title: LLL03 miRNA-seq

city: Nanning

first: Dong-Liang

last: Huang

email: hdl666@163.com, Huangdl@gxaas.net

address: 174 Daxue Road

institute: Sugarcane Research Institure of Guangxi Academy of Agricultural Sciences

description:
LLL03
All_mirna.exp_profile.txt

data_processing:
For RNA-seq, raw data were curated by removing reads containing adapters, and ploy-N and low-quality reads.The high-quality reads were then assembled by Trinity.Unigenes were annotated based on NR, Pfam, KOG/COG/eggNOG , Swiss-Prot , KEGG  and GO.
For miRNA-seq, raw data were quality-checked, and reads with adapters, polyA and low-quality reads (reads containing Ns or with more than one base Q＜20) were removed. The high-quality clean reads were then aligned with small RNAs in GeneBank database (Release 209.0) and Rfam database (Release 11.0) to identify and remove rRNA, snoRNA, snRNA, tRNA, and scRNA. The remaining clean tags were searched against miRBase (Release 22) to identify known miRNAs. The unannotated reads were used for identifying novel miRNA candidates using software mirDeep2. The candidate target genes of the known and novel miRNAs were predicted using software patmatch (Version 1.2) with default parameters.
For degradome-seq, reads with adapters, and low-quality reads were filtered from raw data to obtain clean reads. These clean reads were aligned with Rfam and Genebank database to remove rRNAs, tRNAs, snoRNAs and repeats. The remaining reads were mapped to the transcriptome data (this study) and the potentially cleaved targets were identified by CleaveLand pipeline.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw counts for every miRNA and every sample
Supplementary_files_format_and_content: Matrix table with raw tags for every cleaved mRNA and every sample

organism: Saccharum hybrid cultivar

source_name: tissue

extract_protocol:
Total RNA from leaf and stem was extracted using Trizol reagent kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.Molecules of 18-30 nt were enriched by polyacrylamide gel electrophoresis, ligated with 3’ and 5’ adapters and then reverse transcribed,cDNA libraries were prepared for small RNA sequencing using standard Illumina protocols.Strapavidin capture of RNA fragments through Biotinylated Random Primers and adaptor ligation to only those RNAs containing 5'-monophosphates; After reverse transcription and PCR,Library was sequenced.

value: leaf

tag: growth phase

value: growth phase at the late stage of sucrose accumulation


title: LLS03 miRNA-seq

status: Public on Dec 30 2021

type: SRA

country: China

description:
LLS03
All_mirna.exp_profile.txt

library_source: transcriptomic

molecule: total RNA

tag: genotype

tag: tissue

value: stem


title: LLS01 miRNA-seq

description:
LLS01
All_mirna.exp_profile.txt


title: MATADOR_RNAseq_X563

city: Amsterdam

first: Mark

last: Opdam

address: 121, Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
RSEM package  Accurate transcript quantification from RNA-Seq data
reads were aligned using STAR
Genome_build: hg38
Supplementary_files_format_and_content: csv file matrix with read counts for all samples per gene

organism: Homo sapiens

source_name: Primairy tumor before treatment FFPE

extract_protocol:
FFPE AllPrep DNA/RNA isolation mini kit according to the manufacturer’s instructions (Qiagen,  Hilden, Germany)
Libraries of cDNA were constructed  with the TruSeq RNA Access Library Prep Kit (Illumina, San Diego, California, USA)

value: Breast

tag: material

value: FFPE

tag: treatment

value: 6 x AC dd


title: 328v

city: Austin

first: Grace

last: Chappell

state: TX

address: 9390 Research Blvd, Bldg 2, Ste. #100

department: Health Sciences

country: USA

institute: ToxStrategies, Inc.

description: RNA extracted from FFPE tissue

data_processing:
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing
fastqs were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches
Genome_build: probe-based targeted sequencing
Supplementary_files_format_and_content: comma-separated text files include raw count values for each gene_probe

organism: Mus musculus

source_name: FFPE duodenum_villus_20ppm Cr(VI) 90 days

growth_protocol: female B6C3F1 mice were bred, reared, and administered test compounds at Charles River Laboratories

extract_protocol:
Crypt and villus compartments from formalin-fixed, paraffin-embedded duedenum tissue were selectively scraped from sections mounted to glass slides directly into lysis buffer.
RNA was amplified using targeted oligomers according to the TempO-Seq (BioSpyder Industries) whole transcriptpome expression assay protocol for library construction.

treatment_protocol: B6C3F1 mice were exposed to 0-180ppm Cr(VI) as sodium dichromate dihydrate (SDD) in the drinking water (ad libitum) for 7 or 90 days.

tag: strain

value: villus

value: 20ppm Cr(VI) 90 days

value: wildtype


title: LLS02 miRNA-seq

description:
LLS02
All_mirna.exp_profile.txt


title: 402v

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_villus_60ppm Cr(VI) 90 days

value: 60ppm Cr(VI) 90 days


title: HLS03 miRNA-seq

description:
HLS03
All_mirna.exp_profile.txt


title: 328c

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_crypt_20ppm Cr(VI) 90 days

value: crypt


title: HLS01 miRNA-seq

description:
HLS01
All_mirna.exp_profile.txt


title: HLS02 miRNA-seq

description:
HLS02
All_mirna.exp_profile.txt


title: MATADOR_RNAseq_X648

value: 6 x TAC


title: MATADOR_RNAseq_X535


title: LLL01 miRNA-seq

description:
LLL01
All_mirna.exp_profile.txt


title: 368v

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_villus_20ppm Cr(VI) 7 days

value: 20ppm Cr(VI) 7 days


title: HLL03 miRNA-seq

description:
HLL03
All_mirna.exp_profile.txt


title: 327v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X544


title: HLL02 miRNA-seq

description:
HLL02
All_mirna.exp_profile.txt


title: HLL01 miRNA-seq

description:
HLL01
All_mirna.exp_profile.txt


title: 327c

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X531


title: LES03 miRNA-seq

description:
LES03
All_mirna.exp_profile.txt

value: growth phase at the early stage of sucrose accumulation


title: 366c

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_crypt_20ppm Cr(VI) 7 days


title: MATADOR_RNAseq_X480


title: LLL02 miRNA-seq

description:
LLL02
All_mirna.exp_profile.txt


title: LES01 miRNA-seq

description:
LES01
All_mirna.exp_profile.txt


title: LEL02 miRNA-seq

description:
LEL02
All_mirna.exp_profile.txt


title: LEL01 miRNA-seq

description:
LEL01
All_mirna.exp_profile.txt


title: 325c

description: RNA extracted from FFPE tissue


title: 323v

description: RNA extracted from FFPE tissue


title: HES03 miRNA-seq

description:
HES03
All_mirna.exp_profile.txt


title: MATADOR_RNAseq_X417


title: MATADOR_RNAseq_X416


title: HES02 miRNA-seq

description:
HES02
All_mirna.exp_profile.txt


title: 323c

description: RNA extracted from FFPE tissue


title: HEL03 miRNA-seq

description:
HEL03
All_mirna.exp_profile.txt


title: HES01 miRNA-seq

description:
HES01
All_mirna.exp_profile.txt


title: MATADOR_RNAseq_X446


title: HEL02 miRNA-seq

description:
HEL02
All_mirna.exp_profile.txt


title: MATADOR_RNAseq_X375


title: MATADOR_RNAseq_X376


title: HEL01 miRNA-seq

description:
HEL01
All_mirna.exp_profile.txt


title: 321c

description: RNA extracted from FFPE tissue


title: 321v

description: RNA extracted from FFPE tissue


title: 290v

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_villus_5ppm Cr(VI) 7 days

value: 5ppm Cr(VI) 7 days


title: MATADOR_RNAseq_X371


title: LMS03 RNA-seq

description:
LMS03
All_gene_expression.txt

value: growth phase at the middle stage of sucrose accumulation


title: LMS01 RNA-seq

description:
LMS01
All_gene_expression.txt


title: LES02 miRNA-seq

description:
LES02
All_mirna.exp_profile.txt


title: 325v

description: RNA extracted from FFPE tissue


title: 290c

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_crypt_5ppm Cr(VI) 7 days


title: LMS02 RNA-seq

description:
LMS02
All_gene_expression.txt


title: LML03 RNA-seq

description:
LML03
All_gene_expression.txt


title: LEL03 miRNA-seq

description:
LEL03
All_mirna.exp_profile.txt


title: MATADOR_RNAseq_X343


title: LML02 RNA-seq

description:
LML02
All_gene_expression.txt


title: MATADOR_RNAseq_X333


title: 289v

description: RNA extracted from FFPE tissue


title: HMS03 RNA-seq

description:
HMS03
All_gene_expression.txt


title: LML01 RNA-seq

description:
LML01
All_gene_expression.txt


title: MATADOR_RNAseq_X323


title: HMS02 RNA-seq

description:
HMS02
All_gene_expression.txt


title: 289c

description: RNA extracted from FFPE tissue


title: HML02 RNA-seq

description:
HML02
All_gene_expression.txt


title: HML03 RNA-seq

description:
HML03
All_gene_expression.txt


title: MATADOR_RNAseq_X31


title: MATADOR_RNAseq_X318


title: HML01 RNA-seq

description:
HML01
All_gene_expression.txt


title: 288c

description: RNA extracted from FFPE tissue


title: 288v

description: RNA extracted from FFPE tissue


title: HMS01 RNA-seq

description:
HMS01
All_gene_expression.txt


title: MATADOR_RNAseq_X29


title: LLS03 RNA-seq

description:
LLS03
All_gene_expression.txt


title: MATADOR_RNAseq_X291


title: LLS01 RNA-seq

description:
LLS01
All_gene_expression.txt


title: 287c

description: RNA extracted from FFPE tissue


title: LLS02 RNA-seq

description:
LLS02
All_gene_expression.txt


title: LLL03 RNA-seq

description:
LLL03
All_gene_expression.txt


title: 286v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X286


title: HLS03 RNA-seq

description:
HLS03
All_gene_expression.txt


title: LLL01 RNA-seq

description:
LLL01
All_gene_expression.txt


title: LLL02 RNA-seq

description:
LLL02
All_gene_expression.txt


title: MATADOR_RNAseq_X267


title: 286c

description: RNA extracted from FFPE tissue


title: HLS02 RNA-seq

description:
HLS02
All_gene_expression.txt


title: 246v

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_villus_5ppm Cr(VI) 90 days

value: 5ppm Cr(VI) 90 days


title: HLS01 RNA-seq

description:
HLS01
All_gene_expression.txt


title: HLL03 RNA-seq

description:
HLL03
All_gene_expression.txt

value: leaf


title: MATADOR_RNAseq_X259


title: 246c

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_crypt_5ppm Cr(VI) 90 days


title: HLL02 RNA-seq

description:
HLL02
All_gene_expression.txt

value: growth phase at the late stage of sucrose accumulation


title: LES02 RNA-seq

description:
LES02
All_gene_expression.txt

value: stem


title: 245c

description: RNA extracted from FFPE tissue


title: HLL01 RNA-seq

description:
HLL01
All_gene_expression.txt


title: LES03 RNA-seq

description:
LES03
All_gene_expression.txt


title: LES01 RNA-seq

description:
LES01
All_gene_expression.txt


title: LEL03 RNA-seq

description:
LEL03
All_gene_expression.txt


title: MATADOR_RNAseq_X227

value: Breast


title: LEL02 RNA-seq

description:
LEL02
All_gene_expression.txt


title: LEL01 RNA-seq

description:
LEL01
All_gene_expression.txt


title: MATADOR_RNAseq_X235

value: FFPE


title: HES03 RNA-seq

description:
HES03
All_gene_expression.txt


title: MATADOR_RNAseq_X221


title: 244c

description: RNA extracted from FFPE tissue


title: 243v

description: RNA extracted from FFPE tissue


title: HES02 RNA-seq

description:
HES02
All_gene_expression.txt


title: HES01 RNA-seq

description:
HES01
All_gene_expression.txt


title: 243c

description: RNA extracted from FFPE tissue


title: HEL03 RNA-seq

description:
HEL03
All_gene_expression.txt


title: MATADOR_RNAseq_X211


title: HEL02 RNA-seq

description:
HEL02
All_gene_expression.txt


title: MATADOR_RNAseq_X250


title: 245v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X208

value: 6 x AC dd


title: MATADOR_RNAseq_X193


title: MATADOR_RNAseq_X226


title: 244v

description: RNA extracted from FFPE tissue

value: villus


title: 210v

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_villus_1.4ppm Cr(VI) 7 days

value: 1.4ppm Cr(VI) 7 days


title: 241v

description: RNA extracted from FFPE tissue

value: wildtype


title: MATADOR_RNAseq_X15


title: 241c

description: RNA extracted from FFPE tissue


title: 210c

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_crypt_1.4ppm Cr(VI) 7 days


title: MATADOR_RNAseq_X212


title: HEL01 RNA-seq

description:
HEL01
All_gene_expression.txt


title: 209v

description: RNA extracted from FFPE tissue


title: Equus caballus_BAL fluid_I3

type: RNA

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

description:
I3
Equus caballus, I3_IAD
Sample of equine BAL fluid.

