title: Sh2

city: Guangzhou

first: Xiaomin

last: Zhong

address: 74 Zhongshan Road 2nd

institute: Sun Yat-Sen University

data_processing:
Phred program was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using HISAT2.
Fragments Per Kilobases per Million fragments (FPKM) were calculated using a protocol from Mortazavi et al., Nat. Methods, 2008. In short, readcounts of all exons were determined with StringTie software. FPKM was calculated with the equation: FPKM = Total exon fragments/[Mapped reads (Millions) * exon length (Kb)].
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files include gene rawcount and FPKM values for each sample

extract_protocol:
Total RNA was harvested using Trizol reagent. NEB Next Ultra RNA Library Prep Kit for Illumina (#E7530S) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colorectal cancer cell

value: DANCR knockdown with shRNA2


title: Profiling of RNA from rRNA-depleted RNA library from HT29 cells [HT29_2]

status: Public on Jan 13 2021

type: SRA

city: Regensburg

first: Gerhard

last: Lehmann

address: Universitaetsstrasse 31

department: Biochemistry 1

country: Germany

institute: University of Regensburg

description:
RNASeq_DE.xlsx
circRNA_DE.xlsx

library_source: transcriptomic

data_processing:
Base calling was performed using CASAVA 1.8.2 software
The data processing was divided into 2 workflows:
CircRNA analysis:
Raw reads were mapped to the human genome (hg19 assembly) using STAR version 2.5.3a with the setting --outFilterMismatchNoverLmax to 0.05. Reads were counted using htseq-count version 0.9.1 with Ensembl release 75 genome annotation reference.
For circRNA detection reads were mapped to the human genome (hg19) using bwa mem version 0.7.5a-r405 with the following options: -t 20 -k 14 -T 1 -L 3,3 -O 6,6 -E 3,3. Bwa mem output was processed using find_circ2 (https://github.com/rajewsky-lab/find_circ2) to detect backspliced reads. circRNA candidates flagged by find_circ2 as SHORT or HUGE were discarded. The list was further filtered by keeping only circRNA candidates that were supported by 2 or more unique reads in a given sample and spliced from annotated splice sites. The number of fragments overlapping head-to-tail junctions were used as a measure of circRNA expression.
Differential expression analysis was performed within R using DESeq2 version 1.22.2. The circRNA head-to-tail junction counts were merged with htseq-count output prior to normalization by DESeq2. CircRNAs and genes that were supported by less than 10 reads in total across all samples were discarded.
Genome_build: hg19
Differential gene expression analysis:
Raw reads were mapped to the human genome (hg38 assembly) using STAR version 2.7.0a with --outFilterMultimapNmax 2000000000 and --outSAMmultNmax 1 settings. Reads were counted using Rsubread 1.34.7 with Ensembl release 98 genome annotation reference.
Differential expression analysis was performed within R using DESeq2 version 1.24.0.
Genome_build: hg38
Supplementary_files_format_and_content: Excel files including count tables and DESeq2 outputs

molecule: total RNA

organism: Homo sapiens

source_name: HT29 cells

growth_protocol: HT29 cells were cultivated in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 µg/mL streptomycin. Cells were grown under standard conditions at 37°C in 5% CO2 atmosphere.

extract_protocol:
Tumor samples (PT and LM) were cutted into smaller pieces before putting them into the lysing matrix tubes, type "D" (MP Biomedicals). Tubes with 1 ml TRIzol (Invitrogen) were cooled on ice before samples were added. Tumors were homogenized using Fastprep-24-System with 1x 45 sec. @ full speed in TRIzol. After homogenisation, total RNA from tumor samples was isolated according to TRIzol's protocol. Total RNA from HT29 cells was isolated using TRIzol according to TRIzol's protocol without homogenisation steps.
Workflow consists of double-stranded cDNA generation using a customizable mixture of random and poly(T) priming, fragmentation of double-stranded cDNA, end repair to generate blunt ends, adaptor ligation, strand selection via nucleotide analog-targeted degradation, InDA-C-mediated adaptor cleavage and PCR amplification to produce the final library. The detailed protocol can be found at the user guide Ovation Human FFPE RNA-Seq System.

treatment_protocol: Three SCID mice were initially used for tumor development to collect RNA for RNA sequencing (RNA-seq) via intrasplenic implantation. HT29 cells were dissociated with trypsin, washed once with DMEM supplemented with 10% FCS, 1% PS and then resuspended to the desired concentration in Hank's Balanced Salt Solution (HBSS, Sigma). All animals receiving tumor cell injections were injected with the same quantity of cells (500 000 cells per animal). Abdominal access was obtained via a left subcostal skin and peritoneal wall incision. The spleen was gently exteriorized. 5 µl of 500 000 tumor cells were injected with a 10 µl Hamilton syringe (BD Biosciences). The needle was slowly retracted and the injection site pressed with a moist cotton swab to prevent leakage. The spleen was returned to the peritoneal cavity; peritoneum and skin were closed by running sutures and wound clips. Bioluminescence measurement was performed weekly or every 3 days. For this purpose, mice were anaesthetized, injected with 100 µl of 30 mg/ml D-luciferin (Biosynth, Staad, Switzerland) for 3 min, and emitted photons were registered for 3 min using Xenogen IVIS Lumina Imaging System (Caliper Life Sciences). Primary tumor (either subcutaneous tumor or in spleen) and metastases in the liver resections were performed when the tumor size was big enough or when the bioluminescence measurement was significant. All tumors were collected in RNAlater (Thermo Scientific).

tag: cell type

value: HT29.hCG.Luc colorectal cancer cell line


title: Sh1

country: China

tag: tissue

tag: treatment

value: DANCR knockdown with shRNA1

tag: cell line


title: 7-day-old mre11 rice seedlings Rep1

city: Wuhan

first: Jie

last: Zhao

address: No. 299, Bayi Road, Wuchang District,

institute: Wuhan University

data_processing:
The transcriptome sequencing experiment process includes RNA extraction, RNA sample quality detection, library construction, library purification, library detection, library quantification, sequencing cluster generation, and computer sequencing
The length we obtained was 150bp, and the numbers of reads were 49948012, 43922662, 43510058 and 52841196. Htseq software (V 0.6.1) was used for gene expression calculation, DESeq2 (V1.6.3) of Bioconductor software was used for gene difference analysis, and DEXSeq (V1.18.4) software was used for differential exon usage analysis
Genome_build: Oryza sativa
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Oryza sativa

source_name: 7-day-old mre11 rice seedlings

extract_protocol:
The samples were lysed with Trizol reagent. RNA was extracted with chloroform and precipitated with isopropanol. 75% alcohol was used to clean the impurities, and finally RNA was dissolved with RNase-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Japonica

tag: age

tag: genotype/variation

value: mre11 mutant

value: seedlings


title: HSC CD74-/- rep3

city: Rehovot

first: Idit

last: Shachar

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome using STAR  v2.4.2a (with the  option alignEndsType set to EndToEnd)
Counting proceeded over genes annotated in Ensembl release 92, using htseq-count
Normalization was performed using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: processed.xlsx (Excel file includes the normalized counts)

organism: Mus musculus

growth_protocol: 1000 hematopoietic stem cells (CD34-/LSK cells) were isolated from bone marrow of 3 WT mice and 3 CD74-/- mice (by sorting using FACS Aria in 70 micron nozzle).

extract_protocol:
HSCs (CD34-/LSK) (1*10e3 cells) were sorted from WT and CD74-/- mice (BD FACS Aria III).
Sequencing libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA kit (Clonetech). Sequencing libraries were constructed containing barcodes. Single end reads were sequenced on one lane of an Illumina HiSeq2500 machine.

treatment_protocol: untreated

tag: strain

tag: genotype

value: Hematopoietic stem cells (CD34-/LSK cells)


title: HSC CD74-/- rep2


title: 23NRandomer9h

city: Princeton

first: Alexei

last: Korennykh

state: NJ

address: Washington Rd

department: Molecular Biology

country: USA

institute: Princeton University

data_processing:
Barcodes splitting to deconvolute and assign reads to samples
Mapping using TopHat 2 set to map first stranded reads with default parameters
Exon and intron counting using HTseq-count run in union mode
Genome_build: HG19
Supplementary_files_format_and_content: Excel sheet with exon counts, BAM and BAI files of reads mapped to HG19 genome.

source_name: Lung carcinoma epithelium

growth_protocol: Grown in RMPI supplemented with 10% FBS

extract_protocol:
At the endpoint, media was aspirated and cells were lysed in 300 uL RLT buffer (RNeasy extraction kit, Qiagen) and total RNA was extracted. RNA integrity was verified by an RNA 6000 Nano Chip, using BioAnalyzer and 2100 Expert software (Agilent Technologies).
rRNA was depleted from the total RNA by hybridization to bead bound rRNA probes. This was followed by fragmentation, first and second strand synthesis for library construction, adapter ligation, PCR amplification and finally sequencing on Illumina HiSEq 2000 platform.

treatment_protocol: A 6-well plate of A549 cells were transfected with 50nM Control or 23N Randomer oligo using Lipofectamine 2000 as per manufracturer's instructions. Treatment duration = 9h and 16h time points

tag: phenotype

value: adherent

value: Lipofectamine based transfection of 50nM 23NRandomerOligo for 9h


title: ControlOligo9h

value: Lipofectamine based transfection of 50nM Control Oligo for 9h


title: 23NRandomer16h

value: Lipofectamine based transfection of 50nM 23NRandomerOligo for 16h


title: LipofectamineControl16h

value: Lipofectamine mock transfection 16h


title: HSC WT rep3

source_name: CD34-/LSK WT

value: WT


title: low autophagy population

city: Ulm

first: Konstantin

middle: MJ

last: Sparrer

address: Meyerhofstr. 1

department: Institute of Molecular Virology

institute: Ulm University Medical Center

description: PCR product of genomic DNA, amplified sgRNA casette

library_source: genomic

data_processing:
Demultiplexing of the raw data
quality and adapter trimming by Trim Galore
aligned raw reads to sgRNA library to get counts using MAGeCK
Genome_build: Human_GeCKOv2_Library_combine.csv
Supplementary_files_format_and_content: Count scores represent the abundance of sgRNAs in an isolated population

molecule: genomic DNA

source_name: GEcKO library / Jurkat

extract_protocol:
Isolated from cell populations sorted by flwo cytometry and fixed with MeOH, genomic DNA extracted with ZymoResearch Midi Preps
as described in Joung at al (2017)

tag: sample type

value: PCR product


title: Input population


title: Profiling of miRNA from total RNA library from HT29 cells [HT29_3]

description:
HT29_3
total small RNA
miRNA_DE.xlsx

data_processing:
HiSeq analysis pipeline: HCS 2.2.38, Casava 1.8.2
The following analysis steps were performed with miRDeep2 version 2.0.0.8 within Galaxy server software (http://galaxyproject.org/):
Clipping of Illumina TruSeq 3'-adapters (recognition sequence: TGGAATTCTCGGGTGCCAAGG). Discarding all resulting sequences shorter than 18 bp. Collapsing the list of all remaining reads to unique insert sequences with corresponding number of appearance. Software: miRDeep2 mapper.
Mapping and counting against human miRNAs from www.mirbase.org (Version 22.1; Oct. 2018) with standard parameters. Software: miRDeep2 Quantifier.
Differential expression analysis was performed within R using DESeq2 version 1.24.0.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: miRNA_DE.xlsx: Excel file including count tables and DESeq2 outputs.

