title: 4sU-seq of YRI individual (NA19119) [19119-30-1_C30BHACXX-3-07]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19119_30min


title: 4sU-seq of YRI individual (NA19119) [19119-60-1_C311JACXX-3-08]

status: Public on Mar 29 2016

type: SRA

city: Stanford

first: Yang

middle: I

last: Li

state: CALIFORNIA

address: Department of Genetics

department: genetics

country: USA

institute: Stanford University

description: processed data file: 4su_60_norm.txt

library_source: transcriptomic

data_processing:
The reads were mapped to hg19 using STAR with option --outSAMstrandField intronMotif
The alignment were filtered to remove mapped reads with quality less than 10 using samtools -q 10
We used the WASP alignment strategy to filter read that may be mismapped owing to the human genome reference allele bias (pmid26366987)
We also used WASP to remove cofounding effect from sample-specific GC biases and read count differences to allow comparison between samples (4su_30_norm.txt, 4su_60_norm.txt).
We standardize the values by genes (row) and qqnorm by individuals (column) to get our final quantitative measurements (4su_30_qqnorm.txt, 4su_60_qqnorm.txt).
Genome_build: hg19

molecule: polyA RNA

organism: Homo sapiens

source_name: 4sU-seq of YRI individual NA19119_60min

growth_protocol: Cell lines were grown to log phase (6.5x10^6 - 8.5x10^6 viable cells/ml, with at least 70% cell viability) in RPMI 1640 (supplemented with 2 mM L-glutamine and 15% fetal bovine serum) using standard procedures (as recommended by Coriell).

extract_protocol:
RNA was isolated using QIAshredder columns (Qiagen) and the RNeasy mini kit (Qiagen), using the protocols provided. RNA concentration was measured using a NanoDrop spectrophotometer, and RNA quality was checked using an Agilent Bioanalyzer.
See PMID 21516085.

treatment_protocol: Culture volumes were sufficient to yield at least 6.4x10^6 viable cells, or enough to yield 300 ng of total RNA for the zero time point, and 300 ng of 4sU-labeled RNA for each of the 30' and 60' time points. At the designated “time 0,” cultures were divided into 10-ml aliquots, and 50 mM 4sU was added to each aliquot to obtain a final 4sU concentration of 2x10-7 uMoles/cell. Aliquots corresponding to the 0' time point were immediately washed in 5 mL PBS, pelleted, and frozen in liquid nitrogen. Aliquots corresponding to subsequent time points were returned to the incubator, and washed and frozen at the appropriate times.

tag: cell type

value: lymphoblastoid cell line (LCL)

tag: cell line id

tag: incubated with 4su for


title: 4sU-seq of YRI individual (NA19119) [19119-30-1_C30NNACXX-3-07]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19116) [19116-60-2_C30NNACXX-2-19]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19116_60min


title: 4sU-seq of YRI individual (NA19119) [19119-30-1_C311JACXX-3-07]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19116) [19116-60-2_C30BHACXX-2-19]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19116) [19116-60-1_C30NNACXX-1-10]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19116) [19116-60-1_C30BHACXX-1-10]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19116) [19116-60-2_C311JACXX-2-19]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19116) [19116-30-2_C311JACXX-2-18]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19116_30min


title: 4sU-seq of YRI individual (NA19116) [19116-30-2_C30NNACXX-2-18]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19116) [19116-30-1_C30BHACXX-1-09]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19116) [19116-30-2_C30BHACXX-2-18]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19128) [19128-30-2_C30NNACXX-8-18]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19128_30min


title: 4sU-seq of YRI individual (NA19108) [19108-60-2_C311JACXX-2-23]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19108_60min


title: 4sU-seq of YRI individual (NA19116) [19116-30-1_C30NNACXX-1-09]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19116) [19116-30-1_C311JACXX-1-09]

description: processed data file: 4su_30_norm.txt


title: ChIP_WT_K27Ac

status: Public on Mar 30 2016

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

library_source: genomic

data_processing:
Bowtie2.2.4 alignment to mouse genome, default
For the detection of  peaks in individual samples, use SICER
with  input DNA as control in SICER
FDR < 0.01
Genome_build: mm10
Supplementary_files_format_and_content: BED

molecule: genomic DNA

organism: Mus musculus

source_name: wildtype TT2 ESC

growth_protocol: standard mouse ES cell culture media and without feeder

extract_protocol:
Native ChIP pulldown DNA fragments
Illumina ChIP TRUESeq kit protocol

tag: strain  background

value: C57BL6 x CBA

tag: genotype/variation

value: wildtype TT2

value: ES cell

tag: passage

value: passage 5 to 10

tag: chip antibody

value: K27Ac (Abcam, ab4729)


title: 4sU-seq of YRI individual (NA19119) [19119-60-1_C30NNACXX-3-08]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19108) [19108-60-2_C30BHACXX-2-23]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19108) [19108-30-2_C30NNACXX-2-22]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19108_30min


title: 4sU-seq of YRI individual (NA19108) [19108-60-2_C30NNACXX-2-23]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19108) [19108-30-2_C30BHACXX-2-22]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19108) [19108-30-2_C311JACXX-2-22]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19108) [19108-30-1_D2775ACXX-5-01]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19102) [19102-60-2_C311JACXX-7-06]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19102_60min


title: 4sU-seq of YRI individual (NA19102) [19102-60-2_C30NNACXX-7-06]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19102) [19102-60-1_D2775ACXX-3-12]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19102) [19102-60-2_C30BHACXX-7-06]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19102) [19102-30-2_C30NNACXX-7-05]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19102_30min


title: 4sU-seq of YRI individual (NA19116) [19116-60-1_C311JACXX-1-10]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19102) [19102-30-1_D2775ACXX-3-11]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19102) [19102-30-2_C311JACXX-7-05]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19101) [19101-60-1_D2775ACXX-2-14]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19101_60min