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%).

data_processing: Data processed with FeatureExtraction v9.5 and normalized using cyclic lowess by R 2.11.1 statistical software.

organism: Equus caballus

source_name: Equus caballus BAL fluid collected aseptically during endoscopy

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

extract_protocol: Extracted using the QiAgen RNeasy Mini Kit protocol for tissue samples.

value: BAL fluid

tag: diagnosis

value: IAD


title: MATADOR_RNAseq_X116


title: Equus caballus_BAL fluid_I4

description:
I4
Equus caballus, I4_IAD
Sample of equine BAL fluid.


title: MATADOR_RNAseq_X130


title: 208v

description: RNA extracted from FFPE tissue


title: Equus caballus_BAL fluid_I2

description:
I2
Equus caballus, I2_IAD
Sample of equine BAL fluid.


title: Equus caballus_BAL fluid_R8

description:
R8
Equus caballus, R8_RAO
Sample of equine BAL fluid.

value: RAO


title: Equus caballus_BAL fluid_I1

description:
I1
Equus caballus, I1_IAD
Sample of equine BAL fluid.


title: Equus caballus_BAL fluid_I5

description:
I5
Equus caballus, I5_IAD
Sample of equine BAL fluid.


title: MATADOR_RNAseq_X76


title: Equus caballus_BAL fluid_R7

description:
R7
Equus caballus, R7_RAO
Sample of equine BAL fluid.


title: MATADOR_RNAseq_X65


title: Equus caballus_BAL fluid_R6

description:
R6
Equus caballus, R6_RAO
Sample of equine BAL fluid.


title: 207v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X14

value: 6 x TAC


title: 208c

description: RNA extracted from FFPE tissue

value: crypt


title: Equus caballus_BAL fluid_R2

description:
R2
Equus caballus, R2_RAO
Sample of equine BAL fluid.


title: Equus caballus_BAL fluid_R5

description:
R5
Equus caballus, R5_RAO
Sample of equine BAL fluid.


title: 209c

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X549


title: 207c

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X528


title: 206v

description: RNA extracted from FFPE tissue


title: Equus caballus_BAL fluid_R4

description:
R4
Equus caballus, R4_RAO
Sample of equine BAL fluid.


title: Equus caballus_BAL fluid_R1

description:
R1
Equus caballus, R1_RAO
Sample of equine BAL fluid.


title: MATADOR_RNAseq_X524


title: Equus caballus_BAL fluid_R3

description:
R3
Equus caballus, R3_RAO
Sample of equine BAL fluid.


title: Equus caballus_BAL fluid_C6

description:
C6
Equus caballus, C6_CONTROL
Sample of equine BAL fluid.

value: Control


title: Equus caballus_BAL fluid_C5

description:
C5
Equus caballus, C5_CONTROL
Sample of equine BAL fluid.


title: 165v

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_villus_1.4ppm Cr(VI) 90 days

value: 1.4ppm Cr(VI) 90 days


title: Equus caballus_BAL fluid_C7

description:
C7
Equus caballus, C7_CONTROL
Sample of equine BAL fluid.


title: Equus caballus_BAL fluid_I10

description:
I10
Equus caballus, I10_IAD
Sample of equine BAL fluid.


title: Equus caballus_BAL fluid_I8

description:
I8
Equus caballus, I8_IAD
Sample of equine BAL fluid.


title: Equus caballus_BAL fluid_C2

description:
C2
Equus caballus, C2_CONTROL
Sample of equine BAL fluid.


title: MATADOR_RNAseq_X520


title: MATADOR_RNAseq_X514


title: MATADOR_RNAseq_X503


title: 165c

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_crypt_1.4ppm Cr(VI) 90 days


title: Equus caballus_BAL fluid_I9

description:
I9
Equus caballus, I9_IAD
Sample of equine BAL fluid.


title: Equus caballus_BAL fluid_C4

description:
C4
Equus caballus, C4_CONTROL
Sample of equine BAL fluid.


title: Equus caballus_BAL fluid_I7

description:
I7
Equus caballus, I7_IAD
Sample of equine BAL fluid.


title: Equus caballus_BAL fluid_C3

description:
C3
Equus caballus, C3_CONTROL
Sample of equine BAL fluid.


title: 164v

description: RNA extracted from FFPE tissue


title: Equus caballus_BAL fluid_I6

description:
I6
Equus caballus, I6_IAD
Sample of equine BAL fluid.


title: 206c

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X496


title: 164c

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X490


title: 163v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X485


title: TAC/Benzene rep2

city: Louisville

first: Igor

middle: N

last: Zelko

state: Kentucky

address: 302 E. Muhammad Ali Blvd, Cardiovascular Innovation Institute bld., Room 310

department: Medicine

institute: University of Louisville

data_processing:
Raw reads of the FASTQ files were processed and quality metrics were visualized using FastQC v 0.11.9
Alignment was performed using STAR version 020201 and the following parameters: --runMode genomeGenerate  --genomeDir $library/STAR/$read_length  --limitIObufferSize 1000000000  --runThreadN 16  --genomeFastaFiles $fasta_ucsc  --outFileNamePrefix $output_dir/  --sjdbGTFfile $gtf_ucsc  --sjdbOverhang $overhang  --limitBAMsortRAM 50000000000  --limitIObufferSize 1000000000  --outSAMtype BAM SortedByCoordinate
Differential expression analysis was perfomred using DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: raw counts for each gene are presented in comma delimited format "rawcounts.csv"

source_name: left ventricle and septum of heart

extract_protocol:
Total RNA was extracted from the hearts of mice using TRIzol kit (Thermo Fisher Scientific, MA, USA), and the purity of RNA was analyzed using NanoDrop One (ThermoScientific, MA, USA). RNA quality was measured by Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA) and samples with high RNA integrity were used for subsequent RNAseq analysis.
mRNA RNA-seq was performed by Novogene (California, U.S.A.) for poly-A mRNAs and sequenced with Illumina NovaSeq 6000 system (pair-end, 2 × 150 bp).

tag: Sex

value: male

tag: treatment 1

value: TAC

tag: treatment 2

value: Benzene

value: left ventricle and septum of heart


title: TAC/Benzene rep4


title: TAC/Air rep5

value: Air


title: TAC/Benzene rep6


title: TAC/Benzene rep5


title: TAC/Benzene rep3


title: TAC/Air rep6


title: TAC/Benzene rep1


title: 163c

description: RNA extracted from FFPE tissue


title: TAC/Air rep3


title: Equus caballus_BAL fluid_C1

description:
C1
Equus caballus, C1_CONTROL
Sample of equine BAL fluid.


title: TAC/Air rep4


title: MATADOR_RNAseq_X468

value: Breast

value: FFPE


title: Sham/Benzene rep6

value: Sham


title: MATADOR_RNAseq_X454

value: 6 x AC dd


title: TAC/Air rep1


title: 162c

description: RNA extracted from FFPE tissue

value: wildtype


title: TAC/Air rep2


title: 162v

description: RNA extracted from FFPE tissue

value: villus


title: Sham/Benzene rep3


title: Sham/Benzene rep5


title: Sham/Benzene rep4


title: MATADOR_RNAseq_X422


title: 161v

description: RNA extracted from FFPE tissue


title: Sham/Benzene rep2


title: 161c

description: RNA extracted from FFPE tissue


title: Sham/Benzene rep1


title: MATADOR_RNAseq_X407


title: MATADOR_RNAseq_X483


title: MATADOR_RNAseq_X397


title: 130v

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_villus_0.1ppm Cr(VI) 7 days

value: 0.1ppm Cr(VI) 7 days


title: 130c

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_crypt_0.1ppm Cr(VI) 7 days


title: Sham/Air rep3


title: MATADOR_RNAseq_X406

source_name: Primairy tumor before treatment FFPE


title: MATADOR_RNAseq_X396


title: Sham/Air rep5


title: Sham/Air rep6


title: 129v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X395


title: Sham/Air rep1


title: MATADOR_RNAseq_X385


title: 129c

description: RNA extracted from FFPE tissue


title: Atad3 nKO [Tania-09]

city: Miami

first: Tania

middle: D

last: Arguello

state: Florida

address: 1420 NW 9TH AVE

department: Neurology

institute: University of Miami

data_processing:
Base calling and demultiplexing were performed in BaseSpace® using default bcl2fastq pair end data.
fastq files were aligned against the mouse reference genome UCSC mm10 using STAR2.6.1a BaseSpace app.
Salmon Quantification version 0.11.2.
Expression data was normalized using the median of ratios method, DESeq2.
Genome_build: Mus_musculus (UCSC mm10)
Supplementary_files_format_and_content: .sf quantification genes and transcripts, abundance in terms of Transcripts Per Million (TPM) and estimated number of reads (NumReads).
Supplementary_files_format_and_content: genes.NormalizedHitsPerSample.tsv: Genes normalized hits per sample.

source_name: cortex tissue

growth_protocol: 2.5-month-old Atad3 nKO male mice and control littermates were transcardially perfused with ice-cold PBS.

extract_protocol:
Total RNA extraction was done using TRIZOL, samples were treated with Turbo TM DNase (Invitrogen) as per manufacturer’s instructions.
RNA-Seq libraries were prepared using Illumina TruSeq Stranded Total RNA Library Prep Gold with a modified RNA fragmentation time of 6 minutes.

treatment_protocol: Cortex tissues were dissected and fast frozen.

tag: background strain

value: Atad3 nKO

value: Male

tag: age

value: 2.5 months

value: Cortex


title: Atad3 nKO [Tania-10]


title: Atad3 nKO [Tania-08]


title: Atad3 nKO [Tania-07]


title: Atad3 nKO [Tania-06]


title: 128c

description: RNA extracted from FFPE tissue

value: crypt


title: MATADOR_RNAseq_X362


title: Atad3 Control [Tania-05]

value: Atad3 control


title: Atad3 Control [Tania-04]


title: 127c

description: RNA extracted from FFPE tissue


title: Atad3 Control [Tania-03]


title: Atad3 Control [Tania-02]


title: Sham/Air rep4

value: male


title: MATADOR_RNAseq_X353


title: Sham/Air rep2


title: 128v

description: RNA extracted from FFPE tissue


title: 126v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X352


title: MATADOR_RNAseq_X345


title: MATADOR_RNAseq_X342

value: 6 x TAC


title: Atad3 Control [Tania-01]


title: MATADOR_RNAseq_X328


title: EN 4DAP rep3

city: Tucson

first: Ramin

last: Yadegari

state: Arizona

address: 1140 E. South Campus Dr.