extract_protocol:
Tumor samples (PT and LM) were cut into smaller pieces before putting them into the lysing matrix tubes, type "D" (MP Biomedicals). Tubes with 1 ml TRIzol (Invitrogen) were cooled on ice before samples were added. Tumors were homogenized using Fastprep-24-System with 1x 45 sec. @ full speed in TRIzol. After homogenisation, total RNA from tumor samples was isolated according to TRIzol's protocol. Total RNA from HT29 cells was isolated using TRIzol according to TRIzol's protocol without homogenisation steps.
In short, an adenylated adapter was ligated to the 3’ end of the total RNA by a truncated T4 RNA Ligase 2, followed by the ligation of a 5’ RNA-adapter by T4 RNA Ligase 1 (NEB). After reverse-transcription using a specific primer, the cDNA was amplified by PCR, gel-fractionated and bands or regions corresponding to miRNA inserts were cut out. PCR products from these gel slices were eluted, precipitated and dissolved in water. The quality of the libraries was assessed by qPCR and Bioanalyzer measurements.

treatment_protocol: Five SCID mice were initially used for tumor development to collect RNA for RNA sequencing (RNA-seq) via intrasplenic implantation. HT29 cells were dissociated with trypsin, washed once with DMEM supplemented with 10% FCS, 1% PS and then resuspended to the desired concentration in Hank's Balanced Salt Solution (HBSS, Sigma). All animals receiving tumor cell injections were injected with the same quantity of cells (500 000 cells per animal). Abdominal access was obtained via a left subcostal skin and peritoneal wall incision. The spleen was gently exteriorized. 5 µl of 500 000 tumor cells were injected with a 10 µl Hamilton syringe (BD Biosciences). The needle was slowly retracted and the injection site pressed with a moist cotton swab to prevent leakage. The spleen was returned to the peritoneal cavity; peritoneum and skin were closed by running sutures and wound clips. Bioluminescence measurement was performed weekly or every 3 days. For this purpose, mice were anaesthetized, injected with 100 µl of 30 mg/ml D-luciferin (Biosynth, Staad, Switzerland) for 3 min, and emitted photons were registered for 3 min using Xenogen IVIS Lumina Imaging System (Caliper Life Sciences). Treated mice (Two mice #4 and # 5) with topotecan received 1mg topotecan per 1 kg of bodyweight. Control mice (Three mice #1, #2, #3) served as control mice. Primary tumor (from spleen) and metastases in the liver resections were collected in RNAlater (Thermo Scientific) when the tumor size was big enough or when the bioluminescence measurement was significant.


title: ControlOligo16h

value: Lipofectamine based transfection of 50nM Control Oligo for 16h


title: HSC WT rep2


title: HSC WT rep1


title: H4: Nrf2-High expression

city: Guiyang

first: Ping

last: Liu

address: 28 Guiyi Street, Yunyan District

institute: Affiliated Hospital of Guizhou Medical University

description: Nrf2-High expression

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: GRCh_38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: adult bone marrow

extract_protocol:
prefrontal cortex were rharvested , flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cytarabine for 7 days with an anthracycline for 3 days

value: human bone marrow

tag: disease state

value: acute myeloid leukemia


title: H3: Nrf2-High expression

description: Nrf2-High expression


title: Control

value: colorectal cancer cell

value: Negative Control


title: H2: Nrf2-High expression

description: Nrf2-High expression


title: HSC CD74-/- rep1


title: H1: Nrf2-High expression

description: Nrf2-High expression


title: L3: Nrf2-Low expression

description: Nrf2-Low expression


title: sham_young [910_2_2]

type: RNA

city: Fougeres

first: Denis

last: Habauzit

address: 10 B rue Claude Bourgelat

department: TC unit

country: France

institute: ANSES

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner G2505C using one color scan setting for 8x60k array slides.

data_processing:
The scanned images were analyzed using default parameters (protocol GE1_107_Sep09 and Grid:028279_D_F_20110601) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Data were extracted from the complete data set then were log 2 transform and normalized by quantile (around 30507 gene entities). Probes were then filtered by data file (exclusion of control types, 30367 probes), by flag (Detected, 19 811 probes), and by expression on raw data (expression upper than 125 UA at least in 75 % of sample in at least one condition (14853  gene entities).

organism: Rattus norvegicus

source_name: skin explants from CD hairless rat_sham

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 30 young (2-3 months) hairless male rats (CD Haireless rats, from Charles River laboratories, Ecully, France). Rats were housed by two during the all experiment and maintained in a temperature-controlled room (22°C), on an automatic 12 h light/dark cycle (06:00 18:00 h). Water and diet were given ad libitinum.

extract_protocol: Rat skin biopsies were stored at -80° C in RNA later (Thermo Fisher scientific, Saint Aubin, France). Between 15 and 20 mg of biopsies were first cut in small fragments and then mix with qiazol solution (Invitrogen, Thermo Fisher scientific, Saint Aubin, France) to be crushed with micro pestle and homogenised at 6300 rpm with ceramic beads in Precellys apparatus (Bertin technology, France), during 5 cycles of 23 s, with 2 min on ice between each cycles. Total homogenate containing skin extract and 1 ml of qiazol was mixed with 300 µl of chloroform and then vortexed during 30 s and centrifuged during 15 min (14000 rpm, 4°C). Aqueous phase was taken, equally mixed with ethanol 70% and transferred on qiagen column of RNeasy lipid tissue kits (Qiagen, Hilden, Germany) for purification following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer (Nanodrop technology, Cambridge, UK).

treatment_protocol: Animals were exposed (6 animals) or Sham exposed (8 animals) to 94 GHz exposure 3h/d, 3 days/w during 5.5 months. At the end of the exposure, animals were sacrified and skin explants were recovered and conserved in RNA later up to the analysis.

value: CD Haireless rat

tag: Sex

value: male

value: young; 2-3 months

value: Sham:unexposed rat

value: skin


title: L1: Nrf2-Low expression

description: Nrf2-Low expression


title: CM-d35_rep1

city: Beijing

address: 30 Shuangqing Rd, Haidian District, Beijing, China

department: School of Medicine

institute: Tsinghua University

data_processing:
Adapter sequences were trimmed using TrimGalore (v0.6.4)
Clean data were mapped to the human reference genome (GRCh38) using STAR (2.7.3a) with --quantMode GeneCounts option to output read count tables
Differential gene expression analysis was performed using DESeq2 (v1.24.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include read count values for all samples

molecule: polyA RNA

source_name: cells under CM differentiation at day 35

growth_protocol: Human iPSCs were routinely maintained on Matrigel (BD Biosciences) - coated plates (Corning) in TeSR-E8 medium (STEMCELL Technologies). hiPSCs were passaged every 4 d using Accutase (Merck) and 10 uM ROCK inhibitor Y27632 (Selleck) was added for the first 24 h after passage.

extract_protocol:
Total RNA are extracted using Trizol.
100ng total RNA in each sample are used for SMART-seq2 library construction.

treatment_protocol: Cells undergo CM differentiation by adding CHIR99021 and IWP2.

tag: cell type source

value: human induced pluripotent stem cells (iPSCs)

tag: cell subtype

value: hPSC-derived cardiomyocytes (CMs)

tag: time point


title: sham_young [908_1_1]


title: expo_young [910_1_1]

source_name: skin explants from CD hairless rat_expo

value: Expo:94 GHz chronic exposed rat


title: sham_young [910_2_1]


title: expo_young [908_1_2]


title: sham_young [909_1_4]


title: sham_young [908_1_3]


title: expo_young [909_2_1]


title: expo_young [908_2_1]


title: L2: Nrf2-Low expression

description: Nrf2-Low expression


title: CM-d21_rep2

source_name: cells under CM differentiation at day 21


title: expo_young [908_2_4]


title: sham_young [077_2_3]


title: expo_young [077_2_1]


title: sham_young [077_1_4]


title: expo_young [077_2_4]


title: expo [910_1_4]

data_processing:
The scanned images were analyzed using default parameters (protocol GE1_107_Sep09 and Grid:028279_D_F_20110601) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Data were extracted from the complete data set then were log 2 transform and normalized by quantile (around 30507 gene entities). Probes were then filtered on data file (exclusion of control types, 30367 probes), by flag (Detected, 19915 gene entities), and by expression on raw data (expression upper than 125 UA at least in 75 % of sample in at least one condition (15168 gene entities).

growth_protocol: 30 hairless male rats (CD Haireless rats, from Charles River laboratories, Ecully, France). Rats were housed by two during the all experiment and maintained in a temperature-controlled room (22°C), on an automatic 12 h light/dark cycle (06:00 18:00 h). Water and diet were given ad libitinum.


title: sham [910_2_4]


title: expo_young [077_1_3]


title: sham [910_1_2]


title: CM-d35_rep2


title: CM-d15_rep2

source_name: cells under CM differentiation at day 15


title: sham [910_2_3]


title: sham [909_2_3]


title: expo [909_2_4]


title: CM-d21_rep1


title: sham [909_1_3]


title: S77 bronchial epithelium

city: Amsterdam

first: Joe

last: Butler

address: Meibergdreef 9

department: Infectious diseases

country: Netherlands

institute: Amsterdam UMC

data_processing:
Reads were trimmed using Trimmomatic version 0.36.
Read alignment done by bowtie2 version 2.3.4.3
Count data were generated by means of the FeatureCounts method.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: bronchial epithelium

growth_protocol: HBE cells were obtained anonymously from 3 patients undergoing a lobectomy for lung cancer at the Academic Medical Center, the Netherlands. Healthy tracheobronchial tissue was isolated from the margin of lung cancer tissue by a pathologist. Epithelial cells were isolated following the Fulcher’s protocol (Fulcher and Randell, 2013) and grown in the air-liquid interface.

extract_protocol:
Total RNA was isolated using the Nucleospin RNA Isolation kit. RNA quality was assessed by bioanalysis (Agilent); samples with RNA integrity number > 7 were included for RNA sequencing.
Libraries were prepared from 100-200 ng total RNA using KAPA RNA Hyperprep with RiboErase (Roche) kits.

treatment_protocol: HBE cells were stimulated with 1 ug/ml flagellin from Pseudomonas aeruginosa or PBS for 24 hours. HBE cells were incubated with vehicle, the mTOR inhibitor rapamycin (10 nM), or IOX2 (50 uM).

