title: Arabidopsis, asf1a1b, Rep1

status: Public on Apr 08 2026

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

country: China

institute: Northwest A&F University

description: Library name: asf1a1b R1

data_processing:
Paired-end reads were subjected to filtering and trimming using the fastp tool (version 0.23.4).
The clean reads were aligned to the TAIR 10 genome (https://www.arabidopsis.org/) using HISAT2 (VERSION 2.2.1).
Quantification was performed with Rsubread package (version 2.12.0) and normalized using TPM (Transcripts Per Kilobase of exon model per Million mapped reads).
Assembly: TAIR 10
Supplementary files format and content: Txt files include TPM values for each sample.
Supplementary files format and content: Txt file includes differential gene analysis between asf1a1b and Columbia.

organism: Arabidopsis thaliana

source_name: fresh seeds

growth_protocol: Plants were grown on soil mixture in a growth chamber under long-day conditions at ~21°C.  seeds were stratified for 4 days at 4°.

extract_protocol:
total RNA was extracted by using RNAprep Pure Polysaccharide Polyphenol Plant Total RNA Extraction Kit (TIANGEN, DP441) following the manufacturer’s instructions.
RNA-Seq libraries  were constructed by BGI company.

treatment_protocol: freshly seeds were harvested within 24 hours.

value: fresh seeds

tag: genotype


title: Arabidopsis, asf1a1b, Rep3

type: SRA

description: Library name: asf1a1b R3

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: Cell62

status: Public on Apr 24 2018

city: St. Louis

first: Haojia

last: Wu

state: MO

address: 4523 Clayton Ave, MSB Rm 820

country: USA

institute: Washington University in St Louis

data_processing: The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script. The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR version 3.0.4.b. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Sailfish version 0.6.3. was used to produce isoform estimated counts.

organism: Mus musculus

source_name: Mouse kidney

extract_protocol:
Kidney dissociation protocol: Mice were euthanized and perfused with sterile PBS via the left ventricle and the kidneys were placed in PBS with 5% FBS. After thoroughly mincing the tissue/organ using a sterile scalpel (Feather), the tissue/organ was placed in gentleMACS C Tubes (Miltenyi Biotec) containing 1.5ml DMEM (Life Technologies) with 0.1mg/ml Liberase TL (Roche). The tissue was then dissociated using the D program of the gentleMacs dissociator (Miltenyi Biotec) followed by 30 min incubation at 37°C.
FACS-seq protocol: Single cell sorting was performed at the Siteman Flow Cytometry Core (Washington University) using an iCyt Synergy sorter (Sony). Single cells were sorted directly into 10x lysis buffer (Clontech) in 96well PCR plates. Data were analyzed by using Flow Jo software (Version 9.6.2, Tree Star Inc).  96-well plates with single cell in each well were sealed and sent to the sequencing core at Washington University in St Louis (Genome Technology Access Center, GTAC). RNA from individual wells were processed with the Clonetech Smarter system and ligated with unique barcodes. Each plate was then pooled into one library and the resulting pools were then ligated to adapters containing unique 7bp index sequences so that samples originating from a single plate can be identified by Illumina conventional indexing strategies and each individual well is defined by barcoades sequenced on the first read of a paired end read pair. All plates were pooled into a single library and subjected to Illumina sequencing (HiSeq2500 2x50bp).
RNA libraries were prepared for sequencing using standard FACS-seq procedure

tag: protocol

value: Single cell FACS-seq

tag: age

value: 8 wks

tag: cell population

tag: batch


title: Cell261


title: Cell256


title: Cell250


title: Cell254


title: Cell247


title: Cell249


title: Cell237


title: Cell112


title: Cell110