department: Plant Sciences

institute: University of Arizona

data_processing:
Illumina HiSeq 2500 System
Because of a failure of two samples within the first bio-replicate set, all samples for this bio-replicate were sequenced a second time from the library construction step through RNA-Seq, and the resulting total reads from both runs were combined for the subsequent analyses.
Raw reads were trimmed using the Trimmomatic program to remove adapter sequences and low-quality bases.
Trimmed and high quality reads were aligned to the maize B73 reference genome using TopHat v2.0.9. Intron length was set to 30 to 8000 nt with maximum number of mismatches per read set to 3 (-i 30 -I 8000 -N 3).
Raw count table of exonic reads built by BEDTools v2.17.0 with the exon coordinates (GTF, EnsemblPlants) were used in the software edgeR, reported as counts per million mapped reads (CPM), and filtered with a lower limit of ≥0.5 in at least three of the 18 samples.
The filtered raw count table was further normalized with the trimmed mean of M-values (TMM) method across the 18 samples, and transformed to CPM table using edgeR.
Genome_build: the maize B73 reference genome (AGPv3.20)
Supplementary_files_format_and_content: Tab-delimited text files include CPM values of gene for all 18 samples.

organism: Zea mays

source_name: Kernel

growth_protocol: Maize (Zea mays) inbred line B73 plants were grown in a greenhouse with a cycle of 16 h of light at ~30°C and 8 h of dark at ~25°C at the University of Arizona during June-October 2012. The unfertilized or self-pollinated ears were harvested 0 to 4 days after pollination for laser-capture microdissection of the RNA. The tissue sections for each biological replicate of each stage of endosperm development and the embryo (samples) were pooled from multiple kernels of a single ear.

extract_protocol:
Total RNA was isolated using the Arcturus PicoPure RNA Isolation kit (Applied Biosystems), treated with TURBO DNase (Ambion), and purified with the Arcturus PicoPure kit again. RNA reverse transcription with oligo(dT) and random primers, second-strand cDNA synthesis, purification, cDNA amplification and second-purification were using the Nugen ovation RNA-Seq kit v2 (Nugen), XP-beads (Beckman Coulter) and the MinElute PCR Purification kit (Qiagen) following the manufacturer’s instructions. In RNA purification of the central cell/early endosperm stages (0-2 DAP) and the embryo (4 DAP), we repeatedly found indications of a carryover product(s) that caused an overestimation of RNA measurements using standard procedures. Instead, we used the height of the 18S-rRNA band from the Bioanalyzer 2100 for measuring the RNA concentration. In all these cases, ~5μg of amplified cDNA was obtained from ~10 ng of captured RNA.
The cDNA paired-end libraries construction and quality test were prepared using TruSeq DNA Sample Preparation kit v2 (Illumina) with around 1μg amplified cDNA by following the manufacturer’s suggested procedures.

value: Endosperm

tag: developmental stage

value: 4 DAP


title: EN 3DAP rep3

value: 3 DAP


title: EMB 4DAP rep1

value: Embryo


title: EN 4DAP rep1


title: EMB 4DAP rep3


title: EN 4DAP rep2


title: EMB 4DAP rep2


title: MATADOR_RNAseq_X327

value: Breast

value: FFPE


title: MATADOR_RNAseq_X316

value: 6 x AC dd


title: 85v

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_villus_0.1ppm Cr(VI) 90 days

value: villus

value: 0.1ppm Cr(VI) 90 days

value: wildtype


title: EN 2DAP rep2

value: 2 DAP


title: EN 2DAP rep3


title: 85c

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_crypt_0.1ppm Cr(VI) 90 days


title: MATADOR_RNAseq_X315


title: EN 2DAP rep1


title: EN 1DAP rep3

value: 1 DAP


title: 84c

description: RNA extracted from FFPE tissue


title: 90v

description: RNA extracted from FFPE tissue

value: 0.1ppm Cr(VI) 7 days


title: 126c

description: RNA extracted from FFPE tissue

value: crypt


title: 90c

description: RNA extracted from FFPE tissue


title: EN 1DAP rep1


title: MATADOR_RNAseq_X308


title: EN 3DAP rep1


title: EN 3DAP rep2


title: EN 1DAP rep2


title: EN 0DAP rep3

value: 0 DAP


title: 83v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X307


title: EN 0DAP rep2


title: MATADOR_RNAseq_X284


title: MATADOR_RNAseq_X270


title: 82v

description: RNA extracted from FFPE tissue


title: EN 0DAP rep1


title: 84v

description: RNA extracted from FFPE tissue


title: 82c

description: RNA extracted from FFPE tissue


title: NR32-1Fast1

city: Bethesda

first: Komudi

last: Singh

address: Building 10

institute: NIH

description:
Arm1/NR
S80

data_processing:
QC performed usinf fastQC
Trimming applied using Trimmomatic
Alignment performed using Hisat2
Quantification with StringTie
Genome_build: hg38
Supplementary_files_format_and_content: gene expression result (FPKM)

extract_protocol:
Primary peripheral blood mononuclear cells (PBMCs) were isolated from human blood by density centrifugation using Lymphocyte Separation Medium (MP Biomedicals). Monocytes were negatively selected (monocytes isolation kit - Miltenyi Biotec). Monocytes were then plated 0.15x106/well onto 96-well plate (for ELISA) or 106/well onto 12-well plates (for RNA isolation or Western blotting) in RPMI media supplemented with 10% human serum. Elutriated monocytes were obtained from blood bank of NIH.
Libraries were prepared using TruSeq stranded mRNA kit (Illumina) and sequenced in a HISeq 3000 (Illumina) by the DNA Sequencing

value: M

tag: bmi


title: NR25-1Fast0

description:
Arm1/NR
S77


title: NR25-1Fast1

description:
Arm1/NR
S78


title: NR24-1Fast1

description:
Arm1/NR
S76


title: MATADOR_RNAseq_X269


title: NR32-1Fast0

description:
Arm1/NR
S79


title: NR24-1Fast0

description:
Arm1/NR
S75


title: 81v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X253

value: 6 x TAC


title: 81c

description: RNA extracted from FFPE tissue


title: NR23-1Fast1

description:
Arm1/NR
S74

value: F


title: MATADOR_RNAseq_X247


title: NR23-1Fast0

description:
Arm1/NR
S73


title: MATADOR_RNAseq_X234


title: 83c

description: RNA extracted from FFPE tissue


title: 50v

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_villus_0ppm Cr(VI) 7 days

value: 0ppm Cr(VI) 7 days


title: NR22-1Fast1

description:
Arm1/NR
S72


title: NR19-1Fast0

description:
Arm1/Placebo
S9


title: MATADOR_RNAseq_X229


title: 50c

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_crypt_0ppm Cr(VI) 7 days


title: NR18-1Fed0

description:
Arm1/Placebo
S7


title: NR18-1Fed1

description:
Arm1/Placebo
S8


title: 49v

description: RNA extracted from FFPE tissue


title: NR16-1Fast1

description:
Arm1/NR
S70


title: MATADOR_RNAseq_X205


title: NR16-1Fast0

description:
Arm1/NR
S69


title: 49c

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X203


title: 48v

description: RNA extracted from FFPE tissue


title: NR14-1Fast1

description:
Arm1/NR
S68


title: 48c

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X191


title: NR14-1Fast0

description:
Arm1/NR
S67


title: MATADOR_RNAseq_X184


title: NR13-1Fast0

description:
Arm1/NR
S65


title: NR13-1Fast1

description:
Arm1/NR
S66


title: 47v

description: RNA extracted from FFPE tissue


title: NR22-1Fast0

description:
Arm1/NR
S71


title: IP

city: xi'an

first: 昕

last: 王

address: yanta west road 76

institute: xi'an jiaotong university

description: DN3 and DN4 cells from the thymic of wild-type mice

library_source: genomic

data_processing:
Raw sequencing data was first filtered by SOAPnuke (v1.5.6)
ChIP-seq reads were aligned to the mm10 genome assembly using SOAPaligner/soap2(Version 2.21t) with default parameters
The MACS2 (Version:2.1.2)  software was used for peak calling.
The Manorm (v1.1) software was used for differential gene analysis
The MEME (v4.10.1) was used for motifs analysis
Genome_build: mm10
Supplementary_files_format_and_content: peak wig files

molecule: genomic DNA

source_name: DN cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The library products corresponding to 100-300 bps were enriched, quantified and finally sequenced on SE150 model.

treatment_protocol: Lineage(CD4/CD8/TCRb/TCRd/NK1.1/CD19/CD11b/CD11c)-CD44-CD25+ DN3 and CD44-CD25- DN4 thymocytes were sorted from the thymic of wild-type mice

value: thymus

tag: genotype/variation

value: wild type


title: NR31-2Fed1

description:
Arm1/Placebo
S64


title: NR31-2Fed0

description:
Arm1/Placebo
S63


title: MATADOR_RNAseq_X158

value: Breast


title: 47c

description: RNA extracted from FFPE tissue


title: NR29-2Fed1

description:
Arm1/Placebo
S62


title: Input


title: 46v

description: RNA extracted from FFPE tissue


title: NR29-2Fed0

description:
Arm1/Placebo
S61


title: DN4 thymocytes, KO1

data_processing:
Illumina Hiseq 2000 sequencer software used for basecalling.
The double-stranded cDNA library was finished through PCR enrichment and size selection. The prepared cDNA library was sequenced with the Illumina Hiseq 2000 sequencer (Illumina HiSeq 2000 v4 Single-Read 50 bp) after pooling according to its expected data volume and effective concentration.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: DN4 thymocytes

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration was detected by the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen). After quality control by RNase free agarose gel and Agilent 2100 (Agilent Technologies, Palo Alto, CA, USA), RNA-Seq libraries were prepared using 200ng total RNA with the TruSeq RNA sample prep kit according to manufacturer’s instructions (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lineage(CD4/CD8/TCRb/TCRd/NK1.1/CD19/CD11b/CD11c)-CD44-CD25- DN4 thymocytes were sorted from the thymuses of LckCre+Zfp335f/f mice and wild-type littermates

value: Zfp335 KO

tag: cell type

value: DN4 thymocytes


title: DN4 thymocytes, KO2


title: 46c

description: RNA extracted from FFPE tissue


title: DN4 thymocytes, WT2

value: WT


title: 8c

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_crypt_0ppm Cr(VI) 90 days

value: 0ppm Cr(VI) 90 days


title: input control Pol2, TAF1, YY1 rep2

city: Huntsville

first: Eric

middle: M

last: Mendenhall

state: AL

address: 601 Genome Way Northwest

institute: HudsonAlpha Institute

description:
SL88940
ChIPBS (ChIP followed by bisulfite sequencing)

data_processing:
Reads were trimmed (2-3 bp from ends) using trim galore (version 0.3.7), powered by cutadapt to trim adaptor sequences for QC purpose
ChIPBS reads were processed with Bismark(bismark-0.11.1) pipeline using Bowtie2(bowtie-2-2.1.0) aligner
Deduplication and PCR duplicates removal was performed using deduplicate_bismark program
Methylation extraction from deduplicated bam files, in CpG context, was performed using bismark_methylation_extractor program
Genome_build: hg19
Supplementary_files_format_and_content: .bedGraph - [Chromosome number, start position, stop position, dataValue], .cov - [Chromosome number, start position, stop position, methylation percent, methylated reads, unmethylated reads]

source_name: HepG2 cell

growth_protocol: HepG2 were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell)

extract_protocol:
Cross-linked chromatin was immunoprecipitated with an antibody. The Protein:DNA crosslinks were then reversed and the DNA fragments were recovered and sequenced. Please see protocol notes below and go to http://hudsonalpha.org/myers-lab/protocols for the most current version of the protocol. The eluted DNA was followed by bisulfite conversion using the EZ DNA Methylation-Gold Kit from Zymo according to manufacturer’s instructions.
Illumina Single End for ChIPBS

tag: cell line

tag: chip antibody


title: JunD rep2

description:
SL94837
ChIPBS (ChIP followed by bisulfite sequencing)

value: JunD


title: YY1 rep2

description:
SL88937
ChIPBS (ChIP followed by bisulfite sequencing)


title: 7v

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_villus_0ppm Cr(VI) 90 days

value: villus

tag: genotype

value: wildtype


title: DN4 thymocytes, WT1

tag: tissue


title: NR28-2Fed0

description:
Arm1/Placebo
S59


title: Pol2 rep2

description:
SL88936
ChIPBS (ChIP followed by bisulfite sequencing)


title: NR27-2Fed1

description:
Arm1/Placebo
S58


title: TAF1 rep2

description:
SL88934
ChIPBS (ChIP followed by bisulfite sequencing)


title: 7c

description: RNA extracted from FFPE tissue


title: 6v

description: RNA extracted from FFPE tissue


title: YY1 rep1

description:
SL83433
ChIPBS (ChIP followed by bisulfite sequencing)


title: input control JunD rep2

description:
SL94838
ChIPBS (ChIP followed by bisulfite sequencing)


title: s2-P0-2-250 K562 Cells SF3B1 WT -- Library --  Day 0 (250bp reads)

city: Seattle

first: Khrystyna

middle: Dilai

last: North

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Research Center

data_processing:
Trim reads using cutadapt
Merge reads using FLASH
Map using bowtie2 --very sensitive
Filter reads for q>1
Genome_build: Intron library provided with paper
Supplementary_files_format_and_content: .csv, raw counts

source_name: K562 cells transduced with synthetic library

growth_protocol: IMDM growth media with 10%FBS

extract_protocol:
DNeasy Blood and Tissue Kit Quiagen
Introns were amplifed first with TK specific primers then Illumana specific pr[imers were added.