tag: donorid

tag: experiment

tag: condition

value: Rapa + Fla


title: CM-d15_rep1


title: S76 bronchial epithelium

value: IOX2 + Fla


title: CM-d5_rep2

source_name: cells under CM differentiation at day 5


title: expo [909_2_2]

tag: treatment

tag: tissue


title: CM-d5_rep1


title: sham_young [910_1_3]


title: S74 bronchial epithelium

value: Fla


title: more_than_50-cell_embryos_sRNA-seq

city: Paris

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 4eme Etage

department: Development and stem cell biology

institute: Institut Pasteur

data_processing:
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) was trimmed from the raw reads using cutadapt (version 1.18)
The trimmed reads were sorted by sequence using fastq-sort (from fastq-tools version 0.8) with option -s and deduplicated using a custom haskell program, keeping the highest quality among duplicates, at any given position
The 5' and 3' 4 nt UMIs were removed from the deduplicated reads using cutadapt (version 1.18) with options -u 4 and -u -4
After removing UMIs, the reads from 18 to 24 nt were selected using bioawk version 20110810 (git commit fd40150b7c557da45e781a999d372abbc634cc21)
The size-selected reads were mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with options -L 6 -i S,1,0.8 -N 0
The reads that failed to map were inspected using grep -E -B 1 -A 2 "^G[ACGTN]{20,25}T+$" to detect possible reads starting with G with 20 to 25 nt followed by a poly-U tail that might have prevented the mapping, and this tail was removed from such reads using a custom haskell program before re-mapping them.
Mapped and remapped reads were used to estimate the abundance of small RNAs derived from structural RNAs using featureCounts (version 1.6.3) with options -O -s 1 --fracOverlap 1 and annotations corresponding to tRNA, snRNA, snoRNA, rRNA or RNA (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The abundance of non-structural RNAs was estimated by subtracting the above counts from the number of mapped and remapped reads.
Initially mapped reads were classified using a custom python program according to their length, composition and on the annotations on which they mapped. Reads that didn't match miRNA and piRNA annotations were considered as potential endo-siRNAs.
The potential endo-siRNAs of size 21 to 23 nt that started with G were classified as “si_22G” if they mapped antisense to annotation belonging to the following categories: DNA transposons, RNA transposons, satellites, simple repeats (as annotated in http://hgdownload.cse.ucsc.edu/goldenPath/ce11/database/rmsk.txt.gz) or pseudogene or protein-coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The “si_22G” reads were re-mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with options -L 6 -i S,1,0.8 -N 0
The resulting alignment was used to generate the normalized bigwig file using millions of non-structural RNAs as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.35) and bedGraphToBigWig (version 4)
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of “si_22G” RNAs along the genome

organism: Caenorhabditis elegans

growth_protocol: Strains were maintained at 20°C, using standard methods (Brenner, 1974).

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food at a density of maximum 40,000 animals per 15 cm Petri dish. Worms were carefully monitored using a stereomicroscope and bleached shortly after worms started to produce the first embryos. Embryos were fixed using 2% Formaldehyde for 30 minutes and sorted using a MoFlo Astrios Cell Sorter. After sorting, embryos were reverse crosslinked at 70˚C for 30 minutes in RIPA buffer prior to RNA extraction to generate small RNA libraries.
The library preparation was performed as essentially described by Jayaprakash et al., 2011, except that a 5’ polyphosphatase (Lucigen RP8092H) treatment was performed to be able to clone tri-phosphate small RNAs, and that the PAGE gel extraction after each ligation was substitute with purification by 1.8 volumes of Agencourt RNAClean XP Beads (Beckman Coulter, NC0068576) and 3 volumes of isopropanol. The multiplexed amplified libraries were further purified using PippinPrep DNA size selection with 3% gel cassettes and the following parameters for the selection: BP start (115) and the BP end (165). The purified libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced either on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005).

treatment_protocol: Formaldehyde fixation was performed by treating early embryos immediately after bleaching with 2% formaldehyde in M9 for 30 minutes.

value: whole embryo

tag: developmental stage

value: formaldehyde fixation

tag: molecule subtype

value: total small RNAs


title: 1-cell_embryos_sRNA-seq

value: early embryos (1-cell_embryos)


title: 4-50_cell_embryos_sRNA-seq

value: early embryos (4-50_cell_embryos)


title: sham [909_1_2]


title: CM-d3_rep2

source_name: cells under CM differentiation at day 3


title: S70 bronchial epithelium


title: sham [077_1_2]


title: 2-cell_embryos_sRNA-seq

value: early embryos (2-cell_embryos)


title: expo [908_1_4]

value: CD Haireless rat


title: expo [908_2_2]

value: male


title: expo [909_1_1]


title: CM-d2_rep2

source_name: cells under CM differentiation at day 2


title: CSR-1_FLAG_adults_IP_rep2_sRNA-seq

description: immunoprecipitated sRNA

data_processing:
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) was trimmed from the raw reads using cutadapt (version 1.18)
The trimmed reads were sorted by sequence using fastq-sort (from fastq-tools version 0.8) with option -s and deduplicated using a custom haskell program, keeping the highest quality among duplicates, at any given position
The 5' and 3' 4 nt UMIs were removed from the deduplicated reads using cutadapt (version 1.18) with options -u 4 and -u -4
After removing UMIs, the reads from 18 to 24 nt were selected using bioawk version 20110810 (git commit fd40150b7c557da45e781a999d372abbc634cc21)
The size-selected reads were mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with options -L 6 -i S,1,0.8 -N 0
The reads that failed to map were inspected using grep -E -B 1 -A 2 "^G[ACGTN]{20,25}T+$" to detect possible reads starting with G with 20 to 25 nt followed by a poly-U tail that might have prevented the mapping, and this tail was removed from such reads using a custom haskell program before re-mapping them.
Mapped and remapped reads were used to estimate the abundance of small RNAs derived from structural RNAs using featureCounts (version 1.6.3) with options -O -s 1 --fracOverlap 1 and annotations corresponding to tRNA, snRNA, snoRNA, rRNA or RNA (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The abundance of non-structural RNAs was estimated by subtracting the above counts from the number of mapped and remapped reads.
Initially mapped reads were classified using a custom python program according to their length, composition and on the annotations on which they mapped. Reads that didn't match miRNA and piRNA annotations were considered as potential endo-siRNAs.
The potential endo-siRNAs of size 21 to 23 nt that started with G were classified as “si_22G” if they mapped antisense to annotation belonging to the following categories: DNA transposons, RNA transposons, satellites, simple repeats (as annotated in http://hgdownload.cse.ucsc.edu/goldenPath/ce11/database/rmsk.txt.gz) or pseudogene or protein-coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The “si_22G” reads were re-mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with options -L 6 -i S,1,0.8 -N 0
The resulting alignment was used to generate the normalized bigwig file using millions of non-structural RNAs as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.35) and bedGraphToBigWig (version 4)
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of “si_22G” RNAs antisense to protein coding genes along the genome

source_name: nematodes

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food at a density of maximum 40,000 animals per 15 cm Petri dish. Worms were carefully monitored using a stereomicroscope and bleached shortly after worms started to produce the first embryos. The harvested early embryos were washed three times with M9 buffer and suspended in the extraction buffer (50 mM Tris, 300 mM NaCl, 1 mM EDTA, 0.1% NP40, protease inhibitor cocktails (Thermo Scientific, 1860932)) followed by 30 strokes using a metal dounce on ice. Crude protein extracts were spun at 12,000 rpm at 4°C for 10 minutes. Protein concentration was quantified by the Bradford assay, and 1 mg of protein extract was incubated with 15 μl of packed Anti-FLAG M2 Magnetic Agarose Beads (Sigma M8823) for 1 hour at 4°C. After four washes with RIP washing buffer (50 mM Tris, 500 mM NaCl, 1 mM EDTA, 0.1% NP40, protease inhibitor cocktails (Thermo Scientific, 1860932)), the beads were resuspended in 750 µL of TRIzol LS reagent (Ambion) to extract the immunoprecipitated RNAs. 750 µL of TRIzol LS reagent (Ambion) was also added to 10% of protein extract before the immunoprecipitation (Input). RNA extracted from IPs and Inputs were size selected from 15% UREA PAGE gel.
The library preparation was performed as essentially described by Jayaprakash et al., 2011, except that a 5’ polyphosphatase (lucigen RP8092H) treatment was performed to be able to clone tri-phosphate small RNAs, and that the PAGE gel extraction after each ligation was substitute with purification by 1.8 volumes of Agencourt RNAClean XP Beads (Beckman Coulter, NC0068576) and 3 volumes of isopropanol. The multiplexed amplified libraries were further purified using PippinPrep DNA size selection with 3% gel cassettes and the following parameters for the selection: BP start (115) and the BP end (165). The purified libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced either on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005).

value: whole anymal

value: yound adults


title: CSR-1_FLAG_adults_Input_rep1_sRNA-seq

value: young adults


title: S68 bronchial epithelium

value: Vehicle


title: CM-d3_rep1

value: human induced pluripotent stem cells (iPSCs)

value: hPSC-derived cardiomyocytes (CMs)


title: his11_egg6_3UTR_early_embryos_CSR-1_FLAG_Input_rep1_sRNA-seq

value: Mex-5P::mCherry::his-11::egg-6 3'UTR::tbb-2 3'UTR II; csr-1(gc017[csr-1::3xFLAG::1HA]) IV

value: early embryos


title: his11_egg6_3UTR_early_embryos_CSR-1_FLAG_Input_rep2_sRNA-seq


title: sham [077_1_1]

value: Sham:unexposed rat

value: skin


title: S66 bronchial epithelium

value: Rapa + Fla


title: S71 bronchial epithelium

value: Rapa


title: his11_egg6_3UTR_early_embryos_CSR-1_FLAG_IP_rep1_sRNA-seq

description: immunoprecipitated sRNA

value: whole embryo


title: S65 bronchial epithelium

value: IOX2 + Fla


title: expo_young [908_2_3]

tag: age

value: young; 2-3 months

value: Expo:94 GHz chronic exposed rat


title: CM-d0_rep2

source_name: human CD34-iPSCs


title: CSR-1_FLAG_adults_Input_rep2_sRNA-seq


title: his11_tbb2_3UTR_early_embryos_CSR-1_FLAG_Input_rep2_sRNA-seq

value: Mex-5P::mCherry::his-11::tbb-2 3'UTR II; csr-1(gc017[csr-1::3xFLAG::1HA]) IV


title: CM-d0_rep1


title: his11_tbb2_3UTR_early_embryos_CSR-1_FLAG_IP_rep2_sRNA-seq

description: immunoprecipitated sRNA


title: HepG2: shTCTP_3rd

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 20 -p 16 --no-discordant. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Qvalue <= 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: HepG2 cells were cultured under standard conditions with Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
The HepG2 cells were ground into fine powder before RNA extraction. Total RNA was extracted by the hot phenol method. The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 10μg of the total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.  For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions. Illumina HiSeq 4000 was used to collect data from 150-bp pair-end sequencing (ABlife Inc., Wuhan, China).

treatment_protocol: shRNA plasmid transfection of HepG2 cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48 h for q-PCR analysis.

tag: cell line

tag: genotype/variation

value: TCTP knock-down


title: CSR-1_FLAG_adults_IP_rep1_sRNA-seq

description: immunoprecipitated sRNA

tag: genotype

value: whole anymal

value: yound adults


title: his11_tbb2_3UTR_early_embryos_CSR-1_FLAG_IP_rep1_sRNA-seq

description: immunoprecipitated sRNA


title: CSR-1_degron_CSR-1_rescue_ADH_embryos_rep1_RNA-seq

description: total RNA, rRNA-depleted

data_processing:
Reads were mapped on the C. elegans genome (WBcel235) using hisat2 (version 2.1.0) with default parameters
Mapped reads were used to estimate the abundance of protein coding genes using featureCounts (version 1.6.3) with options -O -M --primary -s 2 --fracOverlap 0 and annotations corresponding to protein coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The alignment was used to generate the normalized bigwig file using millions of summed forward reads per kilobase in protein coding genes as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.35) and bedGraphToBigWig (version 4)
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of RNAs along the genome

growth_protocol: Strains were maintained at 20°C, using standard methods (Brenner, 1974). Bristol N2 was the wild-type strain used.