title: 4sU-seq of YRI individual (NA19101) [19101-30-1_D2775ACXX-2-13]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19101_30min


title: 4sU-seq of YRI individual (NA19099) [19099-60-2_C311JACXX-6-14]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19099_60min


title: 4sU-seq of YRI individual (NA19099) [19099-60-2_C30NNACXX-6-14]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19099) [19099-60-2_C30BHACXX-6-14]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19099) [19099-60-1_C311JACXX-5-10]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19108) [19108-60-1_D2775ACXX-5-02]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19099) [19099-60-1_C30NNACXX-5-10]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19099) [19099-60-1_C30BHACXX-5-10]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19099) [19099-30-2_C311JACXX-6-13]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19099_30min


title: 4sU-seq of YRI individual (NA19099) [19099-30-2_C30NNACXX-6-13]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19099) [19099-30-1_C30NNACXX-5-09]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19099) [19099-30-2_C30BHACXX-6-13]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19099) [19099-30-1_C30BHACXX-5-09]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19098) [19098-60-1_C311JACXX-2-21]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19098_60min


title: 4sU-seq of YRI individual (NA19098) [19098-30-1_C311JACXX-2-20]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19098_30min


title: 4sU-seq of YRI individual (NA19098) [19098-60-1_C30BHACXX-2-21]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19098) [19098-30-1_C30NNACXX-2-20]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19098) [19098-60-1_C30NNACXX-2-21]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19102) [19102-30-2_C30BHACXX-7-05]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19098) [19098-30-1_C30BHACXX-2-20]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19092) [19092-60-2_C311JACXX-8-14]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19092_60min


title: 4sU-seq of YRI individual (NA19092) [19092-30-2_C30NNACXX-8-13]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19092_30min


title: 4sU-seq of YRI individual (NA19092) [19092-60-2_C30BHACXX-8-14]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19092) [19092-60-2_C30NNACXX-8-14]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19092) [19092-30-2_C311JACXX-8-13]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19092) [19092-60-1_D2775ACXX-7-12]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18913) [18913-60-2_C311JACXX-6-16]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18913_60min


title: 4sU-seq of YRI individual (NA19092) [19092-30-1_D2775ACXX-7-11]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19092) [19092-30-2_C30BHACXX-8-13]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18913) [18913-60-2_C30NNACXX-6-16]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19099) [19099-30-1_C311JACXX-5-09]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18913) [18913-60-2_C30BHACXX-6-16]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18913) [18913-60-1_C311JACXX-5-04]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18913) [18913-30-2_C311JACXX-6-15]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18913_30min


title: 4sU-seq of YRI individual (NA18913) [18913-30-1_C30NNACXX-5-03]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18913) [18913-30-2_C30BHACXX-6-15]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18912) [18912-60-2_C30NNACXX-6-21]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18912_60min


title: 4sU-seq of YRI individual (NA18912) [18912-60-1_C30NNACXX-4-27]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18913) [18913-30-1_C311JACXX-5-03]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18912) [18912-60-1_C30BHACXX-4-27]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18912) [18912-30-1_C30BHACXX-4-25]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18912_30min


title: 4sU-seq of YRI individual (NA18912) [18912-30-1_C30NNACXX-4-25]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18907) [18907-60-1_C311JACXX-3-09]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18907_60min


title: 4sU-seq of YRI individual (NA18912) [18912-30-2_C30BHACXX-6-20]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18912) [18912-30-2_C30NNACXX-6-20]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18907) [18907-60-1_C30BHACXX-3-09]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18907) [18907-60-1_C30NNACXX-3-09]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18907) [18907-30-1_C311JACXX-3-03]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18907_30min


title: 4sU-seq of YRI individual (NA18907) [18907-30-1_C30BHACXX-3-03]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18870) [18870-60-1_C30BHACXX-1-06]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18870_60min


title: 4sU-seq of YRI individual (NA18870) [18870-60-1_C30NNACXX-1-06]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18870) [18870-60-1_C311JACXX-1-06]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18870) [18870-30-1_C30NNACXX-1-05]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18870_30min


title: 4sU-seq of YRI individual (NA18870) [18870-30-1_C311JACXX-1-05]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18912) [18912-60-2_C311JACXX-6-21]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18912) [18912-60-2_C30BHACXX-6-21]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18870) [18870-30-1_C30BHACXX-1-05]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18861) [18861-60-2_D2775ACXX-7-02]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18861_60min


title: 4sU-seq of YRI individual (NA18861) [18861-30-2_D2775ACXX-7-01]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18861_30min


title: 4sU-seq of YRI individual (NA18861) [18861-60-1_D2775ACXX-3-10]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18913) [18913-30-1_C30BHACXX-5-03]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18861) [18861-30-1_D2775ACXX-3-09]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18913) [18913-60-1_C30BHACXX-5-04]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18907) [18907-30-1_C30NNACXX-3-03]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18859) [18859-60-2_C30BHACXX-8-27]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18859_60min


title: 4sU-seq of YRI individual (NA18859) [18859-60-2_C311JACXX-8-27]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18859) [18859-60-2_C30NNACXX-8-27]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18859) [18859-60-1_D2775ACXX-7-10]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18913) [18913-60-1_C30NNACXX-5-04]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18859) [18859-30-2_C30BHACXX-8-25]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18859_30min


title: 4sU-seq of YRI individual (NA18859) [18859-30-2_C30NNACXX-8-25]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18912) [18912-30-2_C311JACXX-6-20]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18859) [18859-30-1_D2775ACXX-7-09]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18858) [18858-60-2_D2775ACXX-6-19]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18858_60min


title: 4sU-seq of YRI individual (NA18856) [18856-60-2_C30BHACXX-1-12]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18856_60min


title: 4sU-seq of YRI individual (NA18856) [18856-60-2_C30NNACXX-1-12]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18858) [18858-30-1_D2775ACXX-4-15]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18858_30min


