo

tag: sample type

value: Sagigital section


title: EKHT1_ROW13_16

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

data_processing:
read1 containing umi sequences are appended at the end of the headers of read2
read2 are mapped with tophat v2.0.13 on the mouse genome GRCm38 considering Ensembl78 genes annotations
bam files are processed with umi_tools to deduplicate reads with identical UMI sequence
gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification and this includes 5' and 3' UTRs.
Genome_build: GRCm38
Supplementary_files_format_and_content: retrobeads.tsv.gz contains the result of gene expression quantification by summarizeOverlaps() for each cell. The integers values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contains information about the genes that are quantified.

source_name: primary somatosensory cortex

extract_protocol:
The primary somatosensory cortex was microdissected as aforementioned. Cells were further dissociated by incubating micro-dissected samples in 0.5 mg/mL pronase (Sigma, #P5147) at 37°C for 10 minutes, followed by incubation in 5% bovine serum albumin for 3 minutes and manual trituration in ACSF using pulled glass pipettes. Cells were then centrifuged for 10 minutes at 600 rpm and resuspended before filtration using a 70 mm cell strainer (ClearLine, # 141379C). Cells were then incubated for 10 minutes at 37°C with Hoechst (0.1 mg/mL) and isolated using a Beckman Coulter Moflo Astrios FAC-sorter. Singlet Hoechst+cells were sorted according to their Forward and Side scattering properties (FSC and SSC), and their negativity for Draq7TM (Viability dye, Far red DNA intercalating agent, Beckman Coulter, #B25595). 5000 to 10 000 cells were FACsorted for each experiment. Three microliters of C1 Suspension Reagent (Fluidigm) was added to 10 ml of FAC-sorted cells GFP+ cells, yielding a 300-500 cells / ml suspension. 12 ml of this suspension mix were loaded on a C1 Single-Cell AutoPrep integrated fluidic circuit (IFC) designed for 10 to 17 mm diameter-cells (Fluidigm, #100-5780). RNA was extracted using an RNeasy kit (Qiagen, #74034), and quality control was done using 2001 Bioanalyzer from Agilent. cDNA libraries were obtained using SMARTseq v4 kit (Clontech, # 634888) and sequenced using HiSeq 2500 sequencer.
SMARTseq v4 kit (Clontech, # 634888)

tag: strain


title: Patient 3 N3

type: RNA

city: Guangzhou

first: Xiaohua

last: Chen

state: Guangdong

address: Fuyudong Road 8，Qiaonan street，Panyu

country: China

institute: Panyu Central Hospital

description:
N3
Tissues obtained from the patients by esophagoscopy or surgery.
Matched normal adjacent tissue of Ca3.

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar).

scan_protocol: The hybridized arrays were scanned using the Agilent Scanner 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 using the R software limma package.

molecule: total RNA

organism: Homo sapiens

source_name: primary esophageal tissue, normal

label_protocol: Circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

growth_protocol: Esophageal carcinoma tissues and normal adjacent tissue were excised and stored at -80°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions. RNA quality and quantity were measured by using NanoDrop spectrophotometer (ND-1000, NanoDrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: After grinded under the ice, the tissues were collected for further total RNA extraction.

tag: disease status

value: esophageal carcinoma

value: normal adjacent tissue

tag: age

tag: gender

value: male

tag: patient


title: Patient 4 N4

description:
N4
Tissues obtained from the patients by esophagoscopy or surgery.
Matched normal adjacent tissue of Ca4.


title: Patient 1 N1

description:
N1
Tissues obtained from the patients by esophagoscopy or surgery.
Matched normal adjacent tissue of Ca1.


title: Patient 3 Ca3

description:
Ca3
Tissues obtained from the patients by esophagoscopy or surgery.
Moderately differentiated squamous esophageal carcinoma.

source_name: primary esophageal tissue, carcinoma

value: esophageal carcinoma tumor tissue


title: Patient 2 Ca2

description:
Ca2
Tissues obtained from the patients by esophagoscopy or surgery.
Moderately differentiated squamous esophageal carcinoma.


title: Patient 5 N5

description:
N5
Tissues obtained from the patients by esophagoscopy or surgery.
Matched normal adjacent tissue of Ca5.


title: EKHT1_ROW12_16


title: Developing mouse embryo sections F05H06_S161


title: Patient 1 Ca1

description:
Ca1
Tissues obtained from the patients by esophagoscopy or surgery.
Moderately differentiated tubular adenocarcinoma of the esophagus.


title: Developing mouse embryo sections F05A04_S65


title: EKHT1_ROW11_16


title: Pb24

organism: Sus scrofa

tag: treatment

tag: cell type


title: Pb0


title: Developing mouse embryo sections F03H06_S159


title: EKHT1_ROW06_16


title: TIP_RNAinput

city: nanjing

first: Zhang

last: Jun

state: jiangsu

address: longmiandadao

institute: China Pharmaceutical University

data_processing:
Library strategy: MeRIP-seq
Trim Galore (v.0.6.5) was initially used to trim the low quality sequences and retain paired reads under -length 100 -paired parameters.
The paired-end reads were aligned to mouse genome (GRCm38) with HISAT2 aligner (v2.1.0) with default parameters and Ensemble genes (GRCm38.102) transcriptome annotation.
Then gene expression were quantified using stringtie (v2.1.4), and differentially expressed genes were identifified using DESeq2 (v1.30.1). The FoldChange > 2 or < 0.5 and p-value < 0.05 genes were considered as differentially expressed genes.
Quality control of MeRIP-seq data was performed using FastQC (v.0.11.9). Low-quality bases and adaptor contamination were removed by Trim Galore Remaining reads were aligned to mouse genome version mm10 with HISAT2 aligner with default parameters.
The mapped reads were filtered with Picard (v2.23.5) to remove PCR duplicates and SAMtools (v1.9) to remove the reads with mapping quality below.
m6A peaks were identified using exomePeak2 R package with default parameters. Peaks were annotated by R package ChIPseeker (v.1.26).
The distribution of m6A peaks was plotted by R package Guitar (v.2.6.0). Motif finding on m6A was performed using HOMER (v.4.11) findMotifs.pl with parameters -rna -p 10 -len 5,6,7,8 -S 10.
The final bam files were transformed to bigwig format by using Deeptools (v3.5.0) with --normalizeUsing BPM parameters. IGV (Integrative genomics viewer, v2.94) was used to visualize the aligned data.
Genome_build: mm10
Supplementary_files_format_and_content: peak csv files
Supplementary_files_format_and_content: bigwig files

growth_protocol: Mouse macrophage RAW264.7 cell lines were cultured in Dulbecco’s modified Eagle medium containing 10% fetal bovine serum, 1% 100×penicillin and streptomycin. Serial subculture dilution was performed when the cell confluence reached 70-80%.

extract_protocol:
Total RNA was extracted using TRIzol Reagent and MeRIP-seq samples were immunoprecipitated by m6A antibody.
Samples were first dephosporylated and 40-60nt region was selected according to 15% polyacrylamide TBE-urea gel separation. Desired RNA species were excised and soaked overnight followed by ethanol precipitation. the purified RNA was processed for Poly-(A) tailing reaction and reverse transcription afterwards. Eventually, PCR amplification was proceeded using Phusion High-Fidelity DNA Polymerase.

treatment_protocol: RAW264.7 cells were treated with 100 μM TCP, TBP and TIP for 24 h.

tag: m6a antibody

value: anti-m6A antibody (Abcam ab151230)

value: macrophage

value: TIP


title: TIP_IP


title: Developing mouse embryo sections F04H06_S160


title: Developing mouse embryo sections F03A04_S63


title: EKHT1_ROW02_16


title: TCP_IP

value: TCP


title: Developing mouse embryo sections F02A04_S62


title: TBP_IP

value: TBP


title: Developing mouse embryo sections F01H06_S157


title: EKHT1_ROW33_15


title: Developing mouse embryo sections F01A04_S61


title: Control_RNAinput


title: EKHT1_ROW28_15


title: Developing mouse embryo sections F06H06_S162


title: Developing mouse embryo sections F04A04_S64


title: EKHT1_ROW27_15


title: EKHT1_ROW07_16


title: EKHT1_ROW40_15


title: N302_input

city: Beijing

first: Jinxiu

last: Li

state: Beijing

address: Yuanmingyuan west road 2#

department: College of biological sciences

institute: China Agricutural University

description: control.fragment.bw

library_source: genomic

data_processing:
paired-end 50bp sequencing on an Illumina NovaSeq platform
ChIP-seq reads were aligned to the mm10 genome assembly using novoalign-4.00.01
peaks were called using MACS2 with following settings: -B --SPMR --pvalue=1e-2 --mfold 15 100
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using multirep_macs2_pipeline.pl; Scores represent a log2 fold enrichment

molecule: genomic DNA

source_name: mouse tumor

extract_protocol:
Nuclei was isolated from snap frozen samples. Lysates were clarified from sonicated nuclei and BAF-DNA complexes were isolated with antibody.
Library was prepared using NEBnext ChIP-seq libraray prep reagent set

tag: chip antibody

value: Input


title: Developing mouse embryo sections F02H06_S158


title: TCP_RNAinput


title: TBP_RNAinput


title: EKHT1_ROW25_15


title: Developing mouse embryo sections E12H06_S156


title: EKHT1_ROW36_15


title: N339_input

description: control.fragment.bw


title: Developing mouse embryo sections E12A04_S60


title: EKHT1_ROW10_16


title: Developing mouse embryo sections E11H06_S155


title: N269_input

description: control.fragment.bw


title: Developing mouse embryo sections E09H06_S153


title: Developing mouse embryo sections E09A04_S57


title: CTRL_5_TR2

city: Bern

first: Daniel

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

institute: University of Bern

description:
CTRL5_Tec2
data.csv

data_processing:
fastq files were aligned to the mouse reference genome with Hisat
sam files were sorted and converted to bam files with SAMtools
reads were counted with featureCounts
Genome_build: mm10 (GRCm38.p6)
Supplementary_files_format_and_content: Matrix table with read per sample

source_name: baseline liver tissue of CLDN3+/+ mouse 1

extract_protocol:
total RNA was extracted with Trizol from whole liver tissue
Libraries were constructed using IlluminaTruSeq Stranded mRNA Prep kit according to the manufacture's protocol.

treatment_protocol: Mice underwent a standard two-thirds surgical hepatectomy. The resected liver tissue served as the baseline, non-regenerating control. The regeneratng liver tissue was harvested 48 hours post resection.