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food at a density of maximum 40,000 animals per 15 cm Petri dish. Worms were carefully monitored using a stereomicroscope and bleached shortly after worms started to produce the first embryos. The harvested early embryos were washed three times with M9 buffer and the embryos pellet was frozen in dry ice with Trizol Reagent (Ambion). After five repetitions of freeze and thaw, total RNA was isolated according to the Trizol Reagent protocol. Ten micrograms of RNA were treated with 2 U of Turbo DNase (Ambion) at 37°C for 30 minutes followed by phenol-extraction and isopropanol precipitation. Agilent 2200 TapeStation System was used to evaluate the RIN indexes of all the RNA preps, and only samples with RIN > 8 was used for downstream applications.  For RNA-seq on FACS sorted embryos, early embryos were crosslinked with formaldehyde to block cell division and were reverse crosslinked at 70˚C for 30 minutes in RIPA buffer prior to RNA extraction.
DNase-treated total RNA with RIN > 8 was used to prepare strand-specific RNA libraries. We developed an RNase H based method to degrade C. elegans and mitochondrial ribosomal RNAs (rRNAs) using 50nt oligos complementary to rRNA and mtRNA C. elegans sequences. 100 ng of DNase-treated total RNA was mixed with 1.5 µg of oligos at equimolar concentration and 1X probe hybridization buffer (200 mM NaCl, 10 mM Tris pH 7.5) and incubated in a thermocycler using the following parameters: 2 minutes at 95°C followed by 0.1°C/sec at 95-45°C, and 2 minutes hold at 45°C. Next 2 µl of Thermostable RNase H (epicentre) was added to the reactions together with 1X RNase H reaction buffer 50 mM Tris pH 7.5, 100 mM NaCl, 10 mM MgCl2) and incubated for 30 minutes at 45°C. Next, digested RNAs were treated with 2 U of Turbo DNase (Ambion) at 37°C for 30 minutes followed by purification using 2.2 volumes of Agencourt RNAClean XP Beads (Beckman Coulter, NC0068576) following the manufacturer’s instructions. 100 ng of Ribosomal-depleted RNAs were then used to generate strand-specific RNA libraries using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (E7760S). Multiplexed RNA libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005).

treatment_protocol: Auxin or Ethanol (auxin control) treatment were performed by placing worms on plates containing 500µM Auxin 0,5% Ethanol or 0,5% Ethanol at the beginning of oogenesis. Formaldehyde fixation was performed by treating early embryos immediately after bleaching with 2% formaldehyde in M9 for 30 minutes.

value: ieSi64 [gld-1p::TIR1::mRuby::gld-1 3'UTR + Cbr-unc-119(+)] II; csr-1(gc029[degron::mCherry::3xflag::ha::csr-1]); gcSi1 [mex-5p::csr1[D769A]::GFP::tbb-2 3'UTR + Cbr-unc-119(+)] IV

value: Auxin (500microM) from beginning of oogenesis


title: CSR-1_degron_CSR-1_rescue_DDH_embryos_rep2_RNA-seq

description: total RNA, rRNA-depleted

value: ieSi64 [gld-1p::TIR1::mRuby::gld-1 3'UTR + Cbr-unc-119(+)] II; csr-1(gc029[degron::mCherry::3xflag::ha::csr-1]); gcSi2 [mex-5p::csr1::GFP::tbb-2 3'UTR + Cbr-unc-119(+)] IV


title: CSR-1_degron_CSR-1_rescue_ADH_embryos_rep2_RNA-seq

description: total RNA, rRNA-depleted


title: S57 bronchial epithelium

value: Vehicle


title: S63 bronchial epithelium

value: Fla


title: S59 bronchial epithelium


title: HepG2: shTCTP_2nd


title: S42 bronchial epithelium


title: HepG2: shTCTP_1st


title: S39 bronchial epithelium


title: HepG2: shCtrl_3rd

value: control


title: his11_tbb2_3UTR_early_embryos_CSR-1_FLAG_Input_rep1_sRNA-seq

value: early embryos


title: CSR-1_degron_CSR-1_rescue_DDH_embryos_rep1_RNA-seq

description: total RNA, rRNA-depleted


title: CM-d2_rep1

value: human induced pluripotent stem cells (iPSCs)

value: hPSC-derived cardiomyocytes (CMs)


title: CSR-1_degron_CSR-1_rescue_ADH_embryos_rep1_Deg-seq

description: 5' monophosphate RNA

data_processing:
Library strategy: Degradome-sequencing
Raw reads were trimmed at their low quality 3' end using seqtk (version 1.3-r115-dirty) as follows: seqtk trimfq -b 4
The trimmed reads were mapped on the C. elegans genome ce11 (WBcel235) using bowtie2 (version 2.3.4.3) with default settings.
Mapped reads were counted against transcript annotations using featureCounts (version v1.6.3) with options -O -M --primary --fracOverlap 0
The alignment was also used to generate the normalized bigwig file using counts per million as normalizer. This was done with a custom bash script using bamCoverage from deepTools (version 3.4.3)
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of reads along the genome

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food at a density of maximum 40,000 animals per 15 cm Petri dish. Worms were carefully monitored using a stereomicroscope and bleached shortly after worms started to produce the first embryos. The harvested early embryos were washed three times with M9 buffer embryo and the embryos pellet was frozen in dry ice with Trizol reagent (Ambion). After five repetitions of freeze and thaw in dry ice, total RNA was isolated according to the Trizol Reagent protocol. Agilent 2200 TapeStation System was used to evaluate the RIN indexes of all the RNA preps, and only samples with RIN > 8 was used for downstream applications. 6 µg of total RNAs with RIN > 8 was size selected from 15% UREA PAGE gel and used to generate small RNA libraries.
DNase-treated total RNA with RIN > 8 was used to prepare strand-specific RNA libraries.  We developed an RNase H based method to degrade C. elegans and mitochondrial ribosomal RNAs (rRNAs) using 50nt oligos complementary to rRNA and mtRNA C. elegans sequences. 1 mg of DNase-treated total RNA was mixed with 1.5 µg of oligos at equimolar concentration and 1X probe hybridization buffer (200 mM NaCl, 10 mM Tris pH 7.5) and incubated in a thermocycler using the following parameters: 2 minutes at 95°C followed by 0.1°C/sec at 95-45°C, and 2 minutes hold at 45°C. Next 2 µl of Thermostable RNase H (epicentre) was added to the reactions together with 1X RNase H reaction buffer 50 mM Tris pH 7.5, 100 mM NaCl, 10 mM MgCl2) and incubated for 30 minutes at 45°C. Next, digested RNAs were treated with 2 U of Turbo DNase (Ambion) at 37°C for 30 minutes followed by purification of >200nt RNA molecules using Zymo RNA Clean & Concentrator-5 (Zymo Research: Cat R1015). 5’ end adapter was ligated to 5’ monophosphate RNA molecules using T4RNA ligase I (Ambion) and incubated at 25 °C for 2h followed by another round of purification of >200nt RNA molecules using Zymo RNA Clean & Concentrator-5. cDNA was synthesized using random hexamer and Superscript IV reverse transcriptase (Thermo Fisher) followed by a first round of PCR amplification using Q5® High-Fidelity DNA Polymerase (New England Biolabs). PCR products >200nt were enriched using 1.8X volumes of AMPure XP for PCR Purification (Beckman Coulter) followed by a second round of PCR amplification. PCR products ranging from 250-450bp were purified on 1% agarose gel and eluted with Qiagen gel extraction kit. The purified libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced either on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005).

value: whole embryo


title: CSR-1_degron_CSR-1_rescue_DDH_embryos_rep1_Deg-seq

description: 5' monophosphate RNA


title: S37 bronchial epithelium


title: HepG2: shCtrl_1st


title: his11_egg6_3UTR_early_embryos_rep2_sRNA-seq

data_processing:
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) was trimmed from the raw reads using cutadapt (version 1.18).
The trimmed reads were sorted by sequence using fastq-sort (from fastq-tools version 0.8) with option -s and deduplicated using a custom haskell program, keeping the highest quality among duplicates, at any given position.
The 5' and 3' 4 nt UMIs were removed from the deduplicated reads using cutadapt (version 1.18) with options -u 4 and -u -4.
After removing UMIs, the reads from 18 to 24 nt were selected using bioawk version 20110810 (git commit fd40150b7c557da45e781a999d372abbc634cc21).
The size-selected reads were mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with options -L 6 -i S,1,0.8 -N 0.
The reads that failed to map were inspected using grep -E -B 1 -A 2 "^G[ACGTN]{20,25}T+$" to detect possible reads starting with G with 20 to 25 nt followed by a poly-U tail that might have prevented the mapping, and this tail was removed from such reads using a custom haskell program before re-mapping them.
Mapped and remapped reads were used to estimate the abundance of small RNAs derived from structural RNAs using featureCounts (version 1.6.3) with options -O -s 1 --fracOverlap 1 and annotations corresponding to tRNA, snRNA, snoRNA, rRNA or RNA (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz).
The abundance of non-structural RNAs was estimated by subtracting the above counts from the number of mapped and remapped reads.
Initially mapped reads were classified using a custom python program according to their length, composition and on the annotations on which they mapped. Reads that didn't match miRNA and piRNA annotations were considered as potential endo-siRNAs.
The potential endo-siRNAs of size 21 to 23 nt that started with G were classified as “si_22G” if they mapped antisense to annotation belonging to the following categories: DNA transposons, RNA transposons, satellites, simple repeats (as annotated in http://hgdownload.cse.ucsc.edu/goldenPath/ce11/database/rmsk.txt.gz) or pseudogene or protein-coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz).
The “si_22G” reads were re-mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with options -L 6 -i S,1,0.8 -N 0.
The resulting alignment was used to generate the normalized bigwig file using millions of non-structural RNAs as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.35) and bedGraphToBigWig (version 4).
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of “si_22G” RNAs along the genome.