treatment_protocol: ganciclovir if specified

tag: sf3b1 mutation

tag: tretment

tag: miseq read length


title: s2-P0-1-250 K562 Cells SF3B1 WT -- Library --  Day 0 (250bp reads)


title: s2-E0-3-250 K562 Cells SF3B1 K700E -- Library --  Day 0 (250bp reads)


title: input control TAF1, YY1 rep1

description:
SL81124
ChIPBS (ChIP followed by bisulfite sequencing)


title: NR28-1Fed1

description:
Arm1/Placebo
S56


title: NR28-2Fed1

description:
Arm1/Placebo
S60


title: NR31-1Fed1

description:
Arm1/Placebo
S55


title: 6c

description: RNA extracted from FFPE tissue

tag: strain

tag: treatment


title: 5v

description: RNA extracted from FFPE tissue


title: s2-E0-2-250 K562 Cells SF3B1 K700E -- Library --  Day 0 (250bp reads)


title: TAF1 rep1

description:
SL81122
ChIPBS (ChIP followed by bisulfite sequencing)


title: NR31-1Fed0

description:
Arm1/Placebo
S54

tag: Sex


title: input control Pol2 rep1

description:
SL68324
ChIPBS (ChIP followed by bisulfite sequencing)


title: NR31-1Fast1

description:
Arm1/Placebo
S53


title: 5c

description: RNA extracted from FFPE tissue


title: s2-E0-1-250 K562 Cells SF3B1 K700E -- Library --  Day 0 (250bp reads)


title: NR18-1Fast1

description:
Arm1/Placebo
S6


title: 3v

description: RNA extracted from FFPE tissue


title: s2-P0-3-250 K562 Cells SF3B1 WT -- Library --  Day 0 (250bp reads)


title: NR27-2Fed0

description:
Arm1/Placebo
S57


title: NR31-1Fast0

description:
Arm1/Placebo
S52


title: s2-P0-3-150 K562 Cells SF3B1 WT -- Library --  Day 0 (150bp reads)


title: ZBTB33 rep1

description:
SL68322
ChIPBS (ChIP followed by bisulfite sequencing)


title: s2-P0-2-150 K562 Cells SF3B1 WT -- Library --  Day 0 (150bp reads)


title: NR20-2Fed1

description:
Arm1/Placebo
S51


title: Pol2 rep1

description:
SL68320
ChIPBS (ChIP followed by bisulfite sequencing)


title: s2-P0-1-150 K562 Cells SF3B1 WT -- Library --  Day 0 (150bp reads)


title: NR20-2Fed0

description:
Arm1/Placebo
S50


title: s2-E0-3-150 K562 Cells SF3B1 K700E -- Library --  Day 0 (150bp reads)


title: JunD rep1

description:
SL60584
ChIPBS (ChIP followed by bisulfite sequencing)


title: s2-E0-2-150 K562 Cells SF3B1 K700E -- Library --  Day 0 (150bp reads)


title: NR18-1Fast0

description:
Arm1/Placebo
S5


title: HepG2 WGBS rep2

description:
Re-analysis of:
GSM2308631
Raw files:
ENCFF706BRZ ENCFF220NMH
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR881XOU/

data_processing:
Fastq files were downloaded from ENCODE portal (https://www.encodeproject.org/) for 2 replicates
Reads were trimmed(3-4bp from ends) using trim galore(version 0.3.7), powered by cutadapt to trim adaptor sequences for QC purpose
WGBS reads were processed with Bismark(bismark-0.11.1) pipeline using Bowtie2(bowtie-2-2.1.0) aligner
Deduplication and PCR duplicates removal was performed using deduplicate_bismark program
Methylation extraction from deduplicated bam files, in CpG context, was performed using bismark_methylation_extractor program
Genome_build: hg19
Supplementary_files_format_and_content: .bedGraph - [Chromosome number, start position, stop position, dataValue], .cov - [Chromosome number, start position, stop position, methylation percent, methylated reads, unmethylated reads]

source_name: HepG2 cells

extract_protocol:
Genomic DNA from HepG2 cells was extracted with the Qiagen DNeasy Blood and Tissue Kit following the manufacturer’s instructions. Extracted DNA was converted with  EZ DNA Methylation-Gold Kit from Zymo.  The extracted DNA was followed by bisulfite conversion using the EZ DNA Methylation-Gold Kit from Zymo according to manufacturer’s instructions.
Illumina Paired End (125 PE) for WGBS


title: NR19-2Fed1

description:
Arm1/Placebo
S49


title: NR19-2Fed0

description:
Arm1/Placebo
S48


title: s2-P8G-3-250 K562 Cells SF3B1 WT -- Library -- Day 8 GCV  (250bp reads)

value: ganciclovir (100ug/mL)


title: Experimental_RNA_Rep4

city: NAN JING

first: Kai

last: Xie

state: NAN JING

address: JIANG SU

institute: NAN JING MEDICAL UNIVERSITY

hyb_protocol: Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

scan_protocol: The hybridized arrays were washed, fixed and scanned with 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.

label: biotin

source_name: preoperative ESCC patients  serum sample

label_protocol: After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

growth_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications

extract_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

treatment_protocol: Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

value: serum

tag: disease state

value: preoperative ESCC patients


title: s2-E0-1-150 K562 Cells SF3B1 K700E -- Library --  Day 0 (150bp reads)


title: Experimental_RNA_Rep2


title: Experimental_RNA_Rep1


title: NR18-2Fed0

description:
Arm1/Placebo
S46

value: M


title: Experimental_RNA_Rep3


title: NR18-2Fed1

description:
Arm1/Placebo
S47


title: 3c

description: RNA extracted from FFPE tissue

value: crypt


title: NR15-2Fed1

description:
Arm1/Placebo
S45

value: F


title: s2-P8G-2-250 K562 Cells SF3B1 WT -- Library -- Day 8 GCV  (250bp reads)


title: s2-E8G-3-250 K562 Cells SF3B1 K700E -- Library -- Day 8 GCV  (250bp reads)


title: NR15-2Fed0

description:
Arm1/Placebo
S44


title: HepG2 WGBS rep1

description:
Re-analysis of:
GSM2308630
Raw files:
ENCFF406GDR ENCFF508BUS
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR881XOU/


title: NR32-1Fed1

description:
Arm1/NR
S43


title: LLL01 Other: degradome-seq

description:
LLL01
degradome.txt

data_processing:
Library strategy: degradome-seq
For RNA-seq, raw data were curated by removing reads containing adapters, and ploy-N and low-quality reads.The high-quality reads were then assembled by Trinity.Unigenes were annotated based on NR, Pfam, KOG/COG/eggNOG , Swiss-Prot , KEGG  and GO.
For miRNA-seq, raw data were quality-checked, and reads with adapters, polyA and low-quality reads (reads containing Ns or with more than one base Q＜20) were removed. The high-quality clean reads were then aligned with small RNAs in GeneBank database (Release 209.0) and Rfam database (Release 11.0) to identify and remove rRNA, snoRNA, snRNA, tRNA, and scRNA. The remaining clean tags were searched against miRBase (Release 22) to identify known miRNAs. The unannotated reads were used for identifying novel miRNA candidates using software mirDeep2. The candidate target genes of the known and novel miRNAs were predicted using software patmatch (Version 1.2) with default parameters.
For degradome-seq, reads with adapters, and low-quality reads were filtered from raw data to obtain clean reads. These clean reads were aligned with Rfam and Genebank database to remove rRNAs, tRNAs, snoRNAs and repeats. The remaining reads were mapped to the transcriptome data (this study) and the potentially cleaved targets were identified by CleaveLand pipeline.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw counts for every miRNA and every sample
Supplementary_files_format_and_content: Matrix table with raw tags for every cleaved mRNA and every sample

source_name: tissue

value: leaf

tag: growth phase

value: growth phase at the middle stage of sucrose accumulation


title: LLS01 Other: degradome-seq

description:
LLS01
degradome.txt

value: stem


title: s2-E8G-2-250 K562 Cells SF3B1 K700E -- Library -- Day 8 GCV  (250bp reads)


title: BM MSC, diagnosis, 12

city: Toulouse

first: Lea

last: Lemaitre

address: IUCT, 1 Av. Irene Joliot-Curie

department: Hematology

country: France

institute: IUCT

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Cartridge Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneShip Scanner GCS3000.

data_processing: The data were analyzed with R/Bioconductor

source_name: BM MSC after 21 days in cultured, from diagnosis patient 4043

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MSCs were obtained from unprocessed BM with red blood lysis and seeded at 5×10^4 cells/cm2 in a 150cm2 flask with complete medium MEMα (minimum essential medium-α, Life Technologies, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (Sigma F7524, France) and 0,5% of ciprofloxacin (Bayer, Puteaux, France). For all MSC cultures, the medium was renewed/replaced twice a week (maintained at 37°C and 5% CO2) until cells were confluent (21 days). MSC were then harvested with trypsine + EDTA.

extract_protocol: Then RNA extraction of total RNA was performed according to the manufacturer's instructions with Qiagen kit.