tag: genotype/variation

tag: Sex

value: female

value: liver

tag: time point

value: baseline


title: N308_input

description: control.fragment.bw


title: Developing mouse embryo sections E11A04_S59


title: Developing mouse embryo sections E08H06_S152


title: Developing mouse embryo sections E08A04_S56


title: N339_180


title: N269_180


title: Control_IP


title: Developing mouse embryo sections E07H06_S151


title: N302_180


title: Aged_KO_2

description:
Aged_KO_2
data.csv

source_name: baseline liver tissue of aged CLDN3-/- mouse 2


title: EKHT1_ROW23_15


title: Developing mouse embryo sections E07A04_S55


title: EKHT1_ROW15_15


title: EKHT1_ROW04_15


title: N308_180


title: Developing mouse embryo sections E06H06_S150


title: Aged_KO_1

description:
Aged_KO_1
data.csv

source_name: baseline liver tissue of aged CLDN3-/- mouse 1


title: Developing mouse embryo sections E10H06_S154


title: EKHT1_ROW18_15


title: EKHT1_ROW09_15


title: EKHT1_ROW19_15


title: EKHT1_ROW20_15


title: Aged_WT2

description:
Aged_WT_2
data.csv

source_name: baseline liver tissue of aged CLDN3+/+ mouse 2


title: EKHT1_ROW39_14


title: EKHT1_ROW01_15


title: EKHT1_ROW07_15


title: Aged_WT3

description:
Aged_WT_3
data.csv

source_name: baseline liver tissue of aged CLDN3+/+ mouse 3


title: Developing mouse embryo sections E10A04_S58


title: Developing mouse embryo sections E05A04_S53


title: EKHT1_ROW37_14


title: EKHT1_ROW35_14


title: Developing mouse embryo sections E05H06_S149


title: EKHT1_ROW03_15


title: Chow_NC_10

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
The STAR aligner (Dobin et al., 2013) was used for mapping against the mouse genome assembly mm10 and UCSC knownGene annotation.
Quantification of the number of mapped reads of each gene was performed using iRNA-seq (v 1.1) in the 'count' mode specifying the "-count gene" option (Madsen et al., 2015)
Differential expression between the conditions (Chow_NC vs FPC_NC, FPC_NC vs FPC_Elf3, FPC_NC vs FPC_Glis2) was determined using DESeq2 (v 1.24.0) (Love et al., 2014)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text with unnormalized gene counts (output from iRNA-seq)
Supplementary_files_format_and_content: Tab-delimited text with log2FC and differential gene expression analyses (output from DESeq2)

source_name: Liver

extract_protocol:
Liver tissue were homogenized directly in Trizol using a Tissuelyzer II (Qiagen) and RNA purification was performed using EconoSpin columns (Epoch).
A total amount of 500ng of total RNA was used and sequencing libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) fol-lowing manufacturer’s protocol.
Prepared PCR products were purified and size-selected on AMPure XP beads (Beckman A63881), and library quality was assessed on the Agilent Bioanalyzer 2100 system. The prepared libraries were sequenced (paired-end) on a Illumina platform.

tag: diet

value: Chow

tag: aav-mir

value: miR-NC

value: Liver


title: EKHT1_ROW02_15


title: Aged_KO_3

description:
Aged_KO_3
data.csv

source_name: baseline liver tissue of aged CLDN3-/- mouse 3


title: Developing mouse embryo sections E03H06_S147

tag: genotype

value: E14 Mouse Embryo

value: Sagigital section


title: Chow_NC_8

tag: tissue


title: EKHT1_ROW06_15


title: Developing mouse embryo sections E06A04_S54

tag: sample type


title: Developing mouse embryo sections E04H06_S148


title: Chow_NC_9


title: Developing mouse embryo sections E04A04_S52


title: Developing mouse embryo sections E03A04_S51


title: EKHT1_ROW33_14

tag: strain


title: Chow_NC_6


title: Chow_NC_5


title: Chow_NC_4


title: EKHT1_ROW31_14


title: Developing mouse embryo sections E01H06_S145


title: EKHT1_ROW30_14


title: Developing mouse embryo sections E02A04_S50


title: Aged_WT1

description:
Aged_WT_1
data.csv

source_name: baseline liver tissue of aged CLDN3+/+ mouse 1


title: EKHT1_ROW17_14


title: Chow_NC_7


title: EKHT1_ROW27_14


title: Chow_NC_3


title: EKHT1_ROW14_14


title: Developing mouse embryo sections E01A04_S49


title: EKHT1_ROW13_14


title: Chow_NC_1


title: EKHT1_ROW24_14


title: Chow_NC_2


title: Developing mouse embryo sections D12A04_S48


title: Developing mouse embryo sections D11H06_S143


title: FPC_NC_11

value: FPC


title: Developing mouse embryo sections D11A04_S47


title: EKHT1_ROW11_14


title: FPC_NC_10


title: FPC_Elf3_10


title: Developing mouse embryo sections D10H06_S142


title: EKHT1_ROW07_14


title: FPC_Elf3_9


title: Developing mouse embryo sections D10A04_S46


title: EKHT1_ROW29_14


title: Developing mouse embryo sections E02H06_S146


title: EKHT1_ROW04_14


title: Developing mouse embryo sections D09H06_S141


title: Developing mouse embryo sections D12H06_S144


title: FPC_Elf3_8


title: FPC_Glis2_10


title: EKHT1_ROW06_14


title: EKHT1_ROW09_14


title: Developing mouse embryo sections D08H06_S140


title: Developing mouse embryo sections D08A04_S44


title: FPC_Elf3_7


title: Patient 5-normal

city: Lanzhou

first: Yuping

last: Wang

state: Gansu

address: Donggang West Road, Chengguan District

department: Department of Gastroenterology

institute: The First Hospital of Lanzhou University

description: Matched adjacent noncancerous tissue (patient 5)

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon).

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Data analyses were performed using R 3.5.2 software. The R’s limma package was used for background correction and normalization between arrays. The RMA algorithm was chosen when doing background correction and the “offset” parameter was set to 50. The expressed data were normalized using the Median normalization. The landing lights (annotated as Hy3™ in the gal-fi le, probe ID 13138) are only included for gal-file orientation and their corresponding data points were removed prior to normalization of the dataset, according to the array manual. For the same probes, the expression data of all samples corresponding to each probe is averaged. The one with the maximum averaged value was retained among the same probes.

source_name: Matched adjacent noncancerous tissue

label_protocol: RNA labeling and array hybridization was according to Exiqon's manual.After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C.Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA from 12 tissue samples was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

tag: lesion location

value: Gastric antrum

tag: histology

value: Adenocarcinoma

value: Female

value: 67 years

tag: Stage


title: Developing mouse embryo sections D07H06_S139


title: EKHT1_ROW37_13


title: FPC_Elf3_6


title: Patient 5-cancer

description: Early gastric cancer tissue (patient 5)

source_name: Early gastric cancer tissue

tag: age


title: EKHT1_ROW03_14


title: Patient 4-cancer

description: Early gastric cancer tissue (patient 4)

value: Cardia

value: Male

value: 45 years

value: IA


title: EKHT1_ROW32_13


title: FPC_Glis2_9


title: FPC_Glis2_8


title: Patient 4-normal

description: Matched adjacent noncancerous tissue (patient 4)


title: EKHT1_ROW31_13


title: FPC_Glis2_6


title: Developing mouse embryo sections D06A04_S42


title: Developing mouse embryo sections D05H06_S137


title: Patient 2-normal

description: Matched adjacent noncancerous tissue (patient 2)

value: 72 years


title: Patient 3-normal

description: Matched adjacent noncancerous tissue (patient 3)

value: Gastric body

value: 46 years


title: EKHT1_ROW02_14


title: Patient 3-cancer

description: Early gastric cancer tissue (patient 3)


title: FPC_NC_8


title: FPC_Glis2_7


title: EKHT1_ROW28_13


title: Patient 1-normal

description: Matched adjacent noncancerous tissue (patient 1)

value: 65 years


title: Developing mouse embryo sections D09A04_S45


title: EKHT1_ROW38_13


title: Developing mouse embryo sections D05A04_S41


title: Developing mouse embryo sections D06H06_S138


title: Developing mouse embryo sections D07A04_S43


title: Patient 2-cancer

description: Early gastric cancer tissue (patient 2)


title: FPC_NC_9

value: miR-NC


title: EKHT1_ROW27_13


title: FPC_NC_7

value: Liver


title: EKHT1_ROW25_13


title: Developing mouse embryo sections D03H06_S135

value: E14 Mouse Embryo


title: FPC_Glis2_4


title: Developing mouse embryo sections D03A04_S39

value: Sagigital section


title: EKHT1_ROW19_13


title: FPC_NC_6

value: FPC


title: EKHT1_ROW35_13


title: FPC_NC_5


title: EKHT1_ROW15_13


title: Developing mouse embryo sections D04A04_S40


title: FPC_Glis2_3


title: Developing mouse embryo sections D02A04_S38


title: Patient 1-cancer

description: Early gastric cancer tissue (patient 1)


title: matched normal adjacent breast tissues 4

city: Harbin

first: Aixin

last: Hao

address: 26 Hexing Road

institute: Northeast Forestry University

description: lncRNA expression data from matched non-tumor tissue of Triple negative breast cancer(TNBC)

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human LncRNA Microarray v3.0, and incubated for 17 hours at 65 degree Celsius 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. Raw signal intensities were then normalized in the quantile method by GeneSpring GX v11.5 (Agilent Technologies), and lncRNAs with low intensity were filtered (LncRNAs that at least 5 out of 10 samples have flags in Present or Marginal were chosen for further analysis).

source_name: non-tumor tissue

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

growth_protocol: TNBC and matched non-tumor tissues

extract_protocol: RNA was extracted using the Trizol reagent (Invitrogen) following the manufacturer's instruction. RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: TNBC tissues excised from the breast cancer patients during mammectomies were immediately frozen in liquid nitrogen and then stored at -80℃ until used for RNA extraction using the Trizol reagent.

tag: gender

value: female

tag: matched sample id


title: Developing mouse embryo sections D01H06_S133


title: EKHT1_ROW13_13


title: matched normal adjacent breast tissues 3

value: matched non-tumor tissue of Triple negative breast cancer(TNBC)


title: EKHT1_ROW23_13


title: matched normal adjacent breast tissues 5


title: EKHT1_ROW12_13


title: Developing mouse embryo sections D04H06_S136


title: TNBC tissue 4

description: lncRNA expression data from  Triple negative breast cancer(TNBC) tumor tissue

source_name: tumor tissue


title: FPC_Glis2_2


title: EKHT1_ROW09_13


title: Developing mouse embryo sections D02H06_S134

source_name: E14 saggital sections 8-10um thick


title: TNBC tissue 5

value: Triple negative breast cancer(TNBC) tumor tissue


title: Developing mouse embryo sections D01A04_S37


title: matched normal adjacent breast tissues 1


title: FPC_NC_4


title: FPC_Glis2_1


title: Developing mouse embryo sections C12H06_S132


title: EKHT1_ROW07_13

source_name: primary somatosensory cortex


title: Developing mouse embryo sections C12A04_S36


title: EKHT1_ROW05_13


title: FPC_Elf3_5


title: FPC_Elf3_4


title: FPC_Glis2_5


title: EKHT1_ROW37_12


title: FPC_Elf3_3


title: EKHT1_ROW02_13


title: EKHT1_ROW35_12


title: TNBC tissue 3


title: FPC_NC_3


title: Developing mouse embryo sections C10H06_S130


title: DU145-RR_spheres_rep3

city: Dresden

first: Vasyl

last: Lukiyanchuk

address: Handelallee 26

country: Germany

institute: OncoRay

description: Gene expression in DU145 redioresistant grown as tumorspheres

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37°C wit GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2505C using scan protocol Agilent G3_GX_1_color for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using protocol GE1_107_Sep09 and Grid: 072363_D_F_20150612 to obtain background subtracted and spatially detrended Processed Signal intensities

source_name: DU145 radioresistant, sphere forming culture, repeat 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer

growth_protocol: Standard tissue culture at 37 ºC in a humidified incubator with 5% CO2. Monolayer - in DMEM supplemented with 10% FBS, 10mM HEPES, and 1x Pen/Strep, in regular tissue culture plates. Spheres - MEBM supplemented with 4 μg/mL insulin, 1x B27, 20 ng/mL EGF, and 20 ng/mL FGF, in ultra low attachment plates

extract_protocol: RNA was isolated with RNeasy mini kit (Qiagen) following the manufacturer's recommendations

treatment_protocol: Radioresistant sub-line was generated from original (parental) DU145 cell line by multiple X-ray irradiations, 4Gy/dose, 1 week recovery between doses.