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food at a density of maximum 40,000 animals per 15 cm Petri dish. Worms were carefully monitored using a stereomicroscope and bleached shortly after worms started to produce the first embryos. The harvested early embryos were washed three times with M9 buffer embryo and the embryos pellet was frozen in dry ice with Trizol reagent (Ambion). After five repetitions of freeze and thaw in dry ice, total RNA was isolated according to the Trizol Reagent protocol. Agilent 2200 TapeStation System was used to evaluate the RIN indexes of all the RNA preps, and only samples with RIN > 8 was used for downstream applications. 6 µg of total RNAs with RIN > 8 was size selected from 15% UREA PAGE gel and used to generate small RNA libraries.
The library preparation was performed as essentially described by Jayaprakash et al., 2011, except that a 5’ polyphosphatase (Lucigen RP8092H) treatment was performed to be able to clone tri-phosphate small RNAs, and that the PAGE gel extraction after each ligation was substitute with purification by 1.8 volumes of Agencourt RNAClean XP Beads (Beckman Coulter, NC0068576) and 3 volumes of isopropanol. The multiplexed amplified libraries were further purified using PippinPrep DNA size selection with 3% gel cassettes and the following parameters for the selection: BP start (115) and the BP end (165). The purified libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced either on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005).

value: total small RNAs


title: S36 bronchial epithelium

value: Rapa


title: his11_tbb2_3UTR_early_embryos_rep2_sRNA-seq


title: S34 bronchial epithelium


title: siBTF3_2

city: Dalian

first: Hailing

last: Cheng

address: 467 Zhongshan Road

institute: The Second Hospital of Dalian Medical University

data_processing:
Illunima Casava 1.8 software used for basecalling.
Clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using Hisat2 v2.0.5 and  paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.  We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of  splice junctions based on the gene model annotation file and thus a better mapping  result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then  FPKM of each gene was calculated based on the length of the gene and reads count  mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript  sequence per Millions base pairs sequenced, considers the effect of sequencing depth  and gene length for the reads count at the same time, and is currently the most  commonly used method for estimating gene expression levels.
Genome_build: GRCh37(hg37)
Supplementary_files_format_and_content: Tab-delimited xls files include FPKM values for all Samples

source_name: PC-3 cell lines

extract_protocol:
RNAs were isolated from PC-3 cells using the TRIzol (Invitrogen) reagent by following the company manual. RNA degradation and contamination was monitored on 1% agarose gels.  RNA purity was checked using the NanoPhotometer® spectrophotometer  (IMPLEN, CA, USA) .  RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0  Flurometer (Life Technologies, CA, USA).  RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer  2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: PC-3 cells were transfected with siControl or siBTF3 for 48 hours.

tag: origin

value: Prostate cancer

tag: morphology

value: Epithelial

value: siBTF3 transfected


title: CSR-1_FLAG_embryos_Input_rep3_sRNA-seq

data_processing:
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) was trimmed from the raw reads using cutadapt (version 1.18).
The trimmed reads were sorted by sequence using fastq-sort (from fastq-tools version 0.8) with option -s and deduplicated using a custom haskell program, keeping the highest quality among duplicates, at any given position.
The 5' and 3' 4 nt UMIs were removed from the deduplicated reads using cutadapt (version 1.18) with options -u 4 and -u -4.
After removing UMIs, the reads from 18 to 24 nt were selected using bioawk version 20110810 (git commit fd40150b7c557da45e781a999d372abbc634cc21).
The size-selected reads were mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with options -L 6 -i S,1,0.8 -N 0.
The reads that failed to map were inspected using grep -E -B 1 -A 2 "^G[ACGTN]{20,25}T+$" to detect possible reads starting with G with 20 to 25 nt followed by a poly-U tail that might have prevented the mapping, and this tail was removed from such reads using a custom haskell program before re-mapping them.
Mapped and remapped reads were used to estimate the abundance of small RNAs derived from structural RNAs using featureCounts (version 1.6.3) with options -O -s 1 --fracOverlap 1 and annotations corresponding to tRNA, snRNA, snoRNA, rRNA or RNA (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz).
The abundance of non-structural RNAs was estimated by subtracting the above counts from the number of mapped and remapped reads.
Initially mapped reads were classified using a custom python program according to their length, composition and on the annotations on which they mapped. Reads that didn't match miRNA and piRNA annotations were considered as potential endo-siRNAs.
The potential endo-siRNAs of size 21 to 23 nt that started with G were classified as “si_22G” if they mapped antisense to annotation belonging to the following categories: DNA transposons, RNA transposons, satellites, simple repeats (as annotated in http://hgdownload.cse.ucsc.edu/goldenPath/ce11/database/rmsk.txt.gz) or pseudogene or protein-coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz).
The “si_22G” reads were re-mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with options -L 6 -i S,1,0.8 -N 0.
The resulting alignment was used to generate the normalized bigwig file using millions of non-structural RNAs as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.35) and bedGraphToBigWig (version 4).
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of “si_22G” RNAs antisense to protein coding genes along the genome.

tag: ip antibody

value: total sRNA


title: CSR-1_FLAG_embryos_Input_rep2_sRNA-seq


title: S32 bronchial epithelium


title: his11_tbb2_3UTR_early_embryos_rep1_sRNA-seq


title: CSR-1_FLAG_embryos_IP_rep2_sRNA-seq

value: Anti-FLAG M2 Magnetic Agarose Beads (Sigma M8823)

value: immunoprecipitated sRNA


title: siBTF3_1


title: CSR-1_FLAG_embryos_IP_rep3_sRNA-seq


title: CSR-1_degron_CSR-1_rescue_DDH_embryos_rep2_Deg-seq

description: 5' monophosphate RNA

value: Auxin (500microM) from beginning of oogenesis


title: S24 bronchial epithelium

value: IOX2 + Fla


title: CSR-1_FLAG_embryos_Input_rep1_sRNA-seq


title: CSR-1_FLAG_embryos_IP_rep1_sRNA-seq


title: siNC_1

value: siControl transfected


title: his11_egg6_3UTR_early_embryos_rep1_Ribo-seq

data_processing:
library strategy: Ribo-seq
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) was trimmed from the raw reads using cutadapt (version 1.18).
The trimmed reads were sorted by sequence using fastq-sort (from fastq-tools version 0.8) with option -s and deduplicated using a custom haskell program, keeping the highest quality among duplicates, at any given position.
The 5' and 3' 4 nt UMIs were removed from the deduplicated reads using cutadapt (version 1.18) with options -u 4 and -u -4.
After removing UMIs, the reads from 28 to 30 nt were selected using bioawk version 20110810 (git commit fd40150b7c557da45e781a999d372abbc634cc21).
The size-selected reads were mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with options -L 6 -i S,1,0.8 -N 0.
Mapped reads were used to estimate the abundance of fragments derived from structural RNAs using featureCounts (version 1.6.3) with options -O -s 1 --fracOverlap 1 and annotations corresponding to tRNA, snRNA, snoRNA, rRNA or RNA (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz).
The abundance of non-structural RNAs was estimated by subtracting the above counts from the number of mapped reads.
Reads mapping on sense orientation on annotated protein coding genes were considered as Ribosome-protected fragments (RPF).
RPF reads were extracted from mapping results using samtools (version 1.9) and bedtools (version 2.27.1).
The 28-30nt and RPF reads were re-mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with options -L 6 -i S,1,0.8 -N 0.
The resulting alignments were used to generate normalized bigwig files using millions of non-structural RNAs as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.35) and bedGraphToBigWig (version 4).
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of 28-30nt or RPF (for N2) along the genome.

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food at a density of maximum 40,000 animals per 15 cm Petri dish. Worms were carefully monitored using a stereomicroscope and bleached shortly after worms started to produce the first embryos. The harvested early embryos were washed three times with M9 buffer and lysate in polysome buffer (140 mM KCl, 5 mM MgCl2, 20 mM Tris HCl pH 8, 1% Triton X-100, Halt protease inhibitor cocktail (Thermo Scientific, 1860932), RiboLock RNase Inhibitor (Thermo Scientific, EO0381) in liquid nitrogen and fractionated on sucrose gradient by ultracentrifugation. RNA from monosome fraction was treated with 2 U of Turbo DNase (Ambion) at 37°C for 30 minutes and fragments of 28-30 nucleotides were size selected after running on a TBE-Urea gel 15%.
3’ phosphate and 5’-OH of 28-30 Ribosome protected fragments was repaired using Polynucleotide kinase (New England biolabs, M0201S). RNA was ligated to 3’end adapter using T4 RNA ligase 2 Truncated KQ and to 5’ adapter using T4 RNA ligase 1 (New England biolabs, M0204S). cDNA was PCR amplified with specific primers using Q5 High-Fidelity 2X Master Mix (New England biolabs, M0492S). The purified libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced either on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005).

value: Ribosome protected RNA


title: S22 bronchial epithelium

value: Fla


title: CSR-1_degron_CSR-1_rescue_ADH_embryos_rep2_Deg-seq

description: 5' monophosphate RNA

value: ieSi64 [gld-1p::TIR1::mRuby::gld-1 3'UTR + Cbr-unc-119(+)] II; csr-1(gc029[degron::mCherry::3xflag::ha::csr-1]); gcSi1 [mex-5p::csr1[D769A]::GFP::tbb-2 3'UTR + Cbr-unc-119(+)] IV

value: early embryos


title: his11_tbb2_3UTR_early_embryos_rep2_Ribo-seq


title: his11_egg6_3UTR_early_embryos_rep1_sRNA-seq


title: HepG2: shCtrl_2nd

value: control


title: Dermal papilla-derived exosomes, P8-Exos3

first: Yuxin

address: Nanfang Dadao Street, Baiyun district

institute: Nanfang Hospital of Southern Medical University

description: small RNA

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina HiSeq X Ten platform and single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. And reads were trimmed and cleaned by removing the sequences smaller than 15 nt or longer than 35 nt. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Use Bowtie tools soft, The Clean Reads respectively with Silva database, GtRNAdb database, Rfam database and Repbase database sequence alignment, filter ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats. The remaining reads were used to detect known miRNA and novel miRNA predicted by comparing with Genome and known miRNAs from miRBase. Randfold tools soft was used for novel miRNA secondary structure prediction.
Genome_build: hg18
Supplementary_files_format_and_content: tab-deimited text files include FPKM values for each Sample.

source_name: dermal papilla-derived exosomes

growth_protocol: Healthy human scalp specimens were obtained from patients undergoing facelift surgery, human hair papilla cells (hDPCs) were isolated and cultured in DMEM (Gibco, Grand Island, NY, US) with 10% exosome-free FBS (HyClone, Logan, UT, US) and 100 U/ml penicillin–streptomycin (Gibco). All cells were incubated with 5% CO2 at 37 °C.