title: 4sU-seq of YRI individual (NA18858) [18858-30-2_D2775ACXX-6-18]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18856) [18856-60-1_D2775ACXX-5-06]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18856) [18856-30-2_C311JACXX-1-11]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18856_30min


title: 4sU-seq of YRI individual (NA18856) [18856-60-2_C311JACXX-1-12]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18856) [18856-30-2_C30BHACXX-1-11]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18856) [18856-30-1_D2775ACXX-5-05]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18855) [18855-60-2_C311JACXX-3-12]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18855_60min


title: 4sU-seq of YRI individual (NA18856) [18856-30-2_C30NNACXX-1-11]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18855) [18855-60-2_C30BHACXX-3-12]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18855) [18855-60-1_D2775ACXX-5-10]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18855) [18855-30-2_C311JACXX-3-11]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18855_30min


title: 4sU-seq of YRI individual (NA18855) [18855-60-2_C30NNACXX-3-12]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18855) [18855-30-2_C30NNACXX-3-11]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18855) [18855-30-2_C30BHACXX-3-11]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18859) [18859-30-2_C311JACXX-8-25]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18853) [18853-60-1_C30NNACXX-1-04]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18853_60min


title: 4sU-seq of YRI individual (NA18858) [18858-60-1_D2775ACXX-4-16]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18853) [18853-60-1_C311JACXX-1-04]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18853) [18853-60-1_C30BHACXX-1-04]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18853) [18853-30-1_C311JACXX-1-03]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18853_30min


title: 4sU-seq of YRI individual (NA18853) [18853-30-1_C30BHACXX-1-03]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18853) [18853-30-1_C30NNACXX-1-03]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18852) [18852-30-2_D2775ACXX-4-13]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18852_30min


title: 4sU-seq of YRI individual (NA18852) [18852-60-1_D2775ACXX-7-04]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18852_60min


title: 4sU-seq of YRI individual (NA18852) [18852-30-1_D2775ACXX-7-03]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18522) [18522-60-1_D2775ACXX-4-21]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18522_60min


title: 4sU-seq of YRI individual (NA18522) [18522-30-2_C30BHACXX-4-13]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18522_30min


title: 4sU-seq of YRI individual (NA18522) [18522-60-2_C30BHACXX-4-14]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18522) [18522-30-1_D2775ACXX-4-20]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18522) [18522-60-2_C30NNACXX-4-14]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18852) [18852-60-2_D2775ACXX-4-14]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18520) [18520-60-1_D2775ACXX-4-23]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18520_60min


title: 4sU-seq of YRI individual (NA18522) [18522-30-2_C30NNACXX-4-13]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18520) [18520-30-1_D2775ACXX-4-22]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18520_30min


title: 4sU-seq of YRI individual (NA18519) [18519-60-1_D2775ACXX-5-12]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18519_60min


title: 4sU-seq of YRI individual (NA18517) [18517-60-1_D2775ACXX-1-12]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18517_60min


title: 4sU-seq of YRI individual (NA18519) [18519-30-1_D2775ACXX-5-11]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18519_30min


title: 4sU-seq of YRI individual (NA18516) [18516-60-1_D2775ACXX-1-04]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18516_60min


title: 4sU-seq of YRI individual (NA18855) [18855-30-1_D2775ACXX-5-09]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18516) [18516-30-1_D2775ACXX-1-03]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18516_30min


title: 4sU-seq of YRI individual (NA18517) [18517-30-1_D2775ACXX-1-11]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18517_30min


title: 4sU-seq of YRI individual (NA18511) [18511-60-2_C311JACXX-8-16]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18511_60min


title: 4sU-seq of YRI individual (NA18511) [18511-60-2_C30BHACXX-8-16]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18511) [18511-60-2_C30NNACXX-8-16]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18511) [18511-60-1_D2775ACXX-8-21]

description: processed data file: 4su_60_norm.txt


title: E14Tg2A_smallRNA_2DIV_ELA_ex2iL

city: Genova

first: Luca

last: Pandolfini

state: Genova

address: Via Enrico Melen 83, Building B

department: Center for Human Technologies

country: Italy

institute: Istituto Italiano di Tecnologia - I

description:
Small RNA
Profile of small RNAs in Epiblast-Like Aggregates obtained from  E14Tg2A ES cells cultured in 2i + LIF

data_processing:
Raw sequencing .bcl files were demultiplexed in FASTQ format using CASAVA v.1.8 (Illumina)
Library adaptors were trimmed with Trimmomatic
Reads were mapped to mouse genome (NCBI37/mm9) with Bowtie
miRNAs reads were annotated according to miRbase20 and summarized using featureCounts
Normalization was performed as Reads per Million (RPM)
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Tab-separated file with normalized RPM counts for each sample

molecule: total RNA

source_name: E14Tg2A ELA cells, from ES in 2i+LIF

growth_protocol: Murine embryonic stem cell line E14Tg2A was cultured on gelatin-coated tissue culture dishes at a density of 40,000 cells/cm2. ES cell medium, which was changed daily, contained GMEM, 10% Fetal Calf Serum, 2mM Glutamine, 1mM sodium Pyruvate, 1mM non-essential amino acids, 0.05mM β-mercaptoethanol, 100 U/mL Penicillin/Streptomycin and 1000 U/mL recombinant mouse LIF. Chemically defined minimal medium (CDMM) consisted of DMEM/F12, 2mM Glutamine, 1mM sodium Pyruvate, 0.1mM non-essential amino acids, 0.05mM β-mercaptoethanol, 100 U/mL Penicillin/Streptomycin supplemented with N2/B27 (no vitamin A). For epiblast-like aggregate (ELA) formation, dissociated ES cells were washed with DMEM/F12, aggregated in agar-coated culture dishes (65,000 cells per cm2) and cultured as floating aggregates in CDMM for 2 days.