tag: cell line

value: DU145 radioresistant

tag: growth condition

value: non-attached sphere forming


title: TNBC tissue 1


title: FPC_NC_2


title: matched normal adjacent breast tissues 2


title: EKHT1_ROW30_12


title: TNBC tissue 2


title: DU145-RR_spheres_rep2

source_name: DU145 radioresistant, sphere forming culture, repeat 2


title: Developing mouse embryo sections C11H06_S131


title: Developing mouse embryo sections C11A04_S35


title: EKHT1_ROW26_12


title: DU145-RR_spheres_rep1

source_name: DU145 radioresistant, sphere forming culture, repeat 1


title: FPC_NC_1


title: FPC_Elf3_2


title: FPC_Elf3_1


title: Developing mouse embryo sections C09A04_S33


title: Developing mouse embryo sections C08H06_S128


title: DU145_spheres_rep2

description: Gene expression in DU145 parental grown as tumorspheres

source_name: DU145 parental, sphere forming culture, repeat 2

value: DU145 parental


title: Developing mouse embryo sections C10A04_S34

description:
Developing mouse embryo sections
sci-Space Slides 7-14
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell


title: Developing mouse embryo sections C09H06_S129


title: Developing mouse embryo sections C08A04_S32


title: DU145_spheres_rep1

source_name: DU145 parental, sphere forming culture, repeat 1


title: EKHT1_ROW21_12


title: DU145-RR_monolayer_rep3

description: Gene expression in DU145 redioresistant grown as monolayer

source_name: DU145 radioresistant, monolayer culture, repeat 3

value: attached monolayer


title: EKHT1_ROW22_12


title: DU145_spheres_rep3

source_name: DU145 parental, sphere forming culture, repeat 3


title: EKHT1_ROW23_12


title: EKHT1_ROW20_12


title: Developing mouse embryo sections C07A04_S31


title: EKHT1_ROW16_12


title: Developing mouse embryo sections C07H06_S127


title: Developing mouse embryo sections C06H06_S126


title: EKHT1_ROW19_12


title: EKHT1_ROW15_12


title: EKHT1_ROW12_12


title: Developing mouse embryo sections C05H06_S125


title: Developing mouse embryo sections C06A04_S30


title: DU145-RR_monolayer_rep2

source_name: DU145 radioresistant, monolayer culture, repeat 2


title: OSC - Piwi-KD - H3K4me3

city: Tokyo

first: Yuka

middle: W.

last: Iwasaki

address: 35 Shinanomachi, Shinjuku-ku,

department: Department of Molecular Biology

country: Japan

institute: Keio University School of Medicine

data_processing:
Hi-C: HiCExplorer v3.3 software (Ramirez et al., 2018) was used for the calculation of HiC matrix, and GENOVA v1.0 was used for visualizing the results. Two replicates were performed per knockdown, and hicCorrelate was used to calculate correlation between replicate samples. Due to the high correlation between replicates, samples were combined by using hicSumMatrices for the further analysis. Bins of too low or high coverage were removed and the HiC matrix was iteratively corrected by ICE using hicCorrectMatrix. HiC matrix was further normalized between different knockdown samples using hicNormalize. TADs were defined using hicFindTADs function and matrixes were converted into ginteractions file using hicConvertFormat.
DamID-seq: Adapters were removed using cutadapt, and reads shorter than 50nt after adapter removal was discarded. damidseq_pipeline (Marshall and Brand, 2015) was used to map the reads to Drosophila melanogaster (dm3) genome, followed by normalization and background reduction. We used q-value cutoff 0 (to include multi-mapped reads), and fragment size of 300. Due to the high correlation of replicate samples, two replicate reads were merged for the further analysis. After mapping of DamID-seq reads to the genome, log2 ratio of LamDam/Dam was calculated and bedgraph file was generated using damidseq_pipeline.
ChIP-seq: For ChIP-seq analysis, adapters were removed from the reads using Cutadapt, and subsequent reads shorter than 50 nt were discarded. ChIP-seq reads were mapped to the Drosophila genome (dm3) using Bowtie 2.2.9 (Langmead and Salzberg, 2012) with the default parameters. MACS 1.4.2 (Zhang et al., 2008) was used for peak calling and generation of wig files.
Genome_build: dm3
Supplementary_files_format_and_content: Hi-C: ginteractions file (tsv format) generated using HiCExplorer v3.3 (Ramirez et al., 2018)
Supplementary_files_format_and_content: DamID-seq: bedgraph file generated using damidseq_pipeline v1.4.5 (Marshall and Brand, 2015)
Supplementary_files_format_and_content: ChIP-seq: wig file generated using MACS v1.4.2 (Zhang, 2008)

organism: Drosophila melanogaster

source_name: Ovarian Somatic Cells

growth_protocol: Ovarian somatic cells (OSCs) was established in the previous studies (Niki et al., 2006; Saito et al., 2009). OSCs were cultured in Shield and Sang M3 Insect Medium (Caisson Laboratories) supplemented with 10% fly extract, 10% fetal bovine serum, 0.6 mg/ml glutathione, and 10 μg/ml insulin.

extract_protocol:
Hi-C: Hi-C using OSCs were performed as described previously (Ulianov et al., 2016) with some minor modifications. OSCs were fixed with 1% formaldehyde for 10min, and stored at -80 degrees before usage. 5 x 10^5 cells were lysed and chromatin digested using 30G needle. Chromatin digestion was performed using HindIII restriction enzyme. Ends were filled with biotin-14-dCTP followed by blunt-end ligation. Proteins were reverse crosslinked form the cells, and DNA purification was performed. Biotin was removed from un-ligated ends and DNA was sonicated using covaris S220 (covaris). Sonicated DNA was used for biotin pull down by streptavidin conjugated to Dynabeads Streptavidin C1 beads (Invitrogen). Pulled-down DNA was used as the template to construct DNA library.
DamID-seq: Dam-ID-seq was performed as described previously (Pickersgill et al., 2006) with some modifications to analyze methylated sequences using deep-sequencing rather than microarray. DamID vectors were transfected into OSCs using Nucleofector, one day before cell harvest. pNDamMyc plasmid (van Steensel and Henikoff, 2000) was a kind gift from Dr. Bas van Steensel. Lamin was cloned into pNDamMyc vector as described previously (Pickersgill et al., 2006). Genome DNA precipitation, DpnI digestion, adapter ligation, DpnII digestion, PCR, and PCR cleanup was performed as described within “Van Steensel Lab version 28/08/2006” protocol. Obtained DNA was used as the template to prepare deep sequencing library.
ChIP-seq: ChIP was performed as described previously (Iwasaki et al., 2016). Briefly, OSCs (3×107) were fixed, lysed, and their nuclei were isolated using truChIP Chromatin Shearing Kits (Covaris), in accordance with the manufacturer’s instructions. DNA was sonicated to ~300 bases using Bioruptor (Cosmobio), and then diluted with ChIP buffer. DNA–protein complexes were incubated with antibody on Dynabeads-Protein G for 4 h, at 4 degrees. Beads were washed with ChIP buffer, high-salt lysis buffer, and wash buffer followed by TE. After reversing cross-linking for 12–16 h at 65 degrees, samples were treated with RNase for 30 min at 37 degrees and Proteinase K for 60 min at 55 degrees. DNA was then recovered.
DNA library was constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), in accordance with the manufacturer’s instructions.

treatment_protocol: For the transfection of siRNAs into OSCs, 200 pmol siRNA duplex was nucleofected into 3.0 × 10^6 cells using the Cell Line 96-well Nucleofector Kit SF (Lonza) and program DG150 of the 96-well Shuttle Device (Lonza). The siRNAs were transfected twice for 4-day KD, and once for 2-day KD. Co-transfection of siRNA and plasmid DNA was performed using the Cell Line Nucleofector Kit V (Lonza) and program T-029 of the Nucleofector II Device (Lonza).

value: Ovarian Somatic Cells

tag: treatment

value: Piwi-KD

tag: chip antibody

value: H3K4me3 (Abcam, ab8580)


title: OSC - Piwi-KD - H3K27Ac

value: H3K27Ac (Abcam, ab4729)


title: DU145-RR_monolayer_rep1

source_name: DU145 radioresistant, monolayer culture, repeat 1


title: Developing mouse embryo sections C04H06_S124


title: EKHT1_ROW11_12


title: OSC - EGFP-KD - H3K27Ac

value: EGFP-KD


title: DU145_monolayer_rep2

description: Gene expression in DU145 parental grown as monolayer

source_name: DU145 parental, monolayer culture, repeat 2


title: OSC - Piwi-KD - InputDNA


title: Developing mouse embryo sections C05A04_S29


title: EKHT1_ROW03_12


title: Developing mouse embryo sections C04A04_S28


title: OSC - EGFP-KD - H3K4me3


title: DU145_monolayer_rep1

source_name: DU145 parental, monolayer culture, repeat 1


title: EKHT1_ROW08_12


title: Developing mouse embryo sections C03A04_S27


title: Developing mouse embryo sections C02H06_S122


title: DU145_monolayer_rep3

source_name: DU145 parental, monolayer culture, repeat 3


title: Anti-him-8 piRNAi,H3K9me3 ChIP

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

description:
Genomic DNA extracted from fragmented chromatin
rawcounts_genebygene_SG0321_lib22_to_27.csv
SG0421_lib27

data_processing:
Genomic alignment was performed by using Bowtie 1.2.3
Genome_build: WS190(ce6)
Supplementary_files_format_and_content: rawcounts_genebygene_SG0321_lib22_to_27.csv

organism: Caenorhabditis elegans

source_name: Young adult animals

extract_protocol:
100-200 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). 50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-Pol II-S2 (ab5095, Abcam) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate was treated similarly to reverse crosslink) and then subject to organic extraction and precipitation of DNA and RNA.
DNA libraries were prepared using KAPA Hyper Prep Kits (KAPA Biosystems) according to the manufacturer's instructions

value: kstEx23 [21ur-1224 anti-him-8 + Pmyo-2::mCherry + Prps-27::hygromycinR]

tag: pirnai target gene

value: Abcam, ab8898, anti-H3K9me3

tag: rna-seq method

tag: 5’ barcodes for srna or rna-seq


title: Developing mouse embryo sections C03H06_S123

tag: genotype

value: E14 Mouse Embryo


title: EKHT1_ROW38_11


title: Developing mouse embryo sections C02A04_S26

tag: tissue

value: Sagigital section


title: EKHT1_ROW37_11


title: Anti-him-8 piRNAi,Pol II ChIP

description:
Genomic DNA extracted from fragmented chromatin
rawcounts_genebygene_SG0321_lib22_to_27.csv
SG0421_lib25

value: Abcam, ab5095, Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody


title: Anti-him-5 piRNAi, H3K9me3 ChIP

description:
Genomic DNA extracted from fragmented chromatin
rawcounts_genebygene_SG0321_lib22_to_27.csv
SG0421_lib26

value: kstEx19 [21ur-1224 anti-him-5 + Pmyo-2::mCherry + Prps-27::hygromycinR]


title: OSC - EGFP-KD - InputDNA


title: EKHT1_ROW36_11


title: Anti-him-5 piRNAi, Pol II ChIP

description:
Genomic DNA extracted from fragmented chromatin
rawcounts_genebygene_SG0321_lib22_to_27.csv
SG0421_lib24


title: EKHT1_ROW34_11


title: Developing mouse embryo sections C01H06_S121

tag: sample type


title: Developing mouse embryo sections B12H06_S120


title: MEF14_Dox+FRG_hypoxia_Day6_rep1

city: Cambridge

first: Jocelyn

last: Charlton

state: MA

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Demultiplexed reads were trimmed using cutadapt and the Nugene diversity adapter trimming python script trimRRBSdiversityAdaptCustomers.py. Reads were then aligned to the mouse mm9 genome using BSMAP with the parameters: -v 0.1 -s 12 -q 20 -w 100 -S 1 -u -R -D C-CGG. Duplicate reads were removed using the Nugen deduplication script nudup.py. Methylation ratios were called using the MOABS mcall module.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Processed data bed files have 15 columns: chrom, start, end, ratio, totalC, methC, strand, next, Plus, totalC, methC, Minus, totalC, methC, localSeq.