extract_protocol:
Media were collected from human dermal papilla cultures (P3 or P8) and stored at -20 °C. Exosomes were isolated using ultracentrifugation (SW 32 Ti swinging-bucket rotor in a Beckman Coulter L8-80M Ultracentrifuge), as described previously.[26] Briefly, 500 ml hDPC culture medium was centrifuged at 2000 × g for 20 minutes, then at 10,000 × g for 20 minutes, to remove cells and debris. The supernatant was filtered through a 0.2 µm syringe filter (Corning, Germany), and ultracentrifuged at 100,000 × g for 60 minutes at 4 °C twice. The final pellet was suspended in 100–200 µl PBS and stored at -80 °C.
Libraries for miRNA sequencing were generated using the NEBNext Multiplex Small RNA Library Prep Kit for Illumina (NEB,USA) according to the manufacturer’s instructions. Briefly, First of all, ligated the 3′ SR Adaptor. Mixed 3′ SR Adaptor for Illumina, RNA and Nuclease-Free Water, mixture system after incubation for 2 minutes at 70 degrees in a preheated thermal cycler. Tube was transfer to ice. Then, add 3′ Ligation Reaction Buffer (2X) and 3′ Ligation Enzyme Mix ligate the 3′ SR Adaptor. Incubated for 1 hour at 25°C in a thermal cycler. To prevent adaptor-dimer formation, the SR RT Primer hybridizes to the excess of 3′ SR Adaptor (that remains free after the 3′ ligation reaction) and transforms the single stranded DNA adaptor into a double-stranded DNA molecule. dsDNAs are not substrates for ligation mediated. The second, ligated the 5′ SR Adaptor. Then, reverse transcription synthetic first chain. Last, PCR amplification and Size Selection. PAGE gel was used to electrophoresis fragment screening purposes, rubber cutting recycling as the pieces get small RNA libraries. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Media were collected from human dermal papilla cultures (P3 or P8).

value: dermal papilla cells derived exosomes

tag: passage

value: passage 8


title: S20 bronchial epithelium

value: Rapa


title: his11_tbb2_3UTR_early_embryos_rep1_Ribo-seq

value: whole embryo


title: N2_embryos_rep3_Ribo-seq


title: S27 bronchial epithelium

value: Rapa + Fla


title: Dermal papilla-derived exosomes, P8-Exos2

description: small RNA


title: N2_embryos_rep2_Ribo-seq


title: siNC_2

value: Prostate cancer

value: Epithelial


title: S18 bronchial epithelium


title: N2_embryos_rep1_Ribo-seq


title: S16 bronchial epithelium

value: Vehicle


title: Dermal papilla-derived exosomes, P8-Exos1

description: small RNA


title: Dermal papilla-derived exosomes, P3-Exos3

description: small RNA

value: passage 3


title: his11_egg6_3UTR_early_embryos_rep2_RNA-seq

data_processing:
Reads were mapped on the C. elegans genome (WBcel235) using hisat2 (version 2.1.0) with default parameters.
Mapped reads were used to estimate the abundance of protein coding genes using featureCounts (version 1.6.3) with options -O -M --primary -s 2 --fracOverlap 0 and annotations corresponding to protein coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz).
The alignment was used to generate the normalized bigwig file using millions of summed forward reads per kilobase in protein coding genes as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.35) and bedGraphToBigWig (version 4).
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of RNAs along the genome.

value: total RNA, rRNA-depleted


title: his11_egg6_3UTR_early_embryos_rep2_Ribo-seq


title: his11_tbb2_3UTR_early_embryos_rep2_RNA-seq


title: Dermal papilla-derived exosomes, P3-Exos2

description: small RNA


title: his11_egg6_3UTR_early_embryos_rep1_RNA-seq


title: S11 bronchial epithelium


title: his11_tbb2_3UTR_early_embryos_rep1_RNA-seq


title: S09 bronchial epithelium

value: IOX2 + Fla


title: N2_embryos_rep2_RNA-seq


title: S08 bronchial epithelium


title: Dermal papilla-derived exosomes, P3-Exos1

description: small RNA


title: N2_embryos_rep1_RNA-seq


title: his11_egg6_3UTR_early_embryos_CSR-1_FLAG_IP_rep2_sRNA-seq

description: immunoprecipitated sRNA

value: Mex-5P::mCherry::his-11::egg-6 3'UTR::tbb-2 3'UTR II; csr-1(gc017[csr-1::3xFLAG::1HA]) IV


title: S05 bronchial epithelium


title: CSR-1_degron_control_late_embryos_rep2_RNA-seq

value: ieSi64 [gld-1p::TIR1::mRuby::gld-1 3'UTR + Cbr-unc-119(+)] II; csr-1(gc029[degron::mCherry::3xflag::ha::csr-1])

value: late embryos

value: Ethanol (auxin control) from beginning of oogenesis


title: CSR-1_degron_control_late_embryos_rep1_RNA-seq


title: delta flox microglia sample 1

city: Toronto

first: Shannon

last: Dunn

state: ON

address: 30 Bond Street, Office Location: 209 Victoria Street, 5th floor, 516

department: Keenan Research Centre for Biomedical Research

country: Canada

institute: St. Michael's Hospital

description:
Disease induction protocol: EAE was induced in mice by immunization with myelin oligodendrocyte glycoprotein (MOG) p35-55/CFA plus pertussis toxin. Mice were followed for clinical signs and were euthanized at 2-3 days after the onset of clinical symptoms.
Microglia isolation protoocol: Microglia were isolated from spinal cord and cerebellum tissue from N=9 mice per genotype.  Ttissue collected from 3 individual mice was pooled for one sample for isolation and sorting. Spinal cords and cerebellums from mice were digested with collagenase type IV and DNAse, central nervous system (CNS) mononuclear cells were separated from other cells and myelin debris using a Percoll gradient. CNS cells were labeled with CD45 and CD11b antibodies and DAPI and CD45low CD11b+ DAPI- cells were FACS sorted using a MoFlo Cell Sorter.
RNA extraction protocol: RNA was isolated using the PicoPure™ RNA Isolation Kit (Thermo Fisher Scientific).

data_processing:
Sample aligned to mouse reference genome GRCm38 using HISAT2
Transcripts assembly with Stringtie
Differential gene expression analysis with ballgown

source_name: microglia

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

tag: mouse strain

tag: Sex

value: Male

tag: disease

value: EAE


title: S03 bronchial epithelium

tag: donorid

tag: experiment


title: delta flox microglia sample 2


title: CSR-1_degron_control_late_embryos_rep3_RNA-seq

tag: treatment


title: CSR-1_degron_late_embryos_rep3_RNA-seq

tag: tissue

value: Auxin (500µM) from beginning of oogenesis


title: CX3CR1 microglia sample 2


title: CSR-1_degron_late_embryos_rep2_RNA-seq

tag: developmental stage


title: CSR-1_degron_late_embryos_rep1_RNA-seq

tag: molecule subtype


title: S01 bronchial epithelium

tag: condition


title: CSR-1_degron_control_early_embryos_rep2_RNA-seq

value: early embryos


title: N2_embryos_rep3_RNA-seq


title: CSR-1_degron_control_early_embryos_rep1_RNA-seq


title: CSR-1_degron_early_embryos_rep3_RNA-seq


title: CX3CR1 microglia sample 1


title: CSR-1_degron_early_embryos_rep2_RNA-seq


title: CSR-1_degron_early_embryos_rep1_RNA-seq


title: Late_embryos_rep2_RNA-seq

value: formaldehyde fixation


title: CSR-1_degron_control_early_embryos_rep3_RNA-seq

value: whole embryo


title: Early_embryos_rep2_RNA-seq


title: Murine intestinal organoids - Sandwich-Forskolin-12h

city: Boston

first: Allon

middle: M

last: Klein

state: MA

address: 210 Longwood Avenue

department: Systems Biology

institute: Harvard Medical School

description: adata_perturbations_merged_annotated_cg_122220.h5ad

data_processing:
Basecalling to obtain fastq files as described in https://github.com/AllonKleinLab/klunctions/tree/master/sam/inDrops_pipeline using the supplementary bash scripts bcl2fastq.sh and  bcl2fastq_perturb2.sh for each of the dome v. sandwich and perturbation experiments, respectively.
Gene expression counts in single cells were obtained from raw fastq files using the indrop.py pipeline  from https://github.com/AllonKleinLab/klunctions/tree/master/sam/inDrops_pipeline on 2020 07 22 and 2020 09 04; parameters are listed in supplementary yaml files:  20200722_sandwich_dome_rc.yaml and 20200904_perturb_rc.yaml for the dome v. sandwich and perturbation experiments, respectively.
The processed data files in for each sample consists of an annotated tsv.gz file with raw unfiltered gene counts (cells x genes), gene names, and barcodes; this file can be parsed into its respective matrix, barcodes, and genes using the following python command: hf.load_annotated_text(
hf.file_opener(input_path + s + '.counts.tsv.gz'),
delim='\t',
read_row_labels=True,
read_column_labels=True)
Genome_build: mm10; supplementary fasta formatted bowtie index with GFP sequences: mouse.GRCm38_withGFP.idx.fa
Supplementary_files_format_and_content: The processed data files in for each sample consists of an annotated tsv.gz file with raw unfiltered gene counts (cells x genes), gene names, and barcodes; this file can be parsed into its respective matrix, barcodes, and genes using the  python command described above.

source_name: Murine instestinal organoids

growth_protocol: Organoids were grown for 96 hours prior to treatment for 12 hours in ENR media.