extract_protocol:
Total RNA was extracted with miRNEasy columns (Qiagenl). RNA from three different sets of experiments was pooled. RNA quality was assessed with Agilent Bioanalyzer RNA 6000 Nano kit.
1 µg of total RNA was used for library preparation using TruSeq Small RNA Sample Prep Kit (Illumina) following the manufacturer’s description.

treatment_protocol: For ground state reprogramming of ES cells , medium was switched for 3-5 passages to 2iL medium: GMEM supplemented with N2/B27 (no vitamin A), 2mM Glutamine, 1mM sodium Pyruvate, 1mM non-essential amino acids, 0.05mM β-mercaptoethanol, 100 U/mL Penicillin/Streptomycin; MEK inhibitor PD0325901 (1 μM); GSK3 inhibitor CHIR99021 (3μM); 1000 U/mL recombinant mouse LIF (2i + LIF).

tag: strain

tag: days in vitro

tag: medium used for es cells

value: 2iL + LIF


title: 4sU-seq of YRI individual (NA18511) [18511-30-2_C311JACXX-8-15]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18511_30min


title: 4sU-seq of YRI individual (NA18511) [18511-30-2_C30NNACXX-8-15]

description: processed data file: 4su_30_norm.txt


title: E14Tg2A_smallRNA_0DIV_ES_SerumLIF

description:
Small RNA
Profile of small RNAs in E14Tg2A ES cells cultured in 10% Fetal Bovine Serum + LIF

source_name: E14Tg2A ES cells, Serum+LIF

value: 10% FCS + LIF


title: E14Tg2A_smallRNA_2DIV_ELA_exSerumLIF

description:
Small RNA
Profile of small RNAs in E14Tg2A ES cells cultured in 2i + LIF

source_name: E14Tg2A ELA cells, from ES in Serum+LIF


title: E14Tg2A_smallRNA_0DIV_ES_2iL

description:
Small RNA
Profile of small RNAs in Epiblast-Like Aggregates obtained from  E14Tg2A ES cells cultured in 10% Fetal Bovine Serum + LIF

source_name: E14Tg2A ES cells, 2i+LIF


title: 4sU-seq of YRI individual (NA18511) [18511-30-1_D2775ACXX-8-20]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18510) [18510-60-1_C311JACXX-2-16]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18510_60min


title: 4sU-seq of YRI individual (NA18510) [18510-30-1_C311JACXX-2-15]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18510_30min


title: E14Tg2A_2DIV_Rpl10a-IP_rep1

description:
Ribosome-depleted RNA
Profile of RNA resulting from Rpl10a immunoprecipitation to capture polysomal mRNA in E14Tg2A ES cells at 2 days of in vitro differentiation (ELA) – Replicate 1

data_processing:
Reads contained in each library were mapped to the Mouse transcriptome (USCS mm10 release) using the software Tophat2. Repeated regions (i.e. transposable elements) were excluded, and a maximum of 2 hits on the genome and 2 mismatches were allowed during mapping.
Mapped reads were assigned to genes using the htseq-count script. Counts were calculated for each gene_id, collapsing eventual splicing isoforms.
Raw counts were normalized using the DESeq2 R package.
Ribosome Enrichment was calculated by dividing the average Ribo IP count by the Input count.
We calculated a log2 fold change in Ribosome Enrichment as ELA average Enrichment / ES average Enrichment
Genome_build: USCS mm10
Supplementary_files_format_and_content: Tab-separated file with normalized counts for each sample, average counts, Ribosome Enrichment and fold change in Ribosome Enrichment

source_name: E14Tg2A at 2DIV, Rpl10a IP, Replicate 1

extract_protocol:
Precipitated ribosomes were washed 4 times in 1mL high-salt buffer (20 mM HEPES/KOH pH 7.3; 350 mM KCl; 10 mM MgCl2; 1% IGEPAL; 0.5 mM DTT; 100 μg/mL Cycloheximide), and RNA was extracted using the RNEasy Micro kit (Qiagen) as per supplier’s protocol. The results were quantified by spectrophotometry (Nanodrop) and capillary electrophoresis (Bioanalyzer RNA Nano kit)
2 μg of RNA were ribosome-depleted using the RIBO-Zero Gold kit (Illumina); sequencing libraries were prepared using the SCRIPTSeq v2 kit (Illumina) according to manufacturer's instructions.

treatment_protocol: Cells were trypsinized and resuspended in the appropriate growth medium supplemented with 100 μg/mL cycloheximide in order to stall ribosomes. After a 15’ incubation at 37°C, cells were recovered and washed with ice-cold PBS + 100μg/mL cycloheximide to remove traces of serum and medium. samples were resuspended in 1ml ice-cold lysis buffer (20 mM HEPES/KOH pH 7.3; 150 mM KCl; 10 mM MgCl2; 1% IGEPAL, 0.5 mM DTT; 100 μg/mL Cycloheximide, 1 pill/10mL protease inhibitor, 3 μL/mL RNAsin RNAse inhibitor; 3 μL/mL SUPERASEin RNAse inhibitor) and incubated on ice for 10 minutes, before being triturated in a chilled dounce homogenizer with approximately 20 strokes. After lysis, cellular debris was removed by centrifugation at 2000 RCF for 10 minutes. After centrifugation, 0.1 volumes of 300 mM 1,2-diheptanoyl-sn-glycero-3-phosphocholine were added to each sample to further solubilize ribosomes, followed by a 10’ incubation on ice and by a second centrifugation at 20000 RCF for 10’. The final clarified lysate was transferred to new low-retention tube and 1/10th volume were removed to be used as “input” sample for the measurements of total RNA levels. To immunoprecipitate ribosomes, 16 μg of anti-Rpl10a antibody (Sigma, cat.no WH0004736M1) or an equivalent amount of anti-GFP antibody (control, Sigma cat. No. G1544) were added to each sample, and incubated overnight with end-to-end agitation at 4°C. The following day, 200μL of 30mg/mL Protein-G Dynabeads were washed in PBS+0.1% Tween 20 (PBST), blocked in PBST + 1% BSA for 1 hour, and added to the lysate/antibody mix. Beads were incubated overnight at 4°C with end-to-end agitation.