treatment_protocol: No treatment was used

tag: tumor type

value: Multiple myeloma

value: mesenchymal stromal cell

tag: Stage

value: Diagnosis

tag: number patient


title: s2-P8G-1-250 K562 Cells SF3B1 WT -- Library -- Day 8 GCV  (250bp reads)

value: WT


title: BM MSC, diagnosis, 10

source_name: BM MSC after 21 days in cultured, from diagnosis patient 3210


title: Control_RNA_Rep3

source_name: normal healthy serum sample

value: healthy


title: Control_RNA_Rep4


title: BM MSC, diagnosis, 11

source_name: BM MSC after 21 days in cultured, from diagnosis patient 3871


title: BM MSC, diagnosis, 9

source_name: BM MSC after 21 days in cultured, from diagnosis patient 3151


title: Control_RNA_Rep1


title: Control_RNA_Rep2


title: BM MSC, diagnosis, 7

source_name: BM MSC after 21 days in cultured, from diagnosis patient 1390


title: HLS01 Other: degradome-seq

description:
HLS01
degradome.txt


title: NR32-1Fed0

description:
Arm1/NR
S42

tag: bmi

tag: age


title: BM MSC, diagnosis, 8

source_name: BM MSC after 21 days in cultured, from diagnosis patient 2406

tag: cell type


title: NR25-1Fed1

description:
Arm1/NR
S41


title: s2-P8G-3-150 K562 Cells SF3B1 WT -- Library -- Day 8 GCV  (150bp reads)


title: HLL01 Other: degradome-seq

description:
HLL01
degradome.txt


title: NR25-1Fed0

description:
Arm1/NR
S40


title: s2-E8G-1-250 K562 Cells SF3B1 K700E -- Library -- Day 8 GCV (250bp reads)


title: s2-E8G-3-150 K562 Cells SF3B1 K700E -- Library -- Day 8 GCV  (150bp reads)


title: NR15-1Fed1

description:
Arm1/Placebo
S4


title: HES01 Other: degradome-seq

description:
HES01
degradome.txt

value: growth phase at the early stage of sucrose accumulation


title: LEL01 Other: degradome-seq

description:
LEL01
degradome.txt


title: s2-P8G-1-150 K562 Cells SF3B1 WT -- Library -- Day 8 GCV  (150bp reads)


title: NR24-1Fed1

description:
Arm1/NR
S39


title: s2-E8G-2-150 K562 Cells SF3B1 K700E -- Library -- Day 8 GCV  (150bp reads)


title: LES01 Other: degradome-seq

description:
LES01
degradome.txt


title: HEL01 Other: degradome-seq

description:
HEL01
degradome.txt


title: NR24-1Fed0

description:
Arm1/NR
S38


title: s2-E8G-1-150 K562 Cells SF3B1 K700E -- Library -- Day 8 GCV (150bp reads)


title: 42_jug_24hr

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

data_processing:
We removed the sequencing adapters using cutadapt (v. 2.8) and the sequences indicated by the manufacturer (Illumina, Inc, San Diego, CA). Next, we aligned the sequences to the cattle genome (Bos_taurus.ARS-UCD1.2.99) obtained from the Ensembl database using hisat2 (v. 2.2.0 [9]). Using samtools (v. 1.10) , we filtered the alignment to remove unmapped reads, secondary alignments, alignments whose reads failed quality control, and duplicates. We then utilized biobambam2 (v. 2.0.95) to mark and eliminate duplicates.
We used featureCounts (subread v. 2.0.1) to count the fragments that matched to the Ensembl cattle annotation gene (Bos_taurus.ARS-UCD1.2.103). Genes annotated as protein coding, long non-coding RNA and pseudogene were retained. Following the calculation of counts per million (CPM) and reads per million per kilobase (FPKM) we retained genes that presented FPKM and CPM greater than one in five or more samples.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: tab delimited file containing the raw fragment counts prior to filtering for lowly expressed genes

organism: Bos taurus

source_name: Peripheral white blood cells

extract_protocol:
Total RNA was extracted from peripheral white blood cells of heifers using TRIzol reagent according to the manufacturer's specifications.
Libraries were prepared by the Virginia Tech Genomic Sequencing Center, with approximately 500 ng of total RNA as input material for each of the samples, using Illumina's TruSeq stranded mRNA library preparation kit.

tag: source

value: Jugular Vein

value: Peripheral white blood cells

tag: heifer id

tag: storage time

value: 24 hours


title: PL_K662 Cells SF3B1 WT_Mini Library_Day 6  (150bp)

description: pilot-PL

extract_protocol:
DNeasy Blood and Tissue Kit Quiagen
Introns were amplifed first with TK specific primers then Illumana specific primers were added.

tag: cell line

tag: sf3b1 mutation


title: EL_K662 Cells SF3B1 K700E_Mini Library_Day 6 (150bp)

description: pilot-EL

tag: tretment


title: BM MSC, remission, 7

source_name: BM MSC after 21 days in cultured, from remission patient 6969-R9

value: Complete Remission


title: BM MSC, early relapse, 2

source_name: BM MSC after 21 days in cultured, from early relapse patient 6961-C2

value: Early relapse


title: RLG_K662 Cells SF3B1 WT_Mini Library_Day 6 GCV (150bp)

description: pilot-PLG

value: ganciclovir (100ug/mL)


title: NR22-1Fed1

description:
Arm1/NR
S35


title: BM MSC, early relapse, 9

source_name: BM MSC after 21 days in cultured, from early relapse patient 6643-C10


title: NR23-1Fed0

description:
Arm1/NR
S36


title: 39_jug_3hr

tag: tissue

value: 3 hours


title: 40_jug_6hr

value: 6 hours


title: NR16-1Fed1

description:
Arm1/NR
S33

value: F


title: 38_jug_1hr

value: 1 hour


title: BM MSC, remission, 8

source_name: BM MSC after 21 days in cultured, from remission patient 6221-R11


title: BM MSC, early relapse, 3

source_name: BM MSC after 21 days in cultured, from early relapse patient 9559-C3


title: BM MSC, early relapse, 6

source_name: BM MSC after 21 days in cultured, from early relapse patient 6659-C7


title: NR23-1Fed1

description:
Arm1/NR
S37


title: HLTE_A23_uninfected

city: Hannover

first: Frank

last: Pessler

address: Feodor-Lynen-Str. 7-9

department: Experimental Infection Research

country: Germany

institute: Center for Experimental and Clinical Infection Research GmbH

data_processing:
Large sets of high‐throughput sequencing reads were mapped against the Homo sapiens hg38 reference genome via STAR 2.7.3a tool.
DESeq2 was used to normalize the counts of each gene to account for differences in sequencing depth and low count variability. The DESeq2 normalization metric is based on the median of ratios method.
Following normalization, DESeq2 was run in a pairwise manner, identifying significantly differentially expressed genes with higher levels of expression in the unstimulated group in comparison to the stimulated group of both WT and KO cells.
Genome_build: human reference genome (hg19, GRCh38)
Supplementary_files_format_and_content: normalized count csv file

source_name: lung

growth_protocol: HLTEs were cultured in RPMI medium without any supplement at 37°C, 5% CO2 for overnight

extract_protocol:
HLTE tissue were snap frozen in liquid nitrogen and stored at -80C. Qiagen miRNeasy kit was used to extract total RNA.
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).
The RNA sequencing library was generated from 100 ng total RNA using NEBNext® Single Cell/Low Input RNA Library to manufacture´s protocols. The libraries were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit (100 cycles, paired end run 2x 50 bp) with an average of 5 x107 reads per RNA sample.

treatment_protocol: For IAV, infection medium containing 2.0 x 105 ffu/ml in RPMI medium was added to a 24 well plate, placing one HLTE piece per well. For BCG, Infection medium containing 5X106 CFU/ml was prepared and HLTEs were subjected to infection in a 24 well plate. For PA, infection medium was prepared containing 1x108 CFU/ml in RPMI medium. HLTEs were incubated in 24 well plates for 2 h at 37°C. After infection, HLTEs were washed and incubated in RPMI medium containing 50 μg/ml gentamycin.

tag: infection group

value: Uninfected

tag: patient number


title: 41_jug_8hr

value: 8 hours


title: BM MSC, early relapse, 4

source_name: BM MSC after 21 days in cultured, from early relapse patient 4618-C4

value: Multiple myeloma

value: mesenchymal stromal cell


title: BM MSC, early relapse, 1

source_name: BM MSC after 21 days in cultured, from early relapse patient 5258-C1


title: NR22-1Fed0

description:
Arm1/NR
S34

tag: Sex


title: HLTE_A23_IAV infection

value: Influenza A virus (IAV)


title: BM MSC, remission, 9

source_name: BM MSC after 21 days in cultured, from remission patient 14474-R10


title: BM MSC, early relapse, 5

source_name: BM MSC after 21 days in cultured, from early relapse patient 13745-C6


title: 36_jug_24hr


title: ELG_K662 Cells SF3B1 K700E_Mini Library_Day 6 GCV (150bp)

description: pilot-ELG

source_name: K562 cells transduced with synthetic library


title: NR14-1Fed1

description:
Arm1/NR
S31


title: NR14-1Fed0

description:
Arm1/NR
S30


title: 35_jug_8hr


title: 37_tail

value: Coccygeal Vein


title: 34_jug_6hr


title: NR15-1Fed0

description:
Arm1/Placebo
S3


title: HLTE_A23_BCG infection

value: Mycobacterium bovis (BCG)


title: NR13-1Fed1

description:
Arm1/NR
S29

value: M


title: 33_jug_3hr

value: Jugular Vein

value: Peripheral white blood cells


title: HLTE_A23_PA infection

value: Pseudomonas aeruginosa (PA)


title: HLTE_A22_uninfected


title: HLTE_A22_IAV infection


title: 32_jug_1hr


title: NR13-1Fed0

description:
Arm1/NR
S28


title: HLTE_A22_PA infection


title: NR29-1Fed1

description:
Arm1/Placebo
S27


title: HLTE_A22_BCG infection


title: 30_jug_24hr

value: 24 hours


title: input control JunD rep1

description:
SL60586
ChIPBS (ChIP followed by bisulfite sequencing)

source_name: HepG2 cell

tag: chip antibody


title: BM MSC, remission, 10

source_name: BM MSC after 21 days in cultured, from remission patient 13104-R12

tag: tumor type

value: Complete Remission


title: 29_jug_8hr


title: BM MSC, early relapse, 8

source_name: BM MSC after 21 days in cultured, from early relapse patient 12571-C9

tag: Stage

value: Early relapse


title: NR29-1Fast1

description:
Arm1/Placebo
S25


title: NR29-1Fed0

description:
Arm1/Placebo
S26


title: HLTE_A21_uninfected


title: BM MSC, healthy donor, 8

source_name: BM MSC after 21 days in cultured, from healthy donor MOS8

value: Healthy donor

value: Healthy

tag: number patient


title: HLTE_A21_IAV infection


title: HLTE_A21_PA infection


title: BM MSC, healthy donor, 10

source_name: BM MSC after 21 days in cultured, from healthy donor VAMST


title: BM MSC, healthy donor, 9

source_name: BM MSC after 21 days in cultured, from healthy donor MOS9


title: BM MSC, healthy donor, 7

source_name: BM MSC after 21 days in cultured, from healthy donor MOS7


title: NR28-1Fed0

description:
Arm1/Placebo
S23

tag: bmi


title: NR29-1Fast0

description:
Arm1/Placebo
S24

tag: age


title: 27_jug_3hr

source_name: Peripheral white blood cells

value: 3 hours


title: 31_tail

value: 1 hour


title: HLTE_A21_BCG infection


title: BM MSC, healthy donor, 6

source_name: BM MSC after 21 days in cultured, from healthy donor MOS6

tag: cell type


title: 26_jug_1hr

tag: source


title: NR28-1Fast1

description:
Arm1/Placebo
S22


title: BM MSC, healthy donor, 4

source_name: BM MSC after 21 days in cultured, from healthy donor MOS4


title: BM MSC, healthy donor, 3

source_name: BM MSC after 21 days in cultured, from healthy donor MOS3


title: HLTE_A20_uninfected

source_name: lung

value: Uninfected


title: 28_jug_6hr

tag: heifer id

value: 6 hours


title: NR28-1Fast0

description:
Arm1/Placebo
S21


title: BM MSC, healthy donor, 5

source_name: BM MSC after 21 days in cultured, from healthy donor MOS5

value: mesenchymal stromal cell


title: 25_tail

tag: storage time


title: 24_jug_24hr


title: NR27-1Fed1

description:
Arm1/Placebo
S20

value: F


title: NR15-1Fast1

description:
Arm1/Placebo
S2


title: NR27-1Fed0

description:
Arm1/Placebo
S19


title: 23_jug_8hr

value: 8 hours


title: HLTE_A20_BCG infection

value: Mycobacterium bovis (BCG)


title: HLTE_A20_PA infection


title: 22_jug_6hr


title: HLTE_A19_uninfected


title: BM MSC, healthy donor, 2

source_name: BM MSC after 21 days in cultured, from healthy donor MOS2


title: 21_jug_3hr


title: NR27-1Fast1

description:
Arm1/Placebo
S18


title: HLTE_A19_IAV infection

value: Influenza A virus (IAV)