extract_protocol:
Organoids were grown in either sandwich or dome culture in glass-bottom 12 well plates (Mattek;  P12G-1.5-14-F). Before dissociation, all pipette tips and transfer vessels were coated with 10% w/v BSA to  prevent loss of material. Media was aspirated and culture wells were washed twice with 1X PBS before  incubating in 1mL TrypLE Express (ThermoFisher Cat No. 12604-021). Upon addition of TrypLE Express,  a 1 mL pipette tip was used to mechanically detach organoids embedded in Matrigel from either sandwich  or dome cultures, taking care to scrape the bottom of the well with such force so as not to detach the glass  bottom coverslip, but to visibly remove the Matrigel from the coverslip. Organoids were incubated at 37°C  for between 20-30 minutes, monitoring every 5 minutes to check on the status of dissociation, and to  repeat brief mechanical disruption by trituration. Multiple wells (between 2 and 10) per condition were  pooled into a 15 mL falcon tube and diluted 1:1 with ice cold DMEM, and strained (40 μm [pluriSelect  43-10040-60]) into a 15 mL falcon tube. This cell solution was then centrifuged at 250xg in a spinning  bucket centrifuge for 1 minute at 4°C, and the suspension was aspirated. Cells were resuspended in 200  μL of 1% w/v BSA in 1X PBS, kept on ice, and cell count and viability were measured with a  hemocytometer immediately prior to single cell encapsulation with the inDrops method.
InDrops single cell RNA sequencing was performed as described before [Zilionis et al., 2019, Immunity, 50, 1317-1334.e10; Zilionis et al., 2017, Nat Protoc, 12, 44-73; Klein et al., 2015, Cell, 161, 1187-1201] with changes made as written in the publication associated with this GEO record. All reads were processed with the indrops.py pipeline found at https://github.com/AllonKleinLab/klunctions/tree/master/sam/inDrops_pipeline using the parameters included in the provided bash script files: submit_indrops_sandwich_dome_rc.sh and submit_indrops_perturb2.sh, for sandwich v. dome and perturbation experiments, respectively.
scRNA-seq

value: Murine instestinal organoids

value: Perturbation

tag: culture type

value: Sandwich

value: 100 µM Forskolin treatment for 12 hours


title: WTC-Day90-rep2

city: San Francisco

first: Bruce

last: Conklin

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

data_processing:
The read preprocessing and sequence alignment were performed using  the nf-core/rnaseq pipeline (Ewels et al., 2019). The input sequence was formatted as FASTQ and gene-level counts were based on NCBI gene annotation, in GTF format. Trim-galore (“Babraham Bioinformatics - Trim Galore!,” n.d.) was used to remove contaminated adapters and low-quality regions. The sequence quality was checked and controlled with FastQC (“Babraham Bioinformatics - FastQC A Quality Control tool for High Throughput Sequence Data,” n.d.).
Sequence reads were aligned to the hg38 reference assembly using STAR 2.6.1d (Dobin et al., 2013).
Gene-level counts were measured using "featureCounts" (Liao et al., 2014), part of the Subread suite (http://subread.sourceforge.net/). For the differentially expressed gene analysis, genes not expressed in at least two samples with at minimum 5 (raw) reads were filtered out at the beginning of the analysis. Then expression values were re-normalized using calcNormFactors in EdgeR (Robinson et al., 2010). Mean expression of each gene was modeled as a function of differentiation time, by comparing expression values at time points D0 and D60, and at time point D60 and D90, for each cell type. Gene-wise dispersions were estimated using a quasi-likelihood (QL) method implemented in glmQLFit in EdgeR (Robinson et al., 2010).
Then an empirical Bayes quasi-likelihood F-based test (glmQLFTest) was used to find DEGs (Lun et al., 2016). DEGs were determined based on an FDR threshold of 0.05, using the R function p.adjust (Benjamini and Hochberg, 1995).
To visualize the genes’ expression patterns during cell differentiation, a glmQLFTest model that includes all three differentiation time points was used. Genes that passed the 0.05 FDR threshold were clustered using the R package hopach (van der Laan and Pollard, 2001) and log2(Counts Per Million + 1) values were used to make a heatmap using the pheatmap package (“CRAN - Package pheatmap,” n.d.). These values were also used to make a heatmap for specific gene sets. Principal Component Analysis (PCA) was performed using the R function prcomp.
Genome_build: hg38
Supplementary_files_format_and_content: logCPM_allsamples.txt: This tab-delimited text file contains LogCPM values – log2(Counts Per Million + 1) – for each sample and each gene. Genes are rows and samples are columns.

source_name: iPSC-derived retinal pigment epithelial-like cells

growth_protocol: Cells were incubated in RPE Maintenance Media (RPE-MM), which was exchanged every Monday and supplemented to double feed volume every Thursday.

extract_protocol:
RNA was extracted using the Quick RNA Miniprep Kit (R1055, Zymo Research) according to the manufacturer’s instructions.
RNA library preparation used NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (New England Biolabs).

tag: differentiation stage

value: Day 90

tag: originating ipsc line

value: WTC

tag: differentiation protocol

value: WTC differentiation protocol:Fig 3A


title: Murine intestinal organoids - Sandwich-CFTRinh172-36h

growth_protocol: Organoids were grown for 96 hours prior to treatment for 36 hours in ENR media.

value: 100 µM CFTRinh-172 treatment for 36 hours


title: WTC-Day90-rep1


title: WTC-Day60-rep3

source_name: iPSC-derived retinal pigment epithelial-like progenitors

value: Day 60


title: Early_embryos_rep1_RNA-seq

tag: genotype

value: total RNA, rRNA-depleted


title: WTC-Day60-rep2


title: Murine intestinal organoids - Sandwich-DMSO-12h

value: DMSO treatment for 12 hours


title: 1cell_embryos_rep2_RNA-seq

value: 1 cell embryos


title: 1cell_embryos_rep1_RNA-seq


title: Murine intestinal organoids - Sandwich-untreated

description: adata_mg_annotated_merged_coarse_grain_no_ss_12092020.h5ad

growth_protocol: Organoids were grown for 166 hours (one week) in ENR media prior to dissociation.

value: Sandwich v. Dome

value: untreated


title: WTC-Day90-rep3


title: WTC-iPSC-rep3

source_name: human induced pluripotent stem cells (iPSC)

growth_protocol: All iPSCs were maintained in ‘complete’ StemFit media–StemFit Basic02 media (StemFit, AS-Bo1R, Ajinomoto) supplemented with 5.8nM bFGF (100-18B, Peprotech)–in Matrigel (356231, Corning)-coated cell culture plates.

value: Day 0


title: CSR-1_degron_embryos_control_rep2_RNA-seq

value: ieSi64 [gld-1p::TIR1::mRuby::gld-1 3'UTR + Cbr-unc-119(+)] II; csr-1(gc029[degron::mCherry::3xflag::ha::csr-1])

value: early embryos

value: Ethanol (auxin control) from beginning of oogenesis


title: WTC-Day60-rep1


title: CSR-1_degron_embryos_rep1_RNA-seq

value: whole embryo

value: Auxin (500µM) from beginning of oogenesis


title: Murine intestinal organoids - Dome-rep3

value: Murine instestinal organoids

value: Dome


title: CSR-1_degron_control_rep2_GRO-seq

data_processing:
library strategy: GRO-seq
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) was trimmed from the raw reads using cutadapt (version 1.18). The reads where the adaptor was not found were nonetheless kept ("untrimmed").
The 5' and 3' 4 nt UMIs were removed from the trimmed reads using cutadapt (version 1.18) with options -u 4 and -u -4.
The 5' 4 nt UMIs as well as 7 nt in 3' (to be sure to eliminate possibly unrecognized first adaptor bases, as well as preceding 3' 4 nt UMIs) were removed from the "untrimmed" reads using cutadapt (version 1.18) options -u 4 and -u -7.
Both types of reads were mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with default parameters, and the resulting alignment files were merged using samtools (version 1.9).
Mapped reads were used to estimate the abundance of protein coding genes using featureCounts (version 1.6.3) with options -O -M --primary -s 1 --fracOverlap 0 and annotations corresponding to protein coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz).
The merged alignment was used to generate the normalized bigwig file using millions of summed forward reads per kilobase in protein coding genes as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.26) and bedGraphToBigWig (version 4).
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of nascent RNAs along the genome.

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food at a density of maximum 40,000 animals per 15 cm Petri dish. Worms were carefully monitored using a stereomicroscope and bleached shortly after worms started to produce the first embryos. The harvested early embryos were washed three times with M9 buffer and nuclei were extracted in Nuclei extraction buffer using a metal dounce on ice. GRO-seq experiments were performed as described by Barucci et al., 2014 with minor modifications.
Biotinylated nascent RNAs were fragmented and immunoprecipitated using streptavidin conjugated beads (Invitrogen, 65001). 5’-OH of fragmented RNAs was repaired using Polynucleotide kinase (New England biolabs, M0201S). RNA was ligated to 3’end adapter using T4 RNA ligase 2 Truncated KQ and subjected to a second round of immunoprecipitation with streptavidin beads. RNA was ligated at 5’ end using T4 RNA ligase 1 (New England biolabs, M0204S) and biotinylated RNA was enriched for a third time. Purified RNA was reverse transcribed using SuperScript IV Reverse Transcriptase (Invitrogen, 18091050). cDNA was PCR amplified with specific primers using Q5 High-Fidelity 2X Master Mix (New England biolabs, M0492S). The purified libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced either on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005).

treatment_protocol: Auxin or Ethanol (auxin control) treatment were performed by placing worms on plates containing 500µM Auxin 0,5% Ethanol or 0,5% Ethanol at the beginning of oogenesis

value: biotinylated RNA


title: Late_embryos_rep1_RNA-seq

value: late embryos

value: formaldehyde fixation


title: CSR-1_degron_control_rep3_GRO-seq


title: Murine intestinal organoids - Dome-rep2


title: Murine intestinal organoids - Sandwich-DMSO-36h

value: Perturbation

value: Sandwich

value: DMSO treatment for 36 hours


title: WTC-iPSC-rep1

value: WTC

value: WTC differentiation protocol:Fig 3A


title: CSR-1_degron_control_rep1_GRO-seq


title: CSR-1_degron_rep2_GRO-seq


title: BTP8-Day90-rep3

value: Day 90

value: BTP8 differentiation protocol:Fig 4A


title: CSR-1_degron_embryos_control_rep1_RNA-seq

value: ieSi64 [gld-1p::TIR1::mRuby::gld-1 3'UTR + Cbr-unc-119(+)] II; csr-1(gc029[degron::mCherry::3xflag::ha::csr-1])

value: total RNA, rRNA-depleted


title: Murine intestinal organoids - Dome-rep1

value: Sandwich v. Dome

value: untreated


title: BTP8-Day90-rep2


title: MLL-AF9/iFLT3-ITD OFF In Vivo 48 hrs Replicate 3

first: Stefan

last: Bjelosevic

address: 450 Brookline Ave

department: Department of Pediatric Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Sequenced reads were demultiplexed using bcl2fastq (v2.17.1.14)
Basic QC performed on fastq files using FASTQC (v0.11.6)
Sequencing reads were trimmed using cutadapt (v1.9.1) and aligned to the mm10 reference genome using HISAT 2 (v2.0.4)
Read counting across genomic regions was performed using the Subread (v1.6.3) featureCounts function and differential gene expression analysis was performed in Rstudio (R v3.6.1) using Voom-Limma (v3.42.2)
Genome_build: mm10
Supplementary_files_format_and_content: Comma separated values file of featureCounts counts; Comma separated values file of normalized (voom-limma) counts

source_name: MLL-AF9/iFLT3-ITD Cell Line

growth_protocol: 1 million MLL-AF9/iFLT3-ITD cells were transplanted into NSG mice via tail vein IV injection. Mice were fed doxycycline-containing chow and water to maintain inducible iFLT3-ITD transgene expression, and leukaemias were allowed to engraft for 96 hours.

extract_protocol:
Mice were all culled after 48 hours and viable leukaemic cells sorted from the bone marrow. Cells were lysed in TriZol reagent and total DNAse-treated RNA isolated using the Zymogen RNA mini-prep kit
RNA libraries were prepared using the Lexogen QuantSeq 3'-mRNA Seq Library Prep kit

treatment_protocol: Half of the cohort of mice (n=3) was then placed on regular chow and water to deplete inducible iFLT3-ITD transgene expression for 48 hours, while the other half of the cohort (n=3) remained on doxycycline-containing chow and water to maintain inducible iFLT3-ITD transgene expression as a control.