growth_protocol: MEFs harboring Rosa-rtTA, Col1a1-tetO-MyoD and Pax7-nGFP were isolated from E13.5 embryos and were maintained in DMEM (GIBCO) containing 1X glutaMAX (GIBCO), 1X MEM non essential Amino Acid Solution (GIBCO), 100 U/ml penicillin, 100 μg/mL streptomycin (GIBCO), 0.1% β-mercaptoethanol (GIBCO) and 10% Fetal Bovine Serum (HyClone). For dedifferentiation into iMPCs, MEFs were maintained in knockout DMEM (GIBCO) containing 1X glutaMAX (GIBCO), 1X MEM non essential Amino Acid Solution (GIBCO), 100 U/ml penicillin, 100 μg/mL streptomycin (GIBCO), 0.1% β-mercaptoethanol (GIBCO), 10% KnockOut Serum Replacement (GIBCO), 10% Fetal Bovine Serum (HyClone), 10ng/ml basic FGF (Peprotech), 5μM Forskolin (Sigma), 5μM RepSox (Sigma), 3μM GSK3β inhibitor CHIR99021 (Tocris) and 2μg/ml Doxycycline (Sigma). For transdifferentiation into myotubes, MEFs were maintained in knockout DMEM (GIBCO) containing 1X glutaMAX (GIBCO), 1X MEM non essential Amino Acid Solution (GIBCO), 100 U/ml penicillin, 100 μg/mL streptomycin (GIBCO), 0.1% β-mercaptoethanol (GIBCO), 10% KnockOut Serum Replacement (GIBCO), 10% Fetal Bovine Serum (HyClone), 10ng/ml basic FGF (Peprotech) and 2μg/ml Doxycycline (Sigma). Hypoxia experiments were performed in 5% O2 level. Primary satellite cells were isolated from adult Pax7-nGFP mice (10-12 weeks). Expanded satellite cells were maintained in F10 (GIBCO) with 20% Horse Serum (GIBCO), 1X glutaMAX (GIBCO) and 100 U/ml penicillin, 100 μg/mL streptomycin (GIBCO). 5ng/ml basic FGF (Sigma) was daily added.

extract_protocol:
Genomic DNA was extracted using PureLink Genomic DNA mini kit according to the manufacturer’s instructions.
Genomic DNA was quantified using a Qubit 3.0 Fluorometer. RRBS was performed on 100 ng of each sample using the NuGen Ovation RRBS Methyl-Seq System following the manufacturer’s recommendations. Bisulfite conversion of DNA was conducted using the Qiagen EpiTect Fast Bisulfite Conversion kit. Libraries were purified with Agencourt RNAclean XP beads and quality-assessed using an Agilent 4150 Tape-Station D1000 ScreenTape. Libraries were then sequenced on the Illumina NovaSeq6000, generating 100-bp single-end reads.

treatment_protocol: Cells were harvested following trypsin treatment and processed for genomic DNA extraction.

tag: cell type

value: Dox+FRG, hypoxia

tag: time point


title: EKHT1_ROW39_11

tag: strain


title: EKHT1_ROW29_11


title: Developing mouse embryo sections B12A04_S24


title: CNQX_24h_rep1

city: New York

first: Kenneth

middle: David

last: Birnbaum

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

data_processing:
Libraries were aligned to the Arabidopsis genome TAIR10 using HISAT2
Counts were generated for each sample
Counts were normalized between samples using DESeq2’s median of ratios method before analyzing for Differentially Expressed Genes.
Genome_build: TAIR10
Supplementary_files_format_and_content: counts for each sample in tab delimited .txt
Supplementary_files_format_and_content: Matrix table with normalized counts including annotation and p-values for all time points vs. control in excel format

organism: Arabidopsis thaliana

source_name: Root tip cells

growth_protocol: Plants were grown on plates (1xMS, 0.5% Sucrose, 0.8% Agar) for 7 DAS

extract_protocol:
About 130µm of root tips were excised on plates with either 50µM CNQX or mock, plants were transferred to new MS plates and kept under growing conditions for 30 min, 4h, 14h or 24h. The reprogramming domain comprising about 100µm above the cutting site was then excised. For controls, two separate sets of uncut roots were transferred to CNQX plates or mock plates and incubated for 14 hrs before collecting root tip tissue, which also consisted of about 100 µm of the uncut root tip. RNA was extracted using the Qiagen MicroRNAeasy Kit.
cDNA construction and library amplification was done with Nugen OvationRNA Amplification System V2 and lNugenibraries were made using the Nugen Ovation Ultralow DR Multiplex System (Tecan). DNA shearing was performed using the Covaris S220.

treatment_protocol: Plants were transferred to MS plates supplemented with either 50µM CNQX or mock for 1h prior cutting.

value: 7 DAS

value: root

tag: hours post root tip excision

value: CNQX


title: EKHT1_ROW06_12


title: EKHT1_ROW30_11


title: EKHT1_ROW28_11


title: MEF10_MN+FRG_Day6_rep2

value: MN+FRG


title: MEF14_Dox+FRG_normoxia_Day6_rep2

value: Dox+FRG, normoxia


title: CNQX_14h_rep1

tag: age


title: Developing mouse embryo sections B11A04_S23

source_name: E14 saggital sections 8-10um thick


title: MEF10_MN+FRG_Day6_rep1


title: MEF14_Dox+FRG_hypoxia_Day6_rep2


title: Developing mouse embryo sections B11H06_S119


title: EKHT1_ROW32_11

source_name: primary somatosensory cortex


title: Developing mouse embryo sections C01A04_S25


title: Developing mouse embryo sections B10A04_S22


title: EKHT1_ROW27_11


title: MEF14_Dox+FRG_normoxia_Day6_rep1


title: Anti-him-5 piRNAi, ChIP input

description:
Genomic DNA extracted from fragmented chromatin
rawcounts_genebygene_SG0321_lib22_to_27.csv
SG0421_lib22


title: CNQX_uncut_rep1

value: uncut


title: Developing mouse embryo sections B09H06_S117


title: CNQX_30min_rep1

value: 30 min


title: MEF10_MyoD+FRG_Day6_rep2

value: MyoD+FRG


title: MEF14_FRG_Day8_rep1

value: FRG


title: Anti-him-8 piRNAi, ChIP input

description:
Genomic DNA extracted from fragmented chromatin
rawcounts_genebygene_SG0321_lib22_to_27.csv
SG0421_lib23


title: EKHT1_ROW23_11


title: EKHT1_ROW19_11


title: Developing mouse embryo sections B08H06_S116


title: CNQX_4h_rep1


title: EKHT1_ROW18_11


title: Mock_14h_rep1

value: mock


title: MEF14_Dox+_Day8_rep1

value: Dox+


title: EKHT1_ROW21_11


title: EKHT1_ROW16_11


title: Mock_30min_rep1


title: CNQX_uncut_rep2


title: MEF14_Dox+_Day4_rep2


title: Developing mouse embryo sections B07A04_S19


title: Developing mouse embryo sections B10H06_S118


title: MEF10_MyoD+FRG_Day6_rep1


title: EKHT1_ROW13_11


title: Developing mouse embryo sections B06H06_S114


title: Mock_uncut_rep1


title: EKHT1_ROW12_11


title: expanded_SCs_rep2

value: Expanded satellite cells


title: Developing mouse embryo sections B06A04_S18

value: E14 Mouse Embryo


title: Mock_24h_rep1


title: Developing mouse embryo sections B09A04_S21

value: Sagigital section


title: expanded_SCs_rep1


title: drm_Tapetum_RNA-seq_rep2

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

description:
RNA-seq
drm_tapetum_3reps_combined_no_rRNA_RNA_seq.log2_RPKM_w50.gff.gz

data_processing:
For BS-seq reads,low-quality reads, adaptor sequence and the the first 9 bp of 5’ end of each reads were removed using TrimGalore version 0.4.1 with default parameters. Filtered reads were then mapped to the Arabidopsis genome (TAIR10) using Bismark version 0.22.2(ref). Duplicated reads were removed using the Picard tools MarkDuplicates version 1.141 (https://github.com/broadinstitute/picard). Subsequent DNA methylation analysis was performed as previously described (ref).
For sRNA-seq, adaptor trimming was performed using Cutadapt( -u 1 -m 21 -M 25 -a TGGAATTCTCGGGTGCCAAGG ). Clean sRNA reads with lengths between 21-nt and 25-nt inclusive were then mapped to TAIR10 Arabidopsis reference genome using Bowtie (ref) with either 0 mismatches (-v 0) or up to 3 mismatches (-v 3). Abundance of 24-nt siRNA at each Hyper TE, cRdDM or MetGene locus was calculated using Reads Per Kilobase per Million (RPKM) of total mapped 24-nt sRNA reads.
For RNA-seq, low-quality reads and potential adaptor sequence were first trimmed using  TrimGalore version 0.4.1 with default parameters. RNA-seq reads were mapped to the reference genome with the TopHat-2.0.10 and Cufflinks-2.2.1 packages.
Genome_build: TAIR10
Supplementary_files_format_and_content: gff files

source_name: Flower bud

growth_protocol: Arabidopsis plants were grown under 16h light/8h dark in a growth chamber (21°C, 70% humidity)

extract_protocol:
Total RNA was extracted from either tapetum or pollen using TRIzol reagent (Invitrogen #15596026).
RNA-sequencing libraries were prepared with ScriptSeq V2 RNA-seq (Illumina, SSV21106) Library Prepararion and Ovarion RNA-Seq Systems (Nugen,0351) kit according to the manual.