tag: treatment


title: E14Tg2A_2DIV_Input_rep1

description:
Ribosome-depleted total RNA
Profile of input RNA in E14Tg2A ES cells at 2 days of in vitro differentiation (ELA) – Replicate 1

source_name: E14Tg2A at 2DIV, Input, Replicate 1

value: Input


title: E14Tg2A_2DIV_Input_rep2

description:
Ribosome-depleted total RNA
Profile of input RNA in E14Tg2A ES cells at 2 days of in vitro differentiation (ELA) – Replicate 2


title: 4sU-seq of YRI individual (NA18913) [18913-30-2_C30NNACXX-6-15]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18913_30min


title: 4sU-seq of YRI individual (NA18510) [18510-30-1_C30NNACXX-2-15]

description: processed data file: 4su_30_norm.txt


title: E14Tg2A_0DIV_Rpl10a-IP_rep2

description:
Ribosome-depleted RNA
Profile of RNA resulting from Rpl10a immunoprecipitation to capture polysomal mRNA in E14Tg2A ES cells at 0 days of in vitro differentiation (ES) – Replicate 2

source_name: E14Tg2A at 0DIV, Rpl10a IP, Replicate 2


title: E14Tg2A_0DIV_Rpl10a-IP_rep1

description:
Ribosome-depleted RNA
Profile of RNA resulting from Rpl10a immunoprecipitation to capture polysomal mRNA in E14Tg2A ES cells at 0 days of in vitro differentiation (ES) – Replicate 1

source_name: E14Tg2A at 0DIV, Rpl10a IP, Replicate 1


title: E14Tg2A_0DIV_Input_rep2

description:
Ribosome-depleted total RNA
Profile of input RNA in E14Tg2A ES cells at 0 days of in vitro differentiation (ES) – Replicate 2

source_name: E14Tg2A at 0DIV, Input, Replicate 1


title: E14Tg2A_0DIV_Input_rep1

description:
Ribosome-depleted total RNA
Profile of input RNA in E14Tg2A ES cells at 0 days of in vitro differentiation (ES) – Replicate 1


title: 4sU-seq of YRI individual (NA18508) [18508-60-1_D2775ACXX-1-10]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18508_60min


title: 4sU-seq of YRI individual (NA18508) [18508-30-1_D2775ACXX-1-09]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18508_30min


title: 4sU-seq of YRI individual (NA18507) [18507-30-1_D2775ACXX-1-07]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18507_30min


title: 4sU-seq of YRI individual (NA18510) [18510-30-1_C30BHACXX-2-15]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18505) [18505-60-1_D2775ACXX-1-02]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18505_60min


title: 4sU-seq of YRI individual (NA18507) [18507-60-1_D2775ACXX-1-08]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18507_60min


title: 4sU-seq of YRI individual (NA18505) [18505-30-1_D2775ACXX-1-01]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18505_30min


title: 4sU-seq of YRI individual (NA18504) [18504-60-2_C30NNACXX-7-10]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18504_60min


title: E14Tg2A_2DIV_Rpl10a-IP_rep2

description:
Ribosome-depleted RNA
Profile of RNA resulting from Rpl10a immunoprecipitation to capture polysomal mRNA in E14Tg2A ES cells at 2 days of in vitro differentiation (ELA) – Replicate 2

source_name: E14Tg2A at 2DIV, Rpl10a IP, Replicate 2


title: 4sU-seq of YRI individual (NA18511) [18511-30-2_C30BHACXX-8-15]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18511_30min


title: 4sU-seq of YRI individual (NA18504) [18504-60-2_C30BHACXX-7-10]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18504) [18504-60-2_C311JACXX-7-10]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18504) [18504-60-1_C311JACXX-6-23]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18504) [18504-60-1_C30BHACXX-6-23]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18504) [18504-60-1_C30NNACXX-6-23]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18504) [18504-30-2_C311JACXX-7-09]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18504_30min


title: 4sU-seq of YRI individual (NA18510) [18510-60-1_C30BHACXX-2-16]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18510_60min


title: 4sU-seq of YRI individual (NA18504) [18504-30-2_C30NNACXX-7-09]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18510) [18510-60-1_C30NNACXX-2-16]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18504) [18504-30-1_C30BHACXX-6-22]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18502) [18502-60-2_C311JACXX-7-08]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18502_60min


title: 4sU-seq of YRI individual (NA18504) [18504-30-2_C30BHACXX-7-09]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18502) [18502-30-2_C311JACXX-7-07]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18502_30min


title: 4sU-seq of YRI individual (NA18502) [18502-60-1_C30NNACXX-4-19]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18502) [18502-60-2_C30BHACXX-7-08]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18504) [18504-30-1_C30NNACXX-6-22]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18502) [18502-60-2_C30NNACXX-7-08]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18501) [18501-60-1_C30NNACXX-5-02]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18501_60min


title: 4sU-seq of YRI individual (NA18502) [18502-30-1_C30BHACXX-4-18]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18502) [18502-60-1_C30BHACXX-4-19]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18501) [18501-60-1_C311JACXX-5-02]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18501) [18501-60-1_C30BHACXX-5-02]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18501) [18501-30-1_C311JACXX-5-01]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18501_30min


title: 4sU-seq of YRI individual (NA18502) [18502-30-2_C30BHACXX-7-07]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18502) [18502-30-2_C30NNACXX-7-07]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18501) [18501-30-1_C30BHACXX-5-01]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18499) [18499-60-1_C30NNACXX-3-06]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18499_60min