tag: cell line

value: Acute myeloid leukaemia cell line (generated by transducing murine foetal liver cells with constitutively expressed MSCV-Luc2-IRES-MLL-AF9 and inducible TRE-tight-DsRED-IRES-FLT3-ITD retroviral vectors)

value: Inducible iFLT3-ITD depleted in vivo  for 48 hours (via feeding of normal chow and water and removal of doxycycline)


title: CSR-1_degron_rep3_GRO-seq

value: whole embryo

value: early embryos

value: Auxin (500µM) from beginning of oogenesis


title: Murine intestinal organoids - Dome-rep4

value: Murine instestinal organoids

value: Dome


title: MLL-AF9/iFLT3-ITD OFF In Vivo 48 hrs Replicate 2


title: LD04:00_2

city: shanghai

first: shiyu

last: sun

address: No.800 dong chuan road

institute: Shnaghai jiao tong university

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to rice  genome using Mapsplice v2.1.8 with  parameters -s 22 -p 15 --ins 6 --del 6 --non-canonical --bam -o
count counting
Genome_build: Tigr7
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Oryza sativa Japonica Group

source_name: the mitosis stages I anther sample at 04:00 in long-day condition rep_2

growth_protocol: Rice variety Oryza sativa L. ssp. japonica 9522 was grown in paddy fields around  Shanghai (China) during the normal rice growing season (June–August).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

treatment_protocol: Photoperiod  treatment was started after panicle initiation and continued until all samples were  collected: LD was the natural daylight condition, with a photoperiod of ~14 h; SD  conditions were simulated by covering plants with black cloth for the last 2 h of natural  daylight to create a 12 h photoperiod.

value: anther

tag: development stage

value: mitosis stages I

value: wide type


title: CSR-1_degron_embryos_rep2_RNA-seq


title: BTP8-Day90-rep1


title: WTC-iPSC-rep2

value: Day 0

value: WTC

value: WTC differentiation protocol:Fig 3A


title: BTP8-Day60-rep3

value: Day 60

value: BTP8 differentiation protocol:Fig 4A


title: MLL-AF9/iFLT3-ITD OFF In Vivo 48 hrs Replicate 1


title: MLL-AF9/iFLT3-ITD In Vivo ON Replicate 3

value: Untreated control – inducible iFLT3-ITD expression maintained in vivo by feeding mice doxycycline-containing chow and water


title: LD04:00_1

source_name: the mitosis stages I anther sample at 04:00 in long-day condition rep_1


title: BTP8-Day60-rep2


title: LD00:00_1

source_name: the mitosis stages I anther sample at 24:00 in long-day condition rep_1


title: LD00:00_2

source_name: the mitosis stages I anther sample at 24:00 in long-day condition rep_2


title: MLL-AF9/iFLT3-ITD In Vivo ON Replicate 2


title: MLL-AF9/iFLT3-ITD In Vivo ON Replicate 1


title: CSR-1_degron_rep1_GRO-seq

value: ieSi64 [gld-1p::TIR1::mRuby::gld-1 3'UTR + Cbr-unc-119(+)] II; csr-1(gc029[degron::mCherry::3xflag::ha::csr-1])

value: biotinylated RNA


title: BTP8-Day60-rep1


title: BTP8-iPSC-rep2


title: BTP8-iPSC-rep3


title: MLL-AF9/iFLT3-ITD OFF 48 hrs Replicate 2

data_processing:
Sequenced reads were demultiplexed using bcl2fastq (v2.17.1.14)
Basic QC performed on fastq files using FASTQC (v0.11.2)
Sequencing reads were trimmed using cutadapt (v1.5) and aligned to the mm10 reference genome using HISAT 2 (v2.0.4)
Read counting across genomic regions was performed using the Subread (v1.5.0-p3) featureCounts function and differential gene expression analysis was performed in Rstudio (R v3.6.1) using Voom-Limma (v3.42.2)
Genome_build: mm10
Supplementary_files_format_and_content: Comma separated values file of featureCounts counts; Comma separated values file of normalized (voom-limma) counts

growth_protocol: Cells were cultured in Anne Kelso Modified DMEM supplemented with 20% heat-inactivated foetal bovine serum, 100U/mL penicillin, 100 µg/mL streptomycin and 100 µM L-asparagine at 37 degrees celcius and 10% carbon dioxide

extract_protocol:
Cells were lysed in TriZol reagent and total DNAse-treated RNA isolated using the Zymogen RNA mini-prep kit
RNA libraries were prepared using the Lexogen QuantSeq 3'-mRNA Seq Library Prep kit

treatment_protocol: MLL-AF9/iFLT3-ITD cells were steady-state cultured in 1 µg/mL doxycycline (refreshed every 48 hours) to maintain iFLT3-ITD transgene expression (including for non-iFLT3-ITD depleted controls). For depletion experiments, cells were washed twice with PBS and cultured in doxycycline-free medium to deplete iFLT3-ITD transgene expression for the specified time period

value: Acute myeloid leukaemia cell line (generated by transducing murine foetal liver cells with constitutively expressed MSCV-Luc2-IRES-MLL-AF9 and inducible TRE-tight-DsRED-IRES-FLT3-ITD retroviral vectors)

value: Inducible iFLT3-ITD depleted for 48 hours (via doxycycline wash off)


title: MLL-AF9/iFLT3-ITD OFF 48 hrs Replicate 1


title: MLL-AF9/iFLT3-ITD OFF 48 hrs Replicate 3


title: LD20:00_2

source_name: the mitosis stages I anther sample at 20:00 in long-day condition rep_2


title: LD20:00_1

source_name: the mitosis stages I anther sample at 20:00 in long-day condition rep_1


title: LD16:00_1

source_name: the mitosis stages I anther sample at 16:00 in long-day condition rep_1


title: LD16:00_2

source_name: the mitosis stages I anther sample at 16:00 in long-day condition rep_2


title: HAEC, PS, 24hr, replicate 3

city: La Jolla

first: Shankar

last: Subramaniam

address: 9500 Gilman Dr MC 0412

department: Bioengineering

institute: University of California, San Diego

description:
haec_ps_24hr_n3
HAEC_Count_Gene_with_GeneInfo.txt

data_processing:
Mapping of the RNA-Seq reads to human genome and transcriptome: RNA-seq fastq files were aligned to the Human Reference Genome (version hg19 / Human.B37.3) and raw gene read counts (Refgene) were generated using the Omicsoft Aligner (OSA) OShell version = 9.0.8.75, using default parameter/options and ExpressionMeasurement=Count, SearchNovelExonJunction=True.
Genome_build: Human.B37.3 (based on NCBI build 37.3)
Supplementary_files_format_and_content: HAEC_Count_Gene_with_GeneInfo.txt: Tab-delimited text file; The first nine columns contain information on the RefSeq (Refgene) genes (such as gene symbol). The remaining columns correspond to samples and contain the raw mapped read counts. _n1, _n2 and _n3 correspond to replicates 1, 2 and 3, respectively.

source_name: HAEC

growth_protocol: HAECs (Cell Applications Cat# 03405A) were cultured in endothelial growth medium (Cell applications Cat#211-500) with 100 U/mL penicillin-streptomycin.

extract_protocol:
Samples for RNA sequencing analysis were collected at 1, 4, and 24 hrs after exposure to shear. Samples for RNA sequencing analysis were collected at 0 hr for the static condition.
The total RNA from HAECs were extracted by using TRizol RNA isolation reagent (Thermo Fisher, Cat#15596026). The RNA quality was assessed by RNA Integrity Numbers (RIN), using an Agilent Bioanalyzer, and all RNA samples used in this study had a RIN over 9.
The RNAs were ribo-depleted, fragmented, and random hexamer primed using Illumina TruSeq stranded mRNA sample preparation kit. Constructed cDNA library was subjected to single-ended 75-bp sequencing on Illumina Hi-seq 4000 instrument.

treatment_protocol: Pulsatile shear (PS) or oscillatory shear (OS) flows were applied to ECs with shear stresses of 12 ± 4 dyn/cm2 or 0.5 ± 4 dyn/cm2, respectively. ECs were also exposed to a “no flow” condition, and designated as a “static” condition.

value: Blood vessel

tag: cell type

value: HAEC

value: PS


title: HAEC, PS, 24hr, replicate 2

description:
haec_ps_24hr_n2
HAEC_Count_Gene_with_GeneInfo.txt


title: MLL-AF9/iFLT3-ITD OFF 24 hrs Replicate 3

value: Inducible iFLT3-ITD depleted for 24 hours (via doxycycline wash off)


title: LD12:00_2

source_name: the mitosis stages I anther sample at 12:00 in long-day condition rep_2

value: anther


title: BTP8-iPSC-rep1


title: MLL-AF9/iFLT3-ITD OFF 24 hrs Replicate 2


title: HAEC, PS, 24hr, replicate 1

description:
haec_ps_24hr_n1
HAEC_Count_Gene_with_GeneInfo.txt


title: LD12:00_1

source_name: the mitosis stages I anther sample at 12:00 in long-day condition rep_1

value: mitosis stages I


title: MLL-AF9/iFLT3-ITD OFF 24 hrs Replicate 1


title: LD08:00_2

source_name: the mitosis stages I anther sample at 08:00 in long-day condition rep_2

value: wide type


title: AFD WT replicate 3

city: Klosterneuburg

first: Thanh

middle: TK

last: Vuong-Brender

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria

description: samples_f1453303.csv_DESeq_norm_read_counts.txt

data_processing:
RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis available at https://github.com/lmb-seq/PRAGUI. PRAGUI integrates RNA-seq processing packages including Trim Galore, FastQC, STAR, DESeq2, HTSeq, Cufflinks and MultiQC.
Genome_build: WS255_WBcel235
Supplementary_files_format_and_content: DESeq normalized read counts

source_name: Neurons

growth_protocol: Synchronized worm grown on 9 cm rich peptone plates

extract_protocol:
Worms were incubated with lysis buffer containing DTT then mechanically (pipetting 12 min) and chemically (Pronase) dissociated. GFP cells were FACS-sorted
NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina®

value: WT

value: Neurons

tag: neuronal class

value: AFD

tag: strain name


title: AFD camt-1 mutant replicate 5


title: HAEC, PS, 4hr, replicate 3

description:
haec_ps_4hr_n3
HAEC_Count_Gene_with_GeneInfo.txt


title: AFD WT replicate 1


title: AFD WT replicate 4


title: AFD WT replicate 5


title: MLL-AF9/iFLT3-ITD ON Replicate 3

value: Untreated control – inducible iFLT3-ITD expression maintained in 1 µg/mL doxycycline


title: AFD WT replicate 2


title: HAEC, PS, 4hr, replicate 2

description:
haec_ps_4hr_n2
HAEC_Count_Gene_with_GeneInfo.txt