treatment_protocol: No special treatment to all of the biological materials

value: Anther

value: Tapetum


title: Developing mouse embryo sections B05A04_S17


title: MEF14_FRG_Day8_rep2


title: primary_SCs_rep2

value: Primary satellite cells


title: Mock_4h_rep1

value: 7 DAS


title: Developing mouse embryo sections B07H06_S115


title: drm_Tapetum_RNA-seq_rep1


title: primary_SCs_rep1


title: EKHT1_ROW22_11


title: MEF14_Dox+_Day8_rep2


title: EKHT1_ROW06_11


title: Developing mouse embryo sections B04A04_S16


title: drm_Tapetum_RNA-seq_rep3


title: EKHT1_ROW15_11


title: EKHT1_ROW05_11


title: Mock_uncut_rep2

value: root


title: Developing mouse embryo sections B03H06_S111


title: MEF14_Dox+FRG_Day10_GFP_rep1

value: Dox+FRG


title: MEF14_Dox+_Day4_rep1


title: WT_Tapetum_RNA-seq_rep1

description:
RNA-seq
WT_tapetum_3reps_combined_no_rRNA_RNA_seq.log2_RPKM_w50.gff.gz

value: WT


title: EKHT1_ROW09_11


title: Developing mouse embryo sections B03A04_S15


title: MEF14_Dox+FRG_Day8_rep2


title: Developing mouse embryo sections B08A04_S20


title: EKHT1_ROW10_11


title: Developing mouse embryo sections B05H06_S113


title: EKHT1_ROW07_11


title: drm_pollen_RNA-seq_rep2

description:
RNA-seq
drm_pollen_3reps_combined_no_rRNA_RNA_seq.log2_RPKM_w50.gff.gz

source_name: Open flower

value: Pollen


title: EKHT1_ROW01_11


title: WT_Tapetum_RNA-seq_rep3


title: MEF14_Dox+FRG_Day8_rep1


title: Developing mouse embryo sections B02A04_S14


title: WT_Tapetum_RNA-seq_rep2


title: drm_pollen_RNA-seq_rep3


title: MEF14_Dox+FRG_Day10_GFP_rep2


title: WT_pollen_RNA-seq_rep3

description:
RNA-seq
WT_pollen_3reps_combined_no_rRNA_RNA_seq.log2_RPKM_w50.gff.gz


title: Developing mouse embryo sections B01H06_S109


title: MEF14_Dox+FRG_Day4_rep1


title: EKHT1_ROW04_11


title: Developing mouse embryo sections B04H06_S112


title: MEF14_Day0_rep2


title: drm_pollen_RNA-seq_rep1


title: EKHT1_ROW02_11


title: EKHT1_ROW27_10


title: Developing mouse embryo sections B01A04_S13


title: Developing mouse embryo sections B02H06_S110


title: MEF14_Dox+FRG_Day4_rep2


title: WT_pollen_RNA-seq_rep1


title: EKHT1_ROW20_10


title: EKHT1_ROW33_10


title: MEF14_Day0_rep1


title: Developing mouse embryo sections A12H06_S108


title: WT_pollen_RNA-seq_rep2


title: EKHT1_ROW18_10


title: Developing mouse embryo sections A12A04_S12


title: E18.5

city: Zürich

first: Michael

last: Brügger

address: Winterthurerstrasse 190

department: Molecular Life Sciences

institute: University of Zürich

data_processing:
The sequencing libraries were de-multiplexed, aligned to the mouse transcriptome (mm10) and unique molecular identifiers (UMI) were counted using Cell Ranger (10x Genomics) version 3.0.1
Further data analysis was performed using the Seurat package version 3.1 (Butler et al., 2018) in R version 3.6.2.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files are read abundance measurements in tab-delimited txt format with genes and barcode sequences corresponding to row and column indices
Supplementary_files_format_and_content: raw count matrix
Supplementary_files_format_and_content: filtered and normalized count matrix

source_name: Embryonic intestinal mesenchymal and epithelial cells

extract_protocol:
Adult colonic tissue was harvested, minced into small pieces (2mm) and subsequently washed with PBS. Tissue pieces were then incubated in Gentle Cell Dissociation Reagent (STEMCELL Technologies) for 30 minutes at room temperature to detach the epithelium. The epithelial fraction was then filtered through a Falcon 70 µm cell strainer (Corning), washed with plain ADMEM/F12 and incubated for 5 minutes at 37 °C in prewarmed TrypLE express (Gibco), followed by single cell dissociation using the m_intestine program on the gentleMACS Octo Dissociator (Miltenyi Biotec). The epithelial single cell suspension was then filtered through a Falcon 40 µm cell strainer (Corning) and stored on ice in ADMEM/F12 (supplemented with 10% FBS). After the detachment of the epithelium the remaining tissue pieces were digested for 1 hour at 37°C under 110 rpm shaking conditions in DMEM supplemented with 2mg/mL collagenase D (Roche) and 0.4 mg/mL Dispase (Gibco). The mesenchymal fraction was then filtered through a Falcon 70 µm cell strainer (Corning), washed with plain ADMEM/F12 and subsequently filtered through a Falcon 40 µm cell strainer (Corning). Both epithelial and mesenchymal cells were stained for 30 minutes on ice with anti-CD45-PE (1:500, eBioscience) and anti-CD326(EpCAM)-FITC (1:500, eBioscience) in ADMEM/F12 (supplemented with 10% FBS). Prior to cell sorting, all cells were stained for 5 minutes on ice with Zombie Violet Fixable Viability Kit in PBS (1:1000, Biolegend). In the case of mesenchymal cell isolation from PdgfraH2BeGFP mice only staining with Zombie Violet Fixable Viability Kit was performed. Cells were detected and sorted at the Cytometry Facility at the University of Zürich using a FACSAria III cell sorter (Gates visible in corresponding Figures) (BD Biosciences). Embryonic hindguts isolated and pooled from each stages including E14.5 (25 embryos), E15.5 (17 embryos) and E18.5 (14 embryos). Tissues were minced into small pieces and then incubated for 60 min @ 37 °C in PBS with 15mg of collagenase  in 100ml. Single cells were centrifuged and resuspended in PBS+ 0.2% BSA. Then cells were subjected to antibody staining prior sorting with EpCAM-TITC (eBioscience) and CD45-PE (eBioscience) for 45 minutes. After washing and resuspension in PBS, samples were incubated with Zombie Violet Fixable Viability Kit in PBS (Biolegend) for 5 minutes on ice. Single cells were then centrifuged, resuspended in BGJb media+ 10% FBS and filtered through Falcon 40 µm cell strainer (Corning) and kept on ice prior sorting. Cells were detected and sorted at the Cytometry Facility at the University of Zürich using a FACSAria III cell sorter (BD Biosciences).
Library preparation was performed according to the manufacturer’s indications (Chromium Next GEM Single Cell 3ʹ Reagent Kits  v3  protocol)

value: hindgut

value: mesenchymal and epithelial

tag: developmental stage


title: clsy4_meiocyte_sRNA-seq_rep2

description: sRNA-seq

extract_protocol:
Meiocyte or tapetum cells was isolated using the same method as for BS-seq.Total RNA was then extracted from isolated pure meiocyte or tapetum cells using Direct-zol RNA Kit (Zymo, #R2061).
sRNA library was constructed using the RealSeq-Biofluids NGS Library Preparation Kit (Biocat,600-00048-SOM).To further enrich the small RNA fractions of the library and remove the potential adaptor dimers, the generated sRNA library was separated by electrophoresis with a 6% TBE gel (Novex, #EC6265BOX). The region containing DNA bands from 147 bp to 157 bp long (corresponding to 20-30 nt sRNA size) was excised with a knife and then resolved in elution buffer (0.5 M ammonium acetate, 10 mM magnesium sulfate, 1 mM EDTA (pH 8.0), 0.1% SDS) for 4 hours at 37°C. The remaining fragments of polyacrylamide were removed by passing the supernatant through a disposable plastic column. Two volumes of ethanol at 4°C were added to the solution and then stored on ice for 30 min. DNA was recovered by centrifugation for 10 min at 4°C in one microcentrifuge tube. Finally, the DNA was washed with 70% ethanol and resolved in Tris-EDTA (TE) buffer (pH 7.6).

value: Meiocyte


title: E15.5


title: Developing mouse embryo sections A11H06_S107

extract_protocol:
Nuclei were extracted with a permeabilization buffer, sonicated and fixed. cDNA molecules within nuclei are extracted after tagmentation through the use of denaturants.
3' end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis, tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it, a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.


title: Developing mouse embryo sections A11A04_S11


title: EKHT1_ROW17_10

extract_protocol:
The primary somatosensory cortex was microdissected as aforementioned. Cells were further dissociated by incubating micro-dissected samples in 0.5 mg/mL pronase (Sigma, #P5147) at 37°C for 10 minutes, followed by incubation in 5% bovine serum albumin for 3 minutes and manual trituration in ACSF using pulled glass pipettes. Cells were then centrifuged for 10 minutes at 600 rpm and resuspended before filtration using a 70 mm cell strainer (ClearLine, # 141379C). Cells were then incubated for 10 minutes at 37°C with Hoechst (0.1 mg/mL) and isolated using a Beckman Coulter Moflo Astrios FAC-sorter. Singlet Hoechst+cells were sorted according to their Forward and Side scattering properties (FSC and SSC), and their negativity for Draq7TM (Viability dye, Far red DNA intercalating agent, Beckman Coulter, #B25595). 5000 to 10 000 cells were FACsorted for each experiment. Three microliters of C1 Suspension Reagent (Fluidigm) was added to 10 ml of FAC-sorted cells GFP+ cells, yielding a 300-500 cells / ml suspension. 12 ml of this suspension mix were loaded on a C1 Single-Cell AutoPrep integrated fluidic circuit (IFC) designed for 10 to 17 mm diameter-cells (Fluidigm, #100-5780). RNA was extracted using an RNeasy kit (Qiagen, #74034), and quality control was done using 2001 Bioanalyzer from Agilent. cDNA libraries were obtained using SMARTseq v4 kit (Clontech, # 634888) and sequenced using HiSeq 2500 sequencer.
SMARTseq v4 kit (Clontech, # 634888)


title: clsy3_meiocyte_sRNA-seq_rep2

description: sRNA-seq


title: clsy4_meiocyte_sRNA-seq_rep1

description: sRNA-seq


title: E14.5


title: EKHT1_ROW34_10


title: EKHT1_ROW16_10


title: Developing mouse embryo sections A09H06_S105


title: DSS

source_name: Adult intestinal mesenchymal and epithelial cells

value: colon

value: Adult


title: clsy3_meiocyte_sRNA-seq_rep1

description: sRNA-seq


title: WT_tapetum_sRNA-seq_rep2

description: sRNA-seq


title: Developing mouse embryo sections A10A04_S10


title: Developing mouse embryo sections A10H06_S106


title: N45-PolII

source_name: mouse tumor

value: Polll


title: EKHT1_ROW13_10


title: EKHT1_ROW10_10


title: EKHT1_ROW07_10


title: WT_tapetum_sRNA-seq_rep1

description: sRNA-seq


title: Developing mouse embryo sections A09A04_S9


title: WT_meiocyte_sRNA-seq_rep2

description: sRNA-seq


title: N45-input

value: Input


title: WT_meiocyte_sRNA-seq_rep1

description: sRNA-seq


title: N45-Baf155


title: EKHT1_ROW06_10


title: Developing mouse embryo sections A08H06_S104

value: E14 Mouse Embryo


title: N45-Brg1


title: EKHT1_ROW05_10


title: 84592-input


title: rdr2_tapetum_scBS-seq_rep3

description:
single cell BS-seq
rdr2_tapetum_3reps_merged_sorted_dedup.CG.w1.gff.gz,rdr2_tapetum_3reps_merged_sorted_dedup.CHG.w1.gff.gz,rdr2_tapetum_3reps_merged_sorted_dedup.CHH.w1.gff.gz

extract_protocol:
Male meiocyte of prophase I (mostly at pachytene stage) was isolated as described previously (Walker et;al 2018). To obtain tapetal cells, flower buds were harvested from the pA9::NTF marker line. Protoplasts were generated from the collected flower buds using a previously described method (ref). Isolated protoplasts were immediately subjected to FACS on a BD FACSMelody cell sorter.
Single cell bisufite sequencing (scBS-seq) libraries of male meiocyte from different genotypes were prepared according to the published low-input bisulfite squencing method (ref) whereas normal bisulfite sequencing libraries were constrcuted using the Ovation Ultralow Methyl-Seq Library System (Nugen, #0336) and EpiTect Fast Bisulfite Conversion (Qiagen, #59802) kits.