title: 4sU-seq of YRI individual (NA18499) [18499-60-1_C30BHACXX-3-06]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18499) [18499-30-1_C311JACXX-3-05]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18499_30min


title: 4sU-seq of YRI individual (NA18501) [18501-30-1_C30NNACXX-5-01]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18499) [18499-60-1_C311JACXX-3-06]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18504) [18504-30-1_C311JACXX-6-22]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18498) [18498-60-2_C30NNACXX-8-23]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18498_60min


title: 4sU-seq of YRI individual (NA18499) [18499-30-1_C30BHACXX-3-05]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18498) [18498-60-2_C30BHACXX-8-23]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18498) [18498-60-1_D2775ACXX-8-27]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18502) [18502-30-1_C30NNACXX-4-18]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18498) [18498-30-2_C30BHACXX-8-22]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18498_30min


title: 4sU-seq of YRI individual (NA18486) [18486-60-2_D2775ACXX-8-19]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18486_60min


title: 4sU-seq of YRI individual (NA18489) [18489-60-1_D2775ACXX-7-06]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA18489_60min


title: 4sU-seq of YRI individual (NA18486) [18486-60-1_D2775ACXX-3-08]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA18498) [18498-30-2_C30NNACXX-8-22]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18489) [18489-30-1_D2775ACXX-7-05]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18489_30min


title: 4sU-seq of YRI individual (NA18486) [18486-30-2_D2775ACXX-8-18]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA18486_30min


title: 4sU-seq of YRI individual (NA18498) [18498-30-2_C311JACXX-8-22]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18499) [18499-30-1_C30NNACXX-3-05]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA18498) [18498-30-1_D2775ACXX-8-25]

description: processed data file: 4su_30_norm.txt


title: H2087 LCC2 1 MLM

city: New York

first: Danilo

middle: G

last: Macalinao

state: NY

address: 1275 York Avenue

institute: MSKCC

description:
Total RNA extracted from the indicated cell lines after 48hr of in vitro culture in either MRM or MLM condition.
Processed data file: H2087_MLM_NormalizedCounts.txt

data_processing:
Reads were quality checked and aligned to the human genome (hg19) using bowtie2-2.2.4.
Feature counts were done with aligned reads using htseq-count 0.6.1p1 using the genes.gtf file obtained from the UCSC Genome Browser. Reads were required to uniquely map to a specific feature in order to be counted.
Raw count files were processed into a data matrix and normalized according to the total number of counts uniquely mapped to a specific gene per sample. Normalization was done using the DESEQ2 (1.8.1) package in R.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files contain normalized count data.
Supplementary_files_format_and_content: H2087_MRM_NormalizedCounts.txt: Normalized counts for H2087 in MRM conditions.
Supplementary_files_format_and_content: H2087_MLM_NormalizedCounts.txt: Normalized counts for H2087 in MLM conditions.
Supplementary_files_format_and_content: HCC1954_MRM_NormalizedCounts.txt: Normalized counts for HCC1954 in MRM conditions.
Supplementary_files_format_and_content: HCC1954_MLM_NormalizedCounts.txt: Normalized counts for HCC1954 in MLM conditions.

source_name: H2087, LCC, MLM, 48hr

growth_protocol: Cells were grown under mitogen-rich or mitogen-low conditions for 48hr (subconfluent).

extract_protocol:
Cells were immediately lysed and total RNA was extracted using the PrepEASE RNA Spin Kit according to the manufacturer's protocols.
Libraries were constructed using standard Illumina protocols.

tag: original cell line

value: H2087 derivative isolated from BLI-negative organ

tag: growth condition

value: mitogen-low media (MLM)

tag: growth time


title: HCC1954 LCC2 PolII

data_processing:
50/50bp paired-end raw FASTQ files were mapped to human genome hg19 by Bowtie2 with default settingS in the aligner(Langmead and Salzberg, 2012). Output SAM files are converted to BAM format with “samtools view”, sorted with “samtools sort” and indexed with “samtools index” from Samtools (Li et al., 2009). Sorted BAM files WERE converted to TDF file format with “igvtools count -z 5 -w 25 -e 250” from IGVTools(Robinson et al., 2011), specifying the maximum zoom level at 5bp, window size of 25bp for averaged coverage, and read extension to 250bp(Robinson et al., 2011). TDF files were loaded to Integrative Genomics Viewer 2.3 for coverage visualization. Coverage was normalized to Reads Per Million Reads (RPM) or Counts Per Million TotalCount prior to visualization for cross sample comparisons(Robinson et al., 2011).
H3K27ac peaks were called by “findPeaks -style histone -F 5 -P 0.00001 -L 5 -LP 0.00001” function from HOMER (v4.2), specifying the ChIP-Seq data style as broad histone modifications, cut-off for fold enrichment over input or local tag count as 5, cut-off for poisson p-value threshold relative to input or local tag count as 0.00001(Heinz et al., 2010). Sequencing data from input samples were used as background control. To identify parental (H2087 or HCC1954 Parental) or derivatives (H2087-LCC2 or HCC1954-LCC2) specific peaks, the same peak calling method was used whiling using the second experiment as the background control sample (Heinz et al., 2010). Sample specific peaks were randomly picked and validated in the IGV visualization window. Tag distribution matrix was calculated with “annotatePeaks.pl hg19 -size 6000 -hist 50 -ghist” function from HOMER (v4.2), specifying calculated region as +/-3000bp from peak center, and window size as 50bp. Heatmap for tag distribution matrix was plotted in R (v3.1.2) with “heatmap.2” function from gplot package.
Genome_build: hg19
Supplementary_files_format_and_content: tdf

source_name: HCC1954 Cancer Cell Line

growth_protocol: Cells were grown in mitogen-low media for 48 hours on standard tissue culture plates