title: BM MSC, remission, 4

source_name: BM MSC after 21 days in cultured, from remission patient 5718-R4

value: Multiple myeloma


title: HLTE_A20_IAV infection


title: 20_jug_1hr

value: Jugular Vein

value: Peripheral white blood cells


title: BM MSC, remission, 1

source_name: BM MSC after 21 days in cultured, from remission patient 5614-R1


title: BM MSC, remission, 6

source_name: BM MSC after 21 days in cultured, from remission patient 4198-R6


title: s2-P8G-2-150 K562 Cells SF3B1 WT -- Library -- Day 8 GCV  (150bp reads)

source_name: K562 cells transduced with synthetic library

value: WT

value: ganciclovir (100ug/mL)

tag: miseq read length


title: NR27-1Fast0

description:
Arm1/Placebo
S17


title: HLTE_A19_PA infection

value: Pseudomonas aeruginosa (PA)


title: BM MSC, remission, 3

source_name: BM MSC after 21 days in cultured, from remission patient 3874-R3

value: Complete Remission


title: HLTE_A19_BCG infection


title: 19_tail

value: Coccygeal Vein


title: 12_jug_24hr

value: 24 hours


title: NR20-1Fed1

description:
Arm1/Placebo
S16


title: NR20-1Fed0

description:
Arm1/Placebo
S15


title: BM MSC, healthy donor, 1

source_name: BM MSC after 21 days in cultured, from healthy donor MOS1

value: Healthy donor

value: Healthy


title: 11_jug_8hr


title: 10_jug_6hr

value: 6 hours


title: NR20-1Fast0

description:
Arm1/Placebo
S13


title: 9_jug_3hr

value: 3 hours


title: NR19-1Fed1

description:
Arm1/Placebo
S12

value: F


title: BM MSC, remission, 5

source_name: BM MSC after 21 days in cultured, from remission patient 12283-R5

value: mesenchymal stromal cell


title: 8_jug_1hr

value: 1 hour


title: NR19-1Fed0

description:
Arm1/Placebo
S11


title: NR20-1Fast1

description:
Arm1/Placebo
S14


title: 7_tail


title: BM MSC, diagnosis, 4

source_name: BM MSC after 21 days in cultured, from diagnosis patient GJL55MO

value: Diagnosis


title: BM MSC, diagnosis, 6

source_name: BM MSC after 21 days in cultured, from diagnosis patient 6035

value: Multiple myeloma


title: BM MSC, remission, 2

source_name: BM MSC after 21 days in cultured, from remission patient 12260-R2


title: BM MSC, diagnosis, 3

source_name: BM MSC after 21 days in cultured, from diagnosis patient VG67MO


title: Patient3 normal

city: ChengDu

first: Jinen

last: Song

address: Renmin road

institute: Sichuan university

data_processing:
Basecalls performed using bcl2fastq2 Conversion Software v2.20
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to GRCh38 and quantified using cellranger  v3.0.0 with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv files with all cell barcodes and features of one sample
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and every cells of one sample

molecule: polyA RNA

source_name: Colorectal

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard 10x Genomics Chromium single-cell v2 reagent kit protocols

value: Colorectal

tag: tumor stage

value: normal


title: testis-sheep, scRNA-seq

city: Lanzhou

first: Yao

middle: jing

last: Yue

address: NO.335 Jiangouyan, Qilihe District Lanzhou 730050, Gansu, P. R. C

department: Lanzhou Institute of Husbandry and Pharmaceutical Sciences,

institute: Chinese Academy of Agricultural Sciences

description: one sample from testis tissue

data_processing:
The cell Ranger software pipeline (version 3.1.0) provide by 10X genomics was used to demultplex cellular barcodes, map reads to the Genome
The Seruat package was used to screen the cells following preliminary quality control, while principal component analysis (PCA) for dimensionality reduction was used to analyze the similarity between qualified cells.
A mutual nearest neighbor (MNN)-clustering algorithm was used for clustering and classifying the cell types
Genome_build: Ovis aries, Oar_rambouillet_v4.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

organism: Ovis aries

source_name: testis- healthy sheep

extract_protocol:
A 3-month-old healthy male Hu sheep was selected and castrated for testis collection, then single cell suspension was obtained using enzymatic digestion method for single cell sequencing.
Single cells were suspended in calcium- and magnesium-free PBS containing 0.25% trypsin/ethylenediaminetetraacetic acid (EDTA),Cells  were resuspended in DMEM/F-12 .
RNA libraries were prepared with Chromium Single cell 3 Reagent v3 Kits according to the manufactures protocol.

tag: breed

value: Hu

value: male

value: 3 month-old

tag: period

value: Sexual maturation

value: testis


title: NR15-1Fast0

description:
Arm1/Placebo
S1


title: wounded with EBw [EB6w]

city: London

first: Chrysanthi

last: Ainali

state: England

address: Strand

country: United Kingdom

institute: KING'S COLLEGE LONDON

description:
7196780073_E_Grn
EB6w

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation in R.

source_name: Epidermolysis Bullosa Wounded

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion).

extract_protocol: RNA extraction was performed using the Ambion mirVana miRNA Isolation kit  according to the manufacturer’s protocol. Quality control was performed with Agilent Bioanalyser.

tag: diagnosis

value: recessive dystrophic epidermolysis bullosa

tag: tissue

value: wounded skin

tag: donor


title: control with HC [C6]

description:
7196780073_F_Grn
C6

source_name: Control

value: healthy

value: control skin


title: BM MSC, diagnosis, 5

source_name: BM MSC after 21 days in cultured, from diagnosis patient 1804


title: Patient3 carcinoma

value: carcinoma


title: S+B-3

city: Yinchuan

first: Xiang

last: Xiao

state: Ningxia

address: Shengli Street

institute: Ningxia Medical University

data_processing:
Oxford Nanopore Technologies Long Read Processing：Raw reads were first filtered with minimum average read quality score=7 and minimum read length=500bp. Ribosomal RNA were discarded after mapping to rRNA database. Next, full-length, non-chemiric (FLNC) transcripts were determined by searching for primer at both ends of reads. Clusters of FLNC transcripts were obtained after mapping to reference genome with mimimap2, and consensus isoforms were obtained after polishing within each cluster by pinfish.
Remove redundant:Consensus sequences were mapped to reference genome using minimap2. Mapped reads were further collapsed by cDNA_Cupcake package with min-coverage=85% and min-identity=90%. 5’ difference was not considered when collapsing redundant transcripts.
Find fusion transcript:The criteria for fusion candidates is that a single transcript must:    (1) must map to 2 or more loci    (2) minimum coverage for each loci is 5% and minimum coverage in bp is >= 1 bp    (3) total coverage is >= 95%    (4) distance between the loci is at least 10kb
Genome_build: tab-delimited text files include CPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Glycyrrhiza uralensis

source_name: Glycyrrhiza uralensis Fisch.

growth_protocol: 75 water-absorbing, full-filled seeds were selected, blotted surface moisture, and sown evenly in each pot filled with 1900 g high-pressure sterilized and fully dried sand medium collected from native desert regions which do not contain any nutrients.

extract_protocol:
Glycyrrhiza uralensis Fisch. seedling were collected and ground. Then RNA was extracted and its purity, concentration and integrity were tested. 1ug total RNA was prepared for cDNA libraries using protocol provided by Oxford Nanopore Technologies (ONT). Briefly, SuperScript IV First-Strand Synthesis System (Invitrogen) was used for full length mRNA reverse transcription and following cDNA PCR for 14 circles with LongAmp Tag (NEB). The PCR products were then subjected to FFPE DNA repair and end-repair (NEB) steps and following adaptor ligation using T4 DNA ligase (NEB). Agencourt XP beads was used for DNA purification according to ONT protocol. The final cDNA libraries were added to FLO-MIN109 flowcells and were run on PromethION platform at Biomarker Technology Company (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: (ⅰ) Control group (CK), plants were watered with 300 mL of distilled water; (ⅱ) Control combined with G2 group (CK+B), plants were watered with 300 mL of distilled water containing centrifuged bacteria culture suspension (108 cfu mL-1 G2); (ⅲ) Salt stress group (S), plants were watered with 300 mL of distilled water containing 75 mM NaCl; (ⅳ) Salt stress combined with G2 group (S+B), plants were watered with 300 mL of distilled water containing 75 mM NaCl and 108 cfu mL-1 G2.

tag: treatment

value: salt and G2 treatment

value: 45 days

tag: stress

value: salt stress


title: S+B-2


title: BM MSC, diagnosis, 2

source_name: BM MSC after 21 days in cultured, from diagnosis patient TG55MO

tag: tumor type

value: mesenchymal stromal cell

tag: Stage

value: Diagnosis


title: NR19-1Fast1

description:
Arm1/Placebo
S10

tag: Sex

value: F

tag: bmi


title: S+B-1

tag: age


title: normal with EBn [EB6n]

description:
7196780073_D_Grn
EB6n

source_name: Epidermolysis Bullosa Normal

value: normal skin


title: BM MSC, diagnosis, 1

source_name: BM MSC after 21 days in cultured, from diagnosis patient HE59MO

value: Multiple myeloma

tag: cell type

tag: number patient


title: normal with EBn [EB5n]

description:
7196780073_B_Grn
EB5n


title: control with HC [C5]

description:
7196780073_C_Grn
C5


title: Patient3 blood

source_name: Blood

value: Blood

value: blood


title: Patient3 adenoma 2

value: Colorectal

value: adenoma


title: wounded with EBw [EB5w]

description:
7196780073_A_Grn
EB5w

value: recessive dystrophic epidermolysis bullosa


title: Patient3 adenoma 1


title: normal with EBn [EB4n]

description:
7196780027_K_Grn
EB4n


title: S-3

value: salt treatment


title: S-2


title: Patient2 para-cancer

value: para-cancer


title: Patient2 normal

value: normal


title: S-1


title: Patient2 carcinoma

value: carcinoma


title: NR16-1Fed0

description:
Arm1/NR
S32


title: wounded with EBw [EB4w]

description:
7196780027_J_Grn
EB4w

value: wounded skin


title: control with HC [C4]

description:
7196780027_L_Grn
C4

value: healthy

value: control skin


title: Patient2 adenoma


title: KF-24h-Al

city: Nanjing

first: Ge

middle: Ju

last: Liu

address: Weigang No.1

institute: Nanjing Agricultural University

description: Gene expression data

hyb_protocol: Following fragmentation and Terminal Labeling, 5 ug of cDNA were hybridized for 16 hr at 45℃ on Affymetrix Soybean Gene 1.1 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 0381.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 3.0 (MAS 3.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Glycine max

source_name: Roots of soybean KF under Al stress at 24h

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 0.1 ug total RNA (Expression Analysis Technical Manual, 2013, Affymetrix).

growth_protocol: Soybean seedlings were germinated in moist sterile sand and grown under a photoperiod of 14-h/10-h (day/night) and 26/24 °C (day/night) temperature circulations for three days.