title: EKHT1_ROW04_10


title: rdr2_tapetum_scBS-seq_rep2


title: 84592-PolII


title: EKHT1_ROW01_10


title: 84592-Baf155


title: 84592-Brg1


title: Developing mouse embryo sections A06H06_S102

value: Sagigital section


title: rdr2_tapetum_scBS-seq_rep1

value: Anther


title: Developing mouse embryo sections A08A04_S8


title: Developing mouse embryo sections A05H06_S101


title: EKHT1_ROW39_1


title: WT_tapetum_scBS-seq_rep1

description:
single cell BS-seq
WT_tapetum_3reps_merged_sorted_dedup.CG.w1.gff.gz, WT_tapetum_3reps_merged_sorted_dedup.CHG.w1.gff.gz, WT_tapetum_3reps_merged_sorted_dedup.CHH.w1.gff.gz

value: Tapetum


title: WT_tapetum_scBS-seq_rep2


title: 84603-Baf155


title: 84603-input


title: EKHT1_ROW33_1


title: 84603-Brg1


title: EKHT1_ROW37_1


title: EKHT1_ROW34_1


title: Developing mouse embryo sections A07H06_S103


title: EKHT1_ROW32_1


title: EKHT1_ROW36_1


title: 84603-PolII


title: Developing mouse embryo sections A07A04_S7


title: HyperTE2_crispr_line2_rep2_meiocyte_scBS-seq

description: single cell BS-seq


title: Developing mouse embryo sections A05A04_S5


title: WT_tapetum_scBS-seq_rep3


title: HyperTE2_crispr_line2_rep1_meiocyte_scBS-seq

description: single cell BS-seq


title: Developing mouse embryo sections A04H06_S100


title: HyperTE2_crispr_line1_meiocyte_scBS-seq

description: single cell BS-seq


title: Developing mouse embryo sections A06A04_S6


title: Developing mouse embryo sections A04A04_S4


title: HyperTE1_crispr_line2_meiocyte_scBS-seq

description: single cell BS-seq


title: N202-input


title: Developing mouse embryo sections A02H06_S98


title: EKHT1_ROW18_1


title: N272-input


title: N202-Baf155


title: Developing mouse embryo sections A03A04_S3


title: Developing mouse embryo sections A03H06_S99


title: N272-Baf155


title: HyperTE1_crispr_line1_meiocyte_scBS-seq

description: single cell BS-seq


title: clsy1,2_meiocyte_rep2_scBS-seq

description: single cell BS-seq


title: clsy3_sperm_BS-seq

description: BS-seq

value: Sperm


title: EKHT1_ROW31_1


title: EKHT1_ROW10_1


title: Osdrm2_leaf_smallRNA-seq

city: Fuzhou

first: mao

last: fei

state: Fujian

address: Shangxiadianlu NO.15

department: National Engineering Research Center of JUNCAO

institute: Fujian Agriculture and Forestry University

data_processing:
For Bisulfite-Seq data, the adaptor sequences and low-quality reads were trimmed using trim_galore(https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The clean data were mapped against genome using bismark(v0.19.0). CGmaptools(v0.1.1) was used to calculate the methylation level of the 2-kb sequences upstream and downstream of all genes and transposable elements (http://rice.plantbiology.msu.edu/). A personal Python script was  used to visualize the methylation level.
For RNA-seq data, the adaptor sequences and low-quality reads were trimmed using trim_galore(https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).The clean reads were mapped against replaced genome using Tophat2 (v2.1.1)[5] with default parameters. Cufflinks (v2.0.0) was used to quantify the relative expression of the genes and calculate any differentially expressed genes (Fold change ≥ 1, adjusted p-value<0.01). To visualize the RNA-seq expression level, bedtools was used to calculate the coverage and normalize the data per million mapped reads. A Python script was used to visualize the data.
For smallRNA-seq data, The adaptor sequences and low-quality RNA-seq reads were trimmed using trim_galore, and reads shorter than 18 nt or longer than 30 nt were discarded. MicroRNA (http://www.mirbase.org/ftp.shtml), transfer RNA (http://rice.plantbiology.msu.edu/analyses_search_tRNA.shtml), ribosomal RNA (Rice Genome Annotation MSU7.0), small nucleolar RNA, and small nuclear RNA  (https://www.arb-silva.de/no_cache/download/archive/release_132/Exports/) sequences were also removed. The remaining clean reads were aligned to the  replaced MSU7.0 rice genome using Bowtie (v 1.1.1), allowing 2 mismatches and requiring mapping to a unique site. The siRNA enrichment was calculated in 10-kb windows with normalized reads, and only windows with at least three reads were further analysed. To visualize the level of siRNA expression, bedtools was used to calculate the coverage and normalize the data per million mapping reads. A  Python script was used to visualize the data.
Genome_build: About 7-kb sequence containing LOC_Os01g41370 was amplified from ZH11 and sequenced. This sequence was used to replace the LOC_Os01g41370 sequence in the MSU7.0 rice genome assembly, which was identified using BLASTn. The replaced MSU7.0 rice genome was used in our analysis.

organism: Oryza sativa Japonica Group

source_name: Osdrm2 leaf

growth_protocol: The Epi-lf mutant was identified in a screen of an anther-cultured population of Japonica rice (Oryza sativa ssp. japonica; variety ZhongHua11; ZH11) in 2005. The mutant phenotype of Epi-lf was stably inherited over more than 20 generations. The mutant and WT rice plants were planted in paddy fields under natural conditions or in glasshouses with a day temperature of 30°C and a night temperature of 24°C.

extract_protocol:
Total RNA was extracted from different tissues using TRIzol reagent (Thermo Fisher Scientific). The first-strand cDNA was synthesized using 1 μg RNA and ReverTra Ace qPCR RT Master Mix with gDNA Remover (Toyobo), according to the manufacturer’s instructions, using 29 PCR cycles to amplify the LF transcripts and 23 PCR cycles for Actin1. The RT-PCR analysis was repeated three times with similar results. Genomic DNA was isolated from the flag leaves of WT and tillers with different phenotypes of Epi-lf using the CTAB method. Briefly, 1 μg of genomic DNA was treated with sodium bisulphite using the Qiagen EpiTect Bisulfite kit, according to the manufacturer’s instructions. The treated DNA was dissolved in 15 mL distilled water, and 3 μL of this solution was used as the template in a 50-μL PCR (94°C for 4 min; followed by 40 cycles of 94°C for 30 s , 55°C for 30 s and 60°C for 30 s; with a final 60°C for 10 min).The PCR products were purified and cloned into pEASY-T5-Blunt Zero Cloning Kit vectors.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: variety

value: leaf


title: N272-PolII

extract_protocol:
Nuclei was isolated from snap frozen samples. Lysates were clarified from sonicated nuclei and BAF-DNA complexes were isolated with antibody.
Library was prepared using NEBnext ChIP-seq libraray prep reagent set


title: clsy3,4_meiocyte_rep1_scBS-seq

description: single cell BS-seq


title: N202-PolII


title: clsy3,4_meiocyte_rep2_scBS-seq

description: single cell BS-seq


title: clsy4_meiocyte_rep2_scBS-seq

description: single cell BS-seq


title: Developing mouse embryo sections A01A04_S1

city: Seattle

first: Sanjay

last: Srivatsan

address: 3720 15TH Ave NE Genome Sciences S Foefe Bldg

institute: University of Washington

data_processing:
Basecalls performed using bcl2fastq version 2.20
Poly-dT adapters were trimmed using Trimmomatic and aligned to mm10 using STAR. Mapped reads were then deduplicated and assigned to a gene (GENCODE vM15 - mouse). UMIs were enumerated for each cell/gene combination and finally a count matrix was made.
Count matrix was loaded into Monocle3 for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: Count Matrix (matrix marker file- .mtx), Cell Metadata (tab separated values- .tsv), Gene Metadata (tab separated values- .tsv)


title: EKHT1_ROW05_1

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

institute: University of Geneva

data_processing:
read1 containing umi sequences are appended at the end of the headers of read2
read2 are mapped with tophat v2.0.13 on the mouse genome GRCm38 considering Ensembl78 genes annotations
bam files are processed with umi_tools to deduplicate reads with identical UMI sequence
gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification and this includes 5' and 3' UTRs.
Genome_build: GRCm38
Supplementary_files_format_and_content: retrobeads.tsv.gz contains the result of gene expression quantification by summarizeOverlaps() for each cell. The integers values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contains information about the genes that are quantified.