extract_protocol:
Cells were grown to 90–95% confluence, fixed with 1% formaldehyde for 15 min at room temperature followed by addition of glycine (1.25mM) for 10 minutes to stop cross linking. Nuclei were prepared and sonicated in lysis buffer (150 mM NaCl, 1% Triton X-100, 20 mM Tris pH 8.0, 0.1% SDS) using a Bioruptor to fragment chromatin to less than 500 base pairs (bp).
Chromatin was pre-cleared with 35 μl Protein-G Dyna magnetic beads, and then immunoprecipitated with 5 μg of antibody over night at 4 °C. The chromatin antibody mix was incubated with 35 μl protein G-conjugated Dyna beads for 4 h at 4 °C, washed three times with wash buffer (1% Triton X-100, 50 mM Tris pH 8.0, 10% glycerol) with increasing concentrations of NaCl (150 mM, 300 mM and 400 mM), and two times with Tris-EDTA buffer. DNA was eluted in 1% SDS in Tris-EDTA buffer for 45 min at 37 °C, crosslinking was reversed overnight at 65 °C, and DNA was purified using Qiagen columns. For each ChIP, one fifth of the cells from 15cm plates were used.

tag: cell line source

tag: source cell type

value: breast adenocarcinoma cell line

tag: cell subtype

value: Latency Competent Cancer Cell (LCC) Derivative

value: PolII

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: H2087 LCC4 1 MLM

tag: cell type


title: H2087 LCC3 1 MLM


title: H2087 LCC1 1 MLM


title: H2087 Parental 3 MLM

source_name: H2087, parental, MLM, 48hr

value: established lung cancer cell line


title: HCC1954 Parental PolII

value: Parental Population


title: H2087 LCC5 1 MLM


title: H2087 Parental PolII

source_name: H2087 Cancer Cell Line

value: lung adenocarcinoma cell line


title: 4sU-seq of YRI individual (NA18498) [18498-60-2_C311JACXX-8-23]

description: processed data file: 4su_60_norm.txt

value: lymphoblastoid cell line (LCL)

tag: cell line id

tag: incubated with 4su for


title: H2087 LCC2 Input PolII


title: H2087 Parental 2 MLM


title: HCC1954 LCC2 H3K27Ac

value: Active Motif


title: H2087 LCC5 1 MRM

description:
Total RNA extracted from the indicated cell lines after 48hr of in vitro culture in either MRM or MLM condition.
Processed data file: H2087_MRM_NormalizedCounts.txt

source_name: H2087, LCC, MRM, 48hr

value: mitogen-rich media (MRM)


title: H2087 Parental 1 MLM


title: H2087 LCC6 1 MRM


title: H2087 LCC4 1 MRM


title: 4sU-seq of YRI individual (NA18486) [18486-30-1_D2775ACXX-3-07]

description: processed data file: 4su_30_norm.txt


title: HCC1954 Parental H3K27Ac


title: H2087 LCC6 1 MLM


title: H2087 LCC3 1 MRM


title: H2087 LCC2 Input H3K27Ac


title: H2087 Parental H3K27Ac


title: H2087 LCC2 1 MRM


title: H2087 Parental 2 MRM

source_name: H2087, parental, MRM, 48hr


title: HCC1954 Parental Input

value: none (Input)


title: H2087 LCC1 1 MRM


title: H2087 LCC2 Input


title: H2087 Parental Input


title: HCC1954 LCC2 1 MLM

description:
Total RNA extracted from the indicated cell lines after 48hr of in vitro culture in either MRM or MLM condition.
Processed data file: HCC1954_MLM_NormalizedCounts.txt

source_name: HCC1954, LCC, MLM, 48hr

value: HCC1954 derivative isolated from BLI-negative mouse organ


title: HCC1954 LCC2 2 MLM


title: HCC1954 LCC1 1 MLM


title: Rep2_TSB_Δhpf_RPF

city: Chicago

first: Mee-Ngan

middle: F.

last: Yap

state: IL

address: 320 E Superior St

department: Microbiology-Immunology

institute: Northwestern University Feinberg School of Medicine

data_processing:
Library strategy: ribosome profiling
CASAVA-1.8.2 basecalling
Raw FastQ sequencing data were processed on local instance of Galaxy platform.  Sequence libraries were pre-processed by clipping the adaptor sequence (5’CTGTAGGCACCATCAAT3’) and trimming the sequences by discarding the first base and all those extending beyond the 50th base.  The sequencing reads were mapped to the rRNA reference genome (CP000255.1) with Bowtie2.
The unaligned output files from Bowtie 2 (rRNA-less sequences) were mapped to the S. aureus USA300_FPR3757 (GeneBank CP000255.1) with Bowtie v.0.12.0. The alignment .map files were used as inputs for the modified Python scripts to obtain normalized read density in "reads per million mapped reads" (RPM) at each nucleotide positions. Original Python scripts have been published in Ref: Becker et al (2013)Nature Protoc 8: 2212-2239
mRNA abundance were determined by custom scripts measured in RPKM (Rragments Per Kilobase of transcript per Million mapped reads)
Genome_build: GenBank CP000255.1
Supplementary_files_format_and_content: Tab-delimited text files include normalized read densities (RPM, reads per millions reads) at each nucleotide position

organism: Staphylococcus aureus

source_name: Bacterial cells

growth_protocol: S. aureus cells (WT and Δhpf mutant) were grown in 1 liter of  tryptic soy broth (TSB) or chemically defined minimal medium (MM) until OD600 ~0.4 at 37°C.