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

treatment_protocol: The seedlings were then exposed to 0.5 mM CaCl2 (pH = 4.3) solution containing either 0 µM AlCl3 (control) or 25 µM AlCl3 (treatment) for 6 h, 12 h and 24 h, respectively.

tag: variety

value: KF

value: Roots

tag: phenotype

value: Al-tolerant


title: GF-24h-Al

description: Gene expression data

source_name: Roots of soybean Guangfengmaliaodu under Al stress at 24h

value: Guangfengmaliaodu

value: Al-sensitive


title: wounded with EBw [EB3w]

description:
7196780027_G_Grn
EB3w


title: control with HC [C3]

description:
7196780027_I_Grn
C3


title: CK+B-1

value: G2 treatment

value: 45 days

value: no stress


title: BM MSC, early relapse, 7

source_name: BM MSC after 21 days in cultured, from early relapse patient 5956-C8

value: Multiple myeloma

value: mesenchymal stromal cell

value: Early relapse


title: GF-24h-CK

description: Gene expression data

source_name: Roots of soybean Guangfengmaliaodu under control condition at 24h


title: Patient1 normal

value: Colorectal

tag: tumor stage


title: CK-3

value: control treatment


title: control with HC [C2]

description:
7196780027_F_Grn
C2


title: Patient1 carcinoma

value: carcinoma


title: CK+B-3


title: KF-12h-Al

description: Gene expression data

source_name: Roots of soybean KF under Al stress at 12h


title: CK+B-2


title: normal with EBn [EB2n]

description:
7196780027_E_Grn
EB2n

value: recessive dystrophic epidermolysis bullosa

value: normal skin


title: Patient1 adenoma

value: adenoma


title: KF-24h-CK

description: Gene expression data

source_name: Roots of soybean KF under control condition at 24h

value: KF


title: CK-1


title: wounded with EBw [EB2w]

description:
7196780027_D_Grn
EB2w

value: wounded skin


title: Patient0 carcinoma


title: CK-2


title: M238P.06

status: Public on Dec 29 2021

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: M238P BRAFV600E mutant melanoma cells sensitive to the BRAF inhibitor Vemurafenib

data_processing:
MinKNOW 4.0.5B software used for primary data acquisition, basecalling using Guppy v4.0.11
Sequenced raw reads were then processed following the FLAIR workflow (A.D. Tang et al., Nat. Commun. 11,1438 2020). In short, reads were aligned to hg38 with minimap2 (version 2.17-r941). Misaligned splice sites were corrected according to the GENCODE v.35 annotations. High confidence isoforms were defined after grouping corrected reads of all samples sharing same unique splice junctions. Selected isoforms were quantified using minimap2 in each sample
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files containing the matrix of isoforms abundance in both samples

extract_protocol:
Sequencing libraries were prepared with the Oxford Nanopore LSK-109 library preparation kit (SQK-PCB109 kit)
Sequence using Ofxord Nanopore PromethION (flowcell_id PAE18991),

tag: cell line

value: human melanoma


title: M238R.07

description: M238R melanoma cells resistant to the BRAF inhibitor Vemurafenib


title: normal with EBn [EB3n]

description:
7196780027_H_Grn
EB3n


title: normal with EBn [EB1n]

description:
7196780027_B_Grn
EB1n


title: GF-12h-Al

description: Gene expression data

source_name: Roots of soybean Guangfengmaliaodu under Al stress at 12h

value: Guangfengmaliaodu

value: Roots


title: KF-12h-CK

description: Gene expression data

source_name: Roots of soybean KF under control condition at 12h

value: Al-tolerant


title: CD19+ B cells AdDL70-3 21d #F

first: David

middle: S.

last: DeLuca

address: Carl-Neuberg-Str 1

department: Biomedical Research in End-stage and Obstructive Lung Disease Hannover

institute: Hannover Medical School

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version 2.16.0.10 (Illumina).
The FASTQ files were adapter and quality trimmed using Trim Galore! (version 0.4.1) with default settings as described in the User Guide except for the setting of the quality cutoff (-q/--quality) which was set to a Phred score of 15. Trim Galore! used Cutadapt (version 1.9.1) as subroutine.Quality control of FASTQ files was performed by FastQC (version 0.11.4) before and after trimming.After sequencing, BCL files were de-multiplexed and converted to FASTQ files (GATC).
After trimming, FASTQ files were mapped against a reference genome with the splice-aware aligner STAR (version 2.5.0c) to generate BAM files. The BAM files were built in a 2-pass Mapping (--twopassMode Basic) and were finally sorted (--outSAMtype BAM SortedByCoordinate). All other setting have been left as default as described in the manual. The genome index files were created by STAR with default settings using Mus musculus sequence and annotation data (UCSC, build mm9) available on illumina’s iGenome site (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
Read counts per gene were calculated using htseq-count with the UCSC GTF for mm9
Normalization and differential expression analysis were performed with DESeq2
Genome_build: UCSC mm9
Supplementary_files_format_and_content: cd11b_expression.data.txt provides the raw read counts as produced by htseq-count

source_name: B Cells

growth_protocol: WT mice (C57BL/6J) were purchased from Janvier Lab (Le Genest-Saint-Isle, France). Female and male B cell-deficient µMT KO mice on a C57BL/6J background were obtained from The Jackson Laboratory (Bar Harbor, Maine, USA). Age- (8-14 weeks) and sex-matched mice were used in experiments. All animal experiments corresponded to the European guideline 2010/63/EU as well as the German Animal Welfare Act and were authorized by the Lower Saxony State Office for Consumer Protection and Food Safety, Germany.

extract_protocol:
RNeasy Micro-Kit from Qiagen
500 ng of total RNA per sample were utilized as input for mRNA enrichment procedure with ‘NEBNext® Poly(A) mRNA Magnetic Isolation Module’ (E7490L; New England Biolabs) followed by stranded cDNA library generation using ‘NEBNext® Ultra Directional RNA Library Prep Kit for Illumina’ (E7420L; New England Biolabs). All steps were performed as recommended in user manualE7420 (Version 6.0_08-2015; NEB) except that all reactions were downscaled to 2/3 of initial volumes. Furthermore, one additional purification step was introduced at the end of the standard procedure, using of 1x ‘Agencourt® AMPure® XP Beads’ (#A63881; Beckman Coulter, Inc.). cDNA libraries were barcoded by single indexing approach, using ‘NEBNext Multiplex Oligos for Illumina – Set 1’ (Index Primer 1 – 12). All generated cDNA libraries were amplified by 10 cycles of final pcr.

treatment_protocol: Adenoviral vectors containing the cDNA encoding porcine biologically active TGF-β1 (AdTGF-β1) and empty control vectors (AdCL) were constructed. Mice were anaesthetized with ketamine (75 mg/kg body weight; Albrecht, Aulendorf, Germany) and xylazine (3 mg/kg body weight; Bayer, Leverkusen, Germany) and were then intubated orotracheally (o.t.) with a 29-gauge Abbocath catheter (Abbott, Wiesbaden, Germany). AdTGF-β1 or AdCL were instilled into the lungs of mice at 1.5x108 PFU/mouse diluted in 50 µl PBS. In additional experiments, mice received intratracheal instillations of 0.02 units/mouse BLM diluted in 50 µl of 0.9 % saline.

value: B Cells

tag: time

tag: disease model status

value: Control


title: CD19+ B cells AdTGFß 21d #554

value: AdTGFBeta

value: Fibrosis activated


title: CD19+ B cells AdTGFß 21d #551


title: CD19+ B cells AdDL70-3 21d #E


title: CD19+ B cells AdTGFß 21d #552


title: KF-6h-Al

description: Gene expression data

source_name: Roots of soybean KF under Al stress at 6h

tag: tissue


title: control with HC [C1]

description:
7196780027_C_Grn
C1

source_name: Control

tag: diagnosis

value: healthy

value: control skin

tag: donor


title: CD19+ B cells AdDL70-3 21d #D

tag: treatment


title: CD19+ B cells AdTGFß 14d #559


title: CD19+ B cells AdTGFß 14d #558


title: CD19+ B cells AdTGFß 14d #557


title: CD19+ B cells AdDL70-3 14d #B


title: KF-6h-CK

description: Gene expression data

source_name: Roots of soybean KF under control condition at 6h


title: CD19+ B cells AdDL70-3 14d #A


title: GF-12h-CK

description: Gene expression data

source_name: Roots of soybean Guangfengmaliaodu under control condition at 12h

value: Al-sensitive


title: CD19+ B cells AdDL70-3 14d #C


title: Bleomycin d21 Pool2 CD19+ Cells

value: Bleomycin


title: Bleomycin d21 Pool3 CD19+ Cells


title: GF-6h-Al

description: Gene expression data

source_name: Roots of soybean Guangfengmaliaodu under Al stress at 6h


title: Bleomycin d21 Pool1 CD19+ Cells


title: wounded with EBw [EB1w]

description:
7196780027_A_Grn
EB1w

source_name: Epidermolysis Bullosa Wounded

value: recessive dystrophic epidermolysis bullosa


title: GF-6h-CK

description: Gene expression data

source_name: Roots of soybean Guangfengmaliaodu under control condition at 6h


title: NaCl d21 Pool2 CD19+ Cells

value: NaCl


title: NaCl d21 Pool3 CD19+ Cells


title: Bleomycin d14 Pool3 CD19+ Cells


title: NaCl d21 Pool1 CD19+ Cells


title: NaCl d14 Pool3 CD19+ Cells


title: Bleomycin d14 Pool1 CD19+ Cells


title: NaCl d14 Pool2 CD19+ Cells


title: Untread E. faecalis rep 1

city: Taipei

first: Kung-Ta

last: Lee

address: No.1, Sec. 4, Roosevelt Road

department: Department of Biochemical Science & Technology

country: Taiwan

institute: National Taiwan University

data_processing:
The raw image data were converted to sequence data using bcl2fastq conversion software v2.20.
After adaptor clipping and sequence quality trimming with Trimmomatic v0.36, the clean reads of the control and treated groups were mapped to the reference genome of the WT strain E. faecalis OG1RF (NC_017316.1) using HISAT2.
Differential expression analysis was performed using cuffdiff (cufflinks v2.2.1).
Genome_build: Reference genome: E. faecalis OG1RF (NC_017316.1)
Supplementary_files_format_and_content: The processed data file include raw gene counts and FPKM values of every gene for each treatment.

organism: Enterococcus faecalis OG1RF

source_name: Untread E. faecalis rep 1

growth_protocol: E. faecalis was statically cultured at 37 °C in M9 medium.

extract_protocol:
E. faecalis cells were lysed with lysozyme (30 mg/mL) and mutanolysin (500 U/mL) in Tris-EDTA (TE) buffer at 37 °C for 10 min. Total RNA was then extracted using an RNeasy Mini Kit (Qiagen Ltd., Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: E. faecalis was cultured with or without B. subtilis natto supernatant (10% v/v) anaerobically at 37 °C for 24 hours.

tag: strain

tag: genotype

value: wild type

value: Untreated


title: Treated E. faecalis rep 1

source_name: Treated E. faecalis rep 1

value: Bacillus subtilis natto Supernatant


title: Dome_mut_rescued_BS_seq

city: Beijing

first: Wei

address: Zhongguancun street, Haidian

department: THU-PKU Center for Life Sciences

institute: Tsinghua University

data_processing:
Library strategy: STEM-seq
All STEM-seq datasets were mapped to the danRer7 reference genome by Bismark (Krueger and Andrews, 2011). Reads were trimmed with cutadaptor (Martin, 2011) using parameters: --minimum-length 20 --pair-filter=any. Alignments were performed with the following parameters: -N 1 -X 600 --score_min L,0,-0.6. Multi-mapped reads and PCR duplicates were removed. bismark_methylation_extractor was used to calculate the DNA methylation level.
Total RNA-seq data were firstly processed using Trim Galore! with default parameters to trim the adapter-containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome (danRer7) by STAR (version: STAR_2.5.3a_modified) (Dobin et al., 2013) with the following parameters: --outSAMstrandField intronMotif --outSAMattributes All --outSAMunmapped Within --outSAMattrIHstart 0 --outWigStrand Stranded --outFilterMultimapNmax 20 --twopassMode Basic. The gene expression level was normalized to fragments per kilobase of transcript per million mapped (FPKM) values using Cufflinks (version 2.2.1) (Trapnell et al., 2012).
The scRNA-seq data were processed with Cell Ranger 3.1 for genome alignment (danRer10), transcript counting, and gene-cell-barcode matrix generation. Before the downstream analysis, cells with unique detected genes lower than <2,000 and higher than 6,000 genes were discarded, and cells with high percentage of mitochondrial genes (>5%) were removed too. Subtypes of cells were identified with Seurat 3.0 through the integrating of control and mKD embryos at dome and shield stages with setting control embryos as reference. To make the data comparable samples, we performed SCTransform normalization separately for each dataset. To further reduce the bais caused by sequencing depth of scRNA-seq and percentage of mitochondrial genes, UMI variance and percent.mt were regressed out from SCTransform normalized data matrix by linear model with negative binomial distribution.
All ChIP-seq reads were aligned to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM). To visualize the STAR ChIP-seq signal in the UCSC genome browser, each read was extended by 250 bp and the coverage for each base was counted. Replicates of STAR ChIP-seq were pooled for the downstream analysis.
The ATAC-seq data were mapped to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM). To minimize the batch and cell type variation, RPKM values across whole genome were further Z-score normalized. To visualize the CUT&RUN signals in the UCSC genome browser, each read was extended by 250 bp and the coverage for each base was counted.
Genome_build: danRer7
Supplementary_files_format_and_content: Matrix for scRNA-seq data, gene expression table for total RNA-seq data, Bigwig and narrowPeak for ChIP-seq and ATAC-seq data

organism: Danio rerio

source_name: embryo

growth_protocol: The wild-type AB strain was used in the experiments. The females after OMIS were fed with live adult brine shrimp thrice a day. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously (Kimmel et al., 2000).