title: Developing mouse embryo sections H12G02_S384

description:
Developing mouse embryo sections
sci-Space Slides 1-6
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell


title: Developing mouse embryo sections H12G06_S192


title: Developing mouse embryo sections A01H06_S97


title: Developing mouse embryo sections H12G01_S288


title: Developing mouse embryo sections H11G06_S191


title: EKHT1_ROW09_1


title: WT_leaf_rep1_smallRNA-seq

source_name: WT leaf rep1

value: Oryza sativa ssp. japonica; variety ZhongHua11


title: Epi-lf_leaf_CHD1_smallRNA-seq

source_name: Epi-lf leaf CHD1


title: 3-input

value: input


title: 4-PolII

value: PolII


title: Epi-lf_leaf_CHD2_smallRNA-seq

source_name: Epi-lf leaf CHD2


title: Developing mouse embryo sections H11G05_S95


title: N272-Brg1


title: N202-Brg1


title: Developing mouse embryo sections A02A04_S2


title: clsy1,2_meiocyte_rep1_scBS-seq

description: single cell BS-seq


title: 4-input


title: 4-Baf155


title: WT_leaf_rep3_smallRNA-seq

source_name: WT leaf rep3


title: 3-Baf155


title: Epi-lf_leaf_Normal_smallRNA-seq

source_name: Epi-lf leaf Normal


title: clsy4_meiocyte_rep1_scBS-seq

description: single cell BS-seq


title: WT_leaf_rep2_smallRNA-seq

source_name: WT leaf rep2


title: 4-Brg1


title: 3-PolII


title: Developing mouse embryo sections H11G02_S383


title: WT_endosperm_smallRNA-seq

source_name: WT endosperm

value: endosperm


title: Developing mouse embryo sections H12G05_S96


title: clsy3_meiocyte_rep1_scBS-seq

description: single cell BS-seq


title: Epi-lf_embryo_smallRNA-seq

source_name: Epi-lf embryo

value: embryo


title: clsy2_meiocyte_rep2_scBS-seq

description: single cell BS-seq


title: pTP::Pol-V pol-v line2 meiocyte rep2_scBS-seq

description: single cell BS-seq

value: pol v


title: WT_embryo_smallRNA-seq

source_name: WT embryo


title: clsy3_meiocyte_rep2_scBS-seq

description: single cell BS-seq

value: Meiocyte


title: clsy1_meiocyte_rep2_scBS-seq

description: single cell BS-seq


title: clsy2_meiocyte_rep1_scBS-seq

description: single cell BS-seq


title: Epi-lf_endosperm_smallRNA-seq

source_name: Epi-lf endosperm


title: 78780-input

value: TATcre;SS18-SSX+ and Snf5-/-


title: clsy1_meiocyte_rep1_scBS-seq

description: single cell BS-seq


title: 78780-PolII

value: polII


title: 3-Brg1


title: pTP::Pol-V pol-v line2 meiocyte rep1_scBS-seq

description: single cell BS-seq


title: pTP::Pol-V pol-v line1 meiocyte rep2_scBS-seq

description: single cell BS-seq


title: Developing mouse embryo sections H10G01_S286

source_name: E14 saggital sections 8-10um thick


title: Developing mouse embryo sections H11G01_S287


title: WT_leaf_smallRNA-seq

source_name: WT leaf


title: 78780-Baf155


title: Epi-lf_leaf_smallRNA-seq

source_name: Epi-lf leaf


title: 78780-Brg1


title: Developing mouse embryo sections H10G06_S190


title: WT_seedling_leaf_smallRNA-seq

source_name: WT seedling leaf

value: seedling leaf


title: Developing mouse embryo sections H10G05_S94


title: Developing mouse embryo sections H09G02_S381


title: 78744-input


title: Developing mouse embryo sections H09G05_S93


title: pol v_meiocyte_rep1_scBS-seq

description: single cell BS-seq

source_name: Flower bud


title: Developing mouse embryo sections H09G06_S189


title: REB058: MG1655 delta hsdSMR stat rep 3

city: Singapore

first: Swaine

middle: L

last: Chen

state: Singapore

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

department: Medicine

country: Singapore

institute: National University of Singapore and Genome Institute of Singapore

data_processing:
Raw sequencing reads were mapped to their respective reference genomes: RefSeq accession GCF_000013265.1 for E. coli UTI89, GCF_000005845.2 for E. coli MG1655 and GCF_000007445.1 for E. coli CFT073 using BWA-MEM (version 0.7.10) with default parameters, then the resulting bam files were sorted and deduplicated using PicardTools v.2.2.2
HTseq was used to quantify sequencing reads mapping to predicted open reading frames (ORFs)
Ribosomal RNA (rRNA) and transfer RNA (tRNA) sequences (based on the corresponding Genbank RefSeq annotation) were filtered out of the data set.
R (version 2.15.1) was used for differential expression analysis, using the edgeR package (samples were normalized by TMM (trimmed median of means), common and tagwise dispersion factors were estimated using a negative binomial model, and then fold change values were calculated from these normalized counts)
Genome_build: RefSeq accession GCF_000013265.1 for E. coli UTI89, GCF_000005845.2 for E. coli MG1655 and GCF_000007445.1 for E. coli CFT073
Supplementary_files_format_and_content: Tab-delimited text files with normalized expression values, fold change, P-values, and FDR values.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: MG1655 delta hsdSMR

growth_protocol: Stationary phase cells were obtained by propagating strains statically for two serial 24 hour passages at 37°C, with a 1:1000 dilution between passages (identical to the inoculum used for mouse infections). Log phase cells were obtained by diluting overnight cultures 1:100 in LB and growing to log phase (OD600 = 0.4 – 0.5) at 37°C with shaking.

extract_protocol:
RNA extraction with the Qiagen RNAEasy Mini Kit; ribosomal depletion with the Ribo Zero rRNA removal kit
RNA libraries were prepared using the ScriptSeq v2 RNA-seq library preparation kit

value: stationary phase

value: delta hsdSMR


title: 78744-Baf155

source_name: mouse tumor


title: 78744-PolII


title: pol v_meiocyte_rep2_scBS-seq

description: single cell BS-seq


title: Epi-lf_seedling_leaf_rep1_smallRNA-seq

source_name: Epi-lf seedling leaf rep1


title: REB049: MG1655 delta hsdSMR stat rep 2


title: Developing mouse embryo sections H10G02_S382

value: E14 Mouse Embryo

value: Sagigital section


title: Epi-lf_seedling_leaf_rep2_smallRNA-seq

source_name: Epi-lf seedling leaf rep2


title: pTP::DCL3 dcl3 line2 meiocyte rep2_scBS-seq

description: single cell BS-seq

value: Anther


title: Developing mouse embryo sections H09G01_S285


title: Developing mouse embryo sections H08G06_S188


title: REB040: MG1655 delta hsdSMR stat rep 1


title: pTP::DCL3 dcl3 line2 meiocyte rep1_scBS-seq

description: single cell BS-seq


title: 1-input

value: Myf5cre;SS18-SSX+ and Snf5-/-


title: 78744-Brg1


title: pTP::DCL3 dcl3 line1 meiocyte rep2_scBS-seq

description: single cell BS-seq


title: REB048: MG1655 wt stat rep 2

source_name: MG1655 wt

value: wt


title: pTP::Pol-V pol-v line1 meiocyte rep1_scBS-seq

description: single cell BS-seq


title: Developing mouse embryo sections H08G02_S380


title: Developing mouse embryo sections H08G05_S92


title: pTP::DCL3 dcl3 line1 meiocyte rep1_scBS-seq

description: single cell BS-seq


title: dcl3_meiocyte_rep2_scBS-seq

description: single cell BS-seq


title: Developing mouse embryo sections H07G06_S187


title: N4_Snf5_SSM2_Myf5Cre

data_processing:
RTA v1.18.61 used for basecalling.
Trim adapters with cutadapt, Align to mm10 with STAR -2.7.5a
Generate count matrices with featureCounts and RSEM
Perform differential expression with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Fresh frozen tumor tissue was disrupted using Homogenizer. RNA was extracted from tissue lysate using the Animal Tissues protocol from the RNeasy Mini kit (Qiagen), with final elution volumes of 50 μL.
Libarary was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: Myf5cre;SS18-SSX+/- and Snf5-/-


title: Developing mouse embryo sections H07G02_S379


title: pTP::RDR2 rdr2  sperm_BS-seq

description: BS-seq

source_name: Open flower

value: Sperm


title: 1-Baf155

data_processing:
paired-end 50bp sequencing on an Illumina NovaSeq platform
ChIP-seq reads were aligned to the mm10 genome assembly using novoalign-4.00.01
peaks were called using MACS2 with following settings: -B --SPMR --pvalue=1e-2 --mfold 15 100
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using multirep_macs2_pipeline.pl; Scores represent a log2 fold enrichment


title: REB039: MG1655 wt stat rep 1


title: 1-Brg1


title: 16hpc_ATACseq_rep3

data_processing:
Libraries were aligned to the Arabidopsis genome TAIR10 using Bowtie2
Duplicates, mtDNA and ctDNA were removed using samtools
Peaks corresponding to accessible chromatin regions were identified with MACS2
Consensus peaks among replicates were obtained with bedops-intersect and the counts were determined using feature counts
The Differential Accessible Chromatin (DAC) Regions between samples were statistically determined by DEseq2 comparing time points vs. uncut roots.
Peak annotation was done using HOMER (annotatePeaks.pl)
Genome_build: TAIR10
Supplementary_files_format_and_content: peak location and counts for each sample in tab delimited .txt
Supplementary_files_format_and_content: Matrix table with normalized counts including annotation and p-values for all time points vs. control in excel format

source_name: Root tip reprograming cells

extract_protocol:
About 130µm of root tips were excised, plants were transferred to new MS plates and kept under growing conditions for 2.5h, 14h or 16h. The reprogramming domain comprising about 200µm above the cutting site was then excised and rapid cell wall digestion (Ortiz-Ramirez, et al., 2018) was performed. For uncut controls, the equivalent root size was excised and digested. GFP positive or DAPI stained protoplast were isolated by FACS. Protoplast lysed deionized water and nuclei were subjected to Tn5 tagmentation protocol accoring to input (Buenrostro et al., 2015). Further steps were followed according to described protocols (Buenrostro et al., 2015; Lu et al., 2017)
Libraries were generated according to Buenrostro et al., 2015. In brief, libraries were aplified using published barcoded primers for 5 cycles. An aliquot of the reaction was used in a qPCRreaction to estimate further amplification cycles. Number of total cycles were estimated individually for each library and then purified using AMPure XP beads (Agencourt) prior sequencing.

value: 7 DAS

value: root

tag: number of nuclei profiled

tag: cell marker used

value: GFP


title: dcl3_meiocyte_rep1_scBS-seq

description: single cell BS-seq


title: 16hpc_ATACseq_rep2


title: 14hpc_ATACseq_rep2


title: 1-PolII

value: PolII


title: Developing mouse embryo sections H08G01_S284


title: N2_Snf5_SSM2_Myf5Cre


title: Developing mouse embryo sections H07G01_S283


title: Developing mouse embryo sections H06G06_S186


title: N3_Snf5_SSM2_Myf5Cre


title: pTP::RDR2 rdr2 line2 meiocyte_BS-seq

description: BS-seq

value: Meiocyte


title: 14hpc_ATACseq_rep1


title: 78777_Snf5_SSM2_TATCre

value: TATcre;SS18-SSX+/- and Snf5-/-


title: 78780_Snf5_SSM2_TATCre


title: 14hpc_ATACseq_rep3


title: rdr2_meiocyte_rep2_scBS-seq

description: single cell BS-seq


title: 16hpc_ATACseq_rep1


title: N1_Snf5_SSM2_Myf5Cre


title: pTP::RDR2 rdr2 line1 meiocyte_BS-seq

description: BS-seq


title: rdr2_meiocyte_rep1_scBS-seq

description: single cell BS-seq


title: Developing mouse embryo sections H06G05_S90


title: 78774_Snf5_SSM2_TATCre


title: Developing mouse embryo sections H06G01_S282


title: Developing mouse embryo sections H07G05_S91


title: 2.5hpc_ATACseq_rep2


title: Developing mouse embryo sections H06G02_S378


title: Developing mouse embryo sections H05G06_S185


title: 2.5hpc_ATACseq_rep3


title: Pooled sera_51471

city: Sydney

first: Antibiotic Resistant Sepsis Pathogens Framework Initiative

last: Bioplatforms Australia

state: NSW

address: Level 4, Building 4WW, Research Park Drive, Macquarie University

country: Australia

institute: Bioplatforms Australia

description: Additional information about the bacterial cultures is available from the Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Initiative website. https://data.bioplatforms.com/organization/about/bpa-sepsis

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900622605.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2

organism: Klebsiella pneumoniae

source_name: Bacteria in growth media

growth_protocol: Complete information about the bacterial cultures is available from the Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Initiative website. https://data.bioplatforms.com/organization/about/bpa-sepsis

extract_protocol: Bacterial rRNA depletion with Illumina Ribo-Zero rRNA Removal Kit (Bacteria) followed by strand RNAseq sample preparation with Illumina TruSeq Stranded mRNA Library Prep Kit

tag: growth media

value: Pooled sera

tag: growth time

value: 2 hrs exposure to sera

tag: growth phase

tag: od600 reading

tag: temperature

tag: bpa identifier

tag: serovar


title: 2.5hpc_ATACseq_rep1

tag: tissue

tag: genotype


title: scRNAseq_ThrbNeg_rep1

city: BOSTON

first: CHANGHEE

last: LEE

address: 77 AVENUE LOUIS PASTEUR

department: Genetics

institute: Harvard Medical School

data_processing:
For 10X Chromium libraries, sequencing output was demultiplexed by Cell Ranger (version 3.0.0), then mapped with dropEst (Petukhov et al, Genome Biology 2018) pipeline
Quality score above 0.9 were filtered and then any cells more than 4,000 features filtered out for doublet removal and cells above 15% mitochondrial content removed
Genome_build: galGal5 (Ensembl, release 94, only protein coding and lincRNA with two additional transgenes MCHERRY and EGFP)
Supplementary_files_format_and_content: Seurat (v3.1.5) object with meta information; equivalent text file in market matrix format (MTX) with rownames (features) and colnames (barcodes)

organism: Gallus gallus

growth_protocol: Retina progenitor cells were cultured in DMEM with 10% FBS

extract_protocol:
Total RNA is extracted using Direct-zol RNA Kits (Zymo Research)
1ug of RNA is used to make the library using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

tag: cell type

value: Retina Progentor Cell

tag: treatment/condition

value: ThrbNeg


title: Pooled sera_51470

tag: strain


title: N30_Myf5_Snf5

city: Beijing

first: Jinxiu

last: Li

address: Yuanmingyuan west road 2#

institute: China Agricutural University


title: N49_Snf5_SSM2_TATCre


title: scRNAseq_ThrbPos_rep1

value: ThrbPos


title: Uncut_ATACseq_rep3

source_name: Root tip cells

tag: age

tag: hours post root tip excision

value: uncut

value: 1uM DAPI stained


title: N33_Myf5_Snf5


title: Pooled sera_51472


title: Uncut_ATACseq_rep2


title: Uncut_ATACseq_rep1


title: Developing mouse embryo sections H05G01_S281

value: E14 Mouse Embryo

tag: sample type

value: Sagigital section


title: Pooled sera_51469


title: Developing mouse embryo sections H04G06_S184


title: Pooled sera_51468


title: Developing mouse embryo sections H05G05_S89


title: MNPAT7_2_5

city: London

first: Graham

middle: A

last: Hitman

address: 4 Newark St

institute: Queen Mary University of London

data_processing:
Raw sequence reads were mapped using kallisto to transcripts using version 89 of ensembl (GRCh38.p10)
Genome_build: GRCh38
Supplementary_files_format_and_content: HDF5

growth_protocol: The THP1 (human acute monocytic leukemia derived; ATCC number TIB-202 purchased from Thermofisher) cell line was regularly maintained in RPMI 1640 medium containing GlutaMAX™, supplemented with 10% FCS (Gibco™ Newborn Calf Serum [heat inactivated], of New Zealand origin; Thermo Fisher Scientific), 5% AA (Gibco® MEM), Non-Essential Amino Acids, 100 U/mL penicillin and 100 μg/mL streptomycin (Thermo Fisher Scientific). Cells were grown at 37 °C in a humidified atmosphere of 5% CO2 in air, and sub-passaged with fresh complete RPMI medium every three days. The cell line was regularly checked to be mycoplasma free using the VenorGeM Mycoplasma detection kit (Cambio Ltd, UK) according to manufacturer’s instructions.

extract_protocol:
Total RNA was extracted from treated cells using QIAGEN RNeasy Kit according to manufacturer's instructions
Fragmented cDNA Sequencing libraries were generated from 100ng of Total RNA using NEBNext Ultra II with polyA isolation module (Illumina, San Diego, California, USA) according to manufacturer’s protocol.

treatment_protocol: Stock solutions of Arecoline (100 mg/ml of methanol) and MNPA (2.5 mg/ml of methanol), were made, aliquoted and stored at -20oC. 1x106 THP1 cells were treated with either 50 g/ml Arecoline or 25 g/ml MNPA in 6-well plates and cells were harvested after 24 h of treatment. Methanol was used as a negative control. Three independent experiments were performed for each exposure. Cell viability and proliferation was assessed by phase contrast light microscopy and using a MTT assay. All chemicals were purchased from Sigma-Aldrich.

tag: cell line

tag: treatment

value: MNPA

tag: experiment


title: Pooled sera_51467

tag: growth media

tag: growth time


title: Developing mouse embryo sections H04G02_S376


title: N31_Myf5_Snf5


title: Developing mouse embryo sections H05G02_S377


title: N43R_Snf5_TATCre


title: Developing mouse embryo sections H04G05_S88


title: MNPAT5_2_5


title: MNPAT6_2_5


title: N1_Snf5_TATCre


title: N51_Snf5_TATCre


title: ArecolineT7_2_6

value: Arecoline


title: Developing mouse embryo sections H04G01_S280


title: RPMI_51465

value: RPMI

value: 1 hr

tag: growth phase

value: Mid log phase

tag: od600 reading


title: RPMI_51466

tag: temperature

tag: bpa identifier


title: N49_Snf5_TATCre


title: Developing mouse embryo sections H03G05_S87

tag: tissue


title: ArecolineT5_2_6


title: RPMI_51464

tag: serovar


title: Developing mouse embryo sections H03G06_S183

tag: genotype


title: N43L_Snf5_TATCre


title: B_SSM2


title: Developing mouse embryo sections H03G02_S375


title: RPMI_51462


title: N2_SSM2


title: Myf5_SSM2_N460


title: Developing mouse embryo sections H02G06_S182


title: A_SSM2


title: DMSO-treated immune cells

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

country: France

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

description:
UST-AS-004
SORT-seq (partially robotized version of the CEL-seq2 protocol).
gene_counts_matrix.tsv

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used for identification of the Illumina library barcode, cel barcode and UMI. R2 was assigned 60 base pairs and used to map to the reference transcriptome of Hg19 with BWA (Anders and Huber, 2010).
Data was demultiplexed as described in Grün et al. 2014.
Mapping and generation of count tables was automated using the MapAndGo script (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: gene_counts_matrix.tsv: Matrix table with raw gene counts for every gene and every cell of every sample.

source_name: Liver immune cells

growth_protocol: CD45+ liver immune cells were isolated from liver tissues of patients with advanced liver disease and HCC by flow cytometry.

extract_protocol: scRNA-Seq was performed by Single-Cell Discoveries B.V. using SORT-seq protocol.

treatment_protocol: Cells were treated for 48h with Nizatidine or DMSO (vehicle). Single cells were sorted into 384 well cell capture plates (Single Cell Discovery, https://www.scdiscoveries.com) using SH800 cell sorter (Sony).

value: Liver tissues from patients with advanced liver disease and HCC

tag: cell type

value: CD45+ immune cells

value: DMSO


title: RPMI_51463

tag: strain


title: Nizatidine-treated immune cells

description:
UST-AS-002
SORT-seq (partially robotized version of the CEL-seq2 protocol).
gene_counts_matrix.tsv

value: Nizatidine


title: Pooled sera_51496

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900622645.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2

value: Pooled sera

value: 2 hrs exposure to sera

value: ethics embargo


title: RPMI_51461


title: Developing mouse embryo sections H03G01_S279


title: Pooled sera_51495


title: Developing mouse embryo sections H02G05_S86


title: Myf5_SSM2_N381


title: Pooled sera_51494


title: ArecolineT6_2_6


title: Developing mouse embryo sections H02G02_S374


title: Myf5_SSM2_N428


title: Developing mouse embryo sections H01G06_S181


title: Pooled sera_51493


title: MCF10A-3

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

data_processing:
Fastq reads Trimmed with Trimmomatic 0.39
Trimmed reads aligned with STAR 2.7.1a
RNAseq Counts obtained by featureCounts 2.0.0
Genome_build: GRCh38 Ensemble release 99 Homo sapiens
Supplementary_files_format_and_content: txt feature counts

source_name: ATCC CRL-10317; derived from benign proliferative breast tissue

growth_protocol: MCF10A cells were cultured in DMEM/F12 supplemented with 20ng/mL hEGF, 100ng/mL cholera toxin, 10ug/mL bovine insulin, 500ng/mL hydrocortisone, 5% horse serum, and 1% Penicillin/Streptomycin. MDA-MB-231 cells were cultured in DMEM and supplemented with 10% FBS and 1% Penicillin/Streptomycin. HCC1937 cells were cultured in RPMI supplemented with 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
RNAseq #74101 (RNAseq)
Illumina TruSeq Stranded mRNA Sample Preparation Kit v2

value: normal breast epithelial


title: MCF10A-4


title: MCF10A-1


title: Developing mouse embryo sections H02G01_S278


title: MDA-231-2

source_name: ATCC HTB-26;  isolated from a pleural effusion of a patient with invasive ductal carcinoma.

value: Triple-Negative Breast Cancer


title: Developing mouse embryo sections H01G05_S85

source_name: E14 saggital sections 8-10um thick


title: MDA-231-3


title: Pooled sera_51492


title: Developing mouse embryo sections H01G02_S373


title: Pooled sera_51491


title: RPMI_51490


title: Developing mouse embryo sections H01G01_S277


title: RPMI_51489


title: HCC1937-8

source_name: ATCC CRL-2336: established from a grade III infiltrating ductal primary breast tumor from a patient with a germ-line BRCA1 mutation

value: BRCA1-wild-type ductal primary breast tumor


title: Developing mouse embryo sections G12G06_S180

value: E14 Mouse Embryo


title: MDA-231-4


title: RPMI_51488


title: HCC1937-7


title: Developing mouse embryo sections G12G05_S84

value: Sagigital section


title: RPMI_51487


title: Developing mouse embryo sections G12G02_S372


title: HCC1937-3


title: Developing mouse embryo sections G11G06_S179


title: HTR-8 shNC_rep1

city: Guangzhou

first: Chonghui

last: Hu

address: 106 Zhongshan Er Road

department: Department of General Surgery

institute: Guangdong Provincial People's Hospital

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = PrimeView
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: HTR-8 shNC

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted using TRIzol reagent (Life technology, Carlsbad, CA, USA) according to the manufacturer's instruction. The RNA concentration was measured and complementary DNA was synthesized using reverse transcriptase kit (Takara, Dalian, China) according to the instruction.

value: placenta

value: human extravillous trophoblast

tag: genotype/variation

value: control


title: RPMI_51486

value: RPMI

value: 1 hr


title: RPMI_51485

value: Mid log phase


title: HTR-8 shNC_rep2


title: HTR-8 shCSRP2BP_rep1

source_name: HTR-8 shCSRP2BP

value: CSRP2BP knockdown by specific shRNA (CSRP2BP-shRNA)


title: HTR-8 shCSRP2BP_rep2