extract_protocol:
The deyolked embryos were lysed with 20 µl lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 mM EDTA, pH 8.0, 0.5% NP-40) and 2 µl protease K (Roche, Cat 10910000) for at least 3hrs at 59℃.
After heat-inactivation, spike-in λ-DNA (Promega, Cat D150A) was added at a mass ratio of 1/200. Bisulfite conversion was performed with the EpiTect Fast Bisulfite Conversion Kit (Qiagen, Cat 59824). The converted DNA was subjected to column purification and desulfonation on MinElute DNA spin columns (Qiagen, Cat 59824) with carrier RNA (Qiagen, Cat 59824) according to the manufacturer’s instructions. The purified DNA was eluted in 30 µl of elution buffer and ready for TELP library preparation (Peng et al., 2020).

treatment_protocol: Briefly, on the first day of OMIS (Wu et al., 2018b), adult females at 5-12 month old were anesthetized in 550 µg/ml tricaine (Sigma, Cat A5040) in a petri dish. Then the fish was placed on a damp sponge with specific buffer (5.4 mM KCl, 136.8 mM NaCl, 4.2 mM NaHCO3, 0.44 mM KH2PO4, 0.25 mM Na2HPO4, and 0.5% (wt/vol) BSA). A cut was made on one side of belly to expose the ovary. The diluted MOs were microinjected into each oocyte. Rhodamine B (Sigma, Cat R8881) was co-injected with MOs as a dye. After injection, the wound on the belly was sewed with a surgical sewing needle carefully and quickly. Once the operation was done, the female was transferred into fish water supplemented with 32 µg/ml tricaine, 10 unit/ml penicillin and 10 µg/ml streptomycin (HyClone, Cat SV30010). Then the fish was transferred to fish water containing gradually reduced concentrations of tricaine. In the evening of the second day, the female was paired with a wild type male. In the morning of the third day, the pair started to chase and lay fertilized eggs naturally. The injected oocyte-derived embryos were identified by co-injected dye (rhodamine B) at very early developmental stages. The injection doses of dnmt1 MO were 5 ng per oocyte in the same assay. MOs were dissolved in RNase-free water, and heated to 65°C for 11 min before microinjection.

value: AB

value: WT

value: Oocyte microinjection with Rhodamine B, dnmt1 MO and mut dnmt1 mRNA at oogenesis III stage (GV)


title: Bleomycin d14 Pool2 CD19+ Cells


title: Dome_WT_rescued_BS_seq

growth_protocol: The wild-type AB strain was used in the experiments. The females after OMIS were fed with live adult brine shrimp thrice a day. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously (Kimmel et al., 1999).

extract_protocol:
The deyolked embryos were lysed with 20 µl lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 mM EDTA, pH 8.0, 0.5% NP-40) and 2 µl protease K (Roche, Cat 10910000) for at least 3hrs at 58℃.
After heat-inactivation, spike-in λ-DNA (Promega, Cat D150A) was added at a mass ratio of 1/200. Bisulfite conversion was performed with the EpiTect Fast Bisulfite Conversion Kit (Qiagen, Cat 59824). The converted DNA was subjected to column purification and desulfonation on MinElute DNA spin columns (Qiagen, Cat 59824) with carrier RNA (Qiagen, Cat 59824) according to the manufacturer’s instructions. The purified DNA was eluted in 30 µl of elution buffer and ready for TELP library preparation (Peng et al., 2019).

treatment_protocol: Briefly, on the first day of OMIS (Wu et al., 2018b), adult females at 5-12 month old were anesthetized in 550 µg/ml tricaine (Sigma, Cat A5040) in a petri dish. Then the fish was placed on a damp sponge with specific buffer (5.4 mM KCl, 136.8 mM NaCl, 4.2 mM NaHCO3, 0.44 mM KH2PO4, 0.25 mM Na2HPO4, and 0.5% (wt/vol) BSA). A cut was made on one side of belly to expose the ovary. The diluted MOs were microinjected into each oocyte. Rhodamine B (Sigma, Cat R8881) was co-injected with MOs as a dye. After injection, the wound on the belly was sewed with a surgical sewing needle carefully and quickly. Once the operation was done, the female was transferred into fish water supplemented with 32 µg/ml tricaine, 10 unit/ml penicillin and 10 µg/ml streptomycin (HyClone, Cat SV30010). Then the fish was transferred to fish water containing gradually reduced concentrations of tricaine. In the evening of the second day, the female was paired with a wild type male. In the morning of the third day, the pair started to chase and lay fertilized eggs naturally. The injected oocyte-derived embryos were identified by co-injected dye (rhodamine B) at very early developmental stages. The injection doses of standard control MO (cMO) were 5 ng per oocyte in the same assay. MOs were dissolved in RNase-free water, and heated to 65°C for 10 min before microinjection.

value: Oocyte microinjection with Rhodamine B, dnmt1 MO and WT dnmt1 mRNA at oogenesis III stage (GV)


title: Dome_dnmt1_mKD_ATAC_seq_rep1

data_processing:
All STEM-seq datasets were mapped to the danRer7 reference genome by Bismark (Krueger and Andrews, 2011). Reads were trimmed with cutadaptor (Martin, 2011) using parameters: --minimum-length 20 --pair-filter=any. Alignments were performed with the following parameters: -N 1 -X 600 --score_min L,0,-0.6. Multi-mapped reads and PCR duplicates were removed. bismark_methylation_extractor was used to calculate the DNA methylation level.
Total RNA-seq data were firstly processed using Trim Galore! with default parameters to trim the adapter-containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome (danRer7) by STAR (version: STAR_2.5.3a_modified) (Dobin et al., 2013) with the following parameters: --outSAMstrandField intronMotif --outSAMattributes All --outSAMunmapped Within --outSAMattrIHstart 0 --outWigStrand Stranded --outFilterMultimapNmax 20 --twopassMode Basic. The gene expression level was normalized to fragments per kilobase of transcript per million mapped (FPKM) values using Cufflinks (version 2.2.1) (Trapnell et al., 2012).
The scRNA-seq data were processed with Cell Ranger 3.1 for genome alignment (danRer10), transcript counting, and gene-cell-barcode matrix generation. Before the downstream analysis, cells with unique detected genes lower than <2,000 and higher than 6,000 genes were discarded, and cells with high percentage of mitochondrial genes (>5%) were removed too. Subtypes of cells were identified with Seurat 3.0 through the integrating of control and mKD embryos at dome and shield stages with setting control embryos as reference. To make the data comparable samples, we performed SCTransform normalization separately for each dataset. To further reduce the bais caused by sequencing depth of scRNA-seq and percentage of mitochondrial genes, UMI variance and percent.mt were regressed out from SCTransform normalized data matrix by linear model with negative binomial distribution.
All ChIP-seq reads were aligned to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM). To visualize the STAR ChIP-seq signal in the UCSC genome browser, each read was extended by 250 bp and the coverage for each base was counted. Replicates of STAR ChIP-seq were pooled for the downstream analysis.
The ATAC-seq data were mapped to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM). To minimize the batch and cell type variation, RPKM values across whole genome were further Z-score normalized. To visualize the CUT&RUN signals in the UCSC genome browser, each read was extended by 250 bp and the coverage for each base was counted.
Genome_build: danRer7
Supplementary_files_format_and_content: Matrix for scRNA-seq data, gene expression table for total RNA-seq data, Bigwig and narrowPeak for ChIP-seq and ATAC-seq data

growth_protocol: The wild-type AB strain was used in the experiments. The females after OMIS were fed with live adult brine shrimp thrice a day. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously (Kimmel et al., 1995).

extract_protocol:
The miniATAC-seq procedure was performed as previously described (Wu et al., 2018a) with modifications to adapt it for zebrafish embryos. Briefly, dispersed cells from deyolked zebrafish embryos were transferred into 6 µl lysis buffer (10 mM Tris-HCl, pH = 7.4; 10 mM NaCl; 3 mM MgCl2; and 0.02% digitonin) in ice for 10 min.
The ATAC reaction was performed by adding 4 µl ddH2O, 4 µl 5 X TTBL, and 5 µl TTE mix V5 (Vazyme, Cat TD502) at 37℃ for 30 min, then stopped by adding 5 µl 5 X TS stop buffer at room temperature for 5 min. The DNA was extracted by phenol chloroform and ethanol purification after adding 40 ng carrier RNA and 103 µl Tris-EDTA. Then the DNA was PCR amplified with 10 µl index (Vayzme, Cat TD202), 10 µl 5 X TAB and 1 µl TAE (Vayzme, Cat TD502), with the program of 72℃ for 3 min, 98℃ for 30s, (98℃ for 15s, 60℃ for 30s, and 72℃ for 3min) with 18 cycles, and 72℃ for 5 min. The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.

tag: developmental stage

value: Dome

value: embryo

value: Oocyte microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage (GV)


title: Dome_dnmt1_mKD_ATAC_seq_rep2


title: NaCl d14 Pool1 CD19+ Cells

value: B Cells

value: Control


title: Shield_ctrl_H3K27ac_rep2

description: STAR ChIP-seq

extract_protocol:
The ChIP procedure was based on a previously described method (Zhang et al., 2018a). Embryos were deyolked by repeatedly blowing with a 200 µl pipette and cell pellets were collected by spinning down at 5000 rpm for 5 min at 4℃. After centrifuge, cell pellet was lysed in 40 µl lysis buffer (0.5% NP-40, 0.5% Tween, 0.1% SDS and proteinase inhibitor) with pipetting up and down several times.
0.1 unit of MNase (Sigma, Cat N3755) was added for chromatin digestion at 37℃ for 5 min. The reaction was then terminated by adding 1 µl 0.5 M EGTA. IP sample was incubated with 1 µg H3K4me3 antibody (Homemade) (Zhang et al., 2016) and 2 µg H3K27me3 antibody (Active Motif, Cat 61017) overnight with rotation at 4℃. In the next day, the sample was incubated with 300 µg protein A or protein G dynabeads (Life technologies, Cat 10001D or 10003D) for 2hrs with rotation at 4℃. The beads were washed 5 times in 150 µl RIPA buffer and once in 150 µl LiCl buffer. After washing, spin tubes briefly and remove the supernatant. For each IP sample, resuspend beads with 27 µl ddH2O and 1 µl 10x Ex-Taq buffer (TaKaRa). 1 µl proteinase K (Roche, Cat 10910000) was then added and the mix was incubated at 55℃ for 90 min to elute DNA from beads. The supernatant was then transferred to a new tube and the proteinase K was inactivated at 72℃ for 40 min. 1 µl rSAP (NEB, Cat M0371) was then added to dephosphorylate 3’ end of DNA at 37℃ for 1hr. rSAP was inactivated at 65℃ for 10 min. The resulting sample was subjected to TELP library preparation as previously described (Peng et al., 2015). The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.

value: Shield

value: Oocyte microinjection with Rhodamine B and control MO at oogenesis III stage (GV)