extract_protocol:
Bacterial cells were disrupted by cryomilling on a Retch MM400 (15 mm grinding balls, 10 ml jars) for 8 set of 3 min cycles at 15 Hz. Ref: Oh et al (2011) Cell 147: 1295-1308
Cell lysates were subjected to micrococcal nuclease digestion, and monosomes were collected by 10-55% sucrose density gradient. Total mRNA and the monosomal mRNAs were isolated by hot-phenol/chloroform method. Total mRNAs were fragmented by alkaline hydrolysis. The fragmented mRNAs and ribosome footprint mRNA (RPF) were ligated to a universal linker. Following rRNA subtraction, PAGE purification, reverse transcription, cDNA circularization, and multiplexing PCR amplification, the cDNA libraries were sequenced on Illumina HiSeq 2000

treatment_protocol: To preserve ribosome occupancy on its mRNA template, 100 μg/ml of chloramphenicol were added to both WT and Δhpf cultures and incubated for 2 min before harvest.

tag: growth phase

value: Exponentially growing S. aureus

tag: media

value: TSB

tag: genotype

tag: cdna type

value: Ribosome protected mRNA fragments


title: Rep2_TSB_WT_Total mRNA

data_processing:
CASAVA-1.8.2 basecalling
Raw FastQ sequencing data were processed on local instance of Galaxy platform.  Sequence libraries were pre-processed by clipping the adaptor sequence (5’CTGTAGGCACCATCAAT3’) and trimming the sequences by discarding the first base and all those extending beyond the 50th base.  The sequencing reads were mapped to the rRNA reference genome (CP000255.1) with Bowtie2.
The unaligned output files from Bowtie 2 (rRNA-less sequences) were mapped to the S. aureus USA300_FPR3757 (GeneBank CP000255.1) with Bowtie v.0.12.0. The alignment .map files were used as inputs for the modified Python scripts to obtain normalized read density in "reads per million mapped reads" (RPM) at each nucleotide positions. Original Python scripts have been published in Ref: Becker et al (2013)Nature Protoc 8: 2212-2239
mRNA abundance were determined by custom scripts measured in RPKM (Rragments Per Kilobase of transcript per Million mapped reads)
Genome_build: GenBank CP000255.1
Supplementary_files_format_and_content: Tab-delimited text files include normalized read densities (RPM, reads per millions reads) at each nucleotide position

tag: strain

value: wildtype

value: total fragmented mRNA


title: HCC1954 Parental 3 MLM

source_name: HCC1954, parental, MLM, 48hr

value: established breast cancer cell line

value: mitogen-low media (MLM)


title: Rep2_TSB_Δhpf_Total mRNA


title: HCC1954 Parental 2 MLM


title: Rep2_TSB_WT_RPF


title: Rep1_TSB_WT_Total mRNA


title: Rep1_TSB_Δhpf_Total mRNA


title: Rep1_TSB_Δhpf_RPF


title: HCC1954 LCC2 2 MRM

description:
Total RNA extracted from the indicated cell lines after 48hr of in vitro culture in either MRM or MLM condition.
Processed data file: HCC1954_MRM_NormalizedCounts.txt

source_name: HCC1954, LCC, MRM, 48hr


title: HCC1954 LCC2 1 MRM


title: Rep2_MM_Δhpf_Total mRNA

value: MM


title: Rep1_TSB_WT_RPF


title: HCC1954 LCC2 Input

value: breast adenocarcinoma cell line

value: Latency Competent Cancer Cell (LCC) Derivative

tag: chip antibody


title: HCC1954 LCC1 2 MRM

tag: original cell line


title: H2087 Parental 1 MRM

value: established lung cancer cell line

tag: growth condition


title: HCC1954 LCC1 1 MRM

tag: growth time


title: Rep2_MM_Δhpf_RPF


title: HCC1954 LCC1 2 MLM


title: Rep1_MM_Δhpf_Total mRNA


title: HCC1954 Parental 1 MRM

source_name: HCC1954, parental, MRM, 48hr


title: Rep1_MM_WT_Total mRNA


title: HCC1954 Parental 2 MRM


title: Rep1_MM_WT_RPF


title: HCC4006_Gef2

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

data_processing:
alignment: TopHat v1.4.1 using default settings
expression levels: Cufflinks v1.3.0 and cuffdiff using default settings
Genome_build: hg19
Supplementary_files_format_and_content: text file with FPKM values

source_name: NSCLC cell lines

growth_protocol: Cells were obtained from the University of Colorado Cancer Center Tissue Culture Core.  The passage controls and TKI-adapted cell lines used in this study were submitted to fingerprint analysis to verify their authenticity relative to established sources and to demonstrate that the control and TKI-resistant cultures were genetically equivalent. All cell lines were routinely cultured in RPMI-1640 growth medium supplemented with 10% fetal bovine serum (Sigma, St. Louis, MO, USA) at 37 °C in a humidified 5% CO2 incubator. Resistant cell population were cultured with the addition of 3 μM gefitinib or 2 μM BIBW2992.

extract_protocol:
Total RNA was extracted with the miRNeasy Kit (Qiagen) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using TruSEQ RNA Sample Prep v2 using standard Illumina protocols.

treatment_protocol: Cells were considered resistant when they could be routinely cultured in growth medium containing 3 μM gefitinib

tag: cell line

value: NSCLC

tag: treatment

value: Gefitinib Treated


title: HCC4006_DMSO2

value: DMSO


title: HCC4006_DMSO1


title: HCC1954 Parental 1 MLM


title: Rep1_MM_Δhpf_RPF


title: HCC827_Gef1


title: HCC827_Gef2


title: HCC827_DMSO1


title: IgG ChIP-Seq

city: Tampa

first: Nupam

last: Mahajan

state: FL

address: 10902 Magnolia Dr

department: Drug Discovery Program

institute: Moffitt Cancer Center

data_processing:
The 75-nt paired end sequence reads were mapped to the genome using the BWA-MEM algorithm. Alignment information for each read was stored in the output file *.bam. Only reads that mapped uniquely with proper pairing were used in the subsequent analysis.
Peak regions were called using the MACS2 software with the following options -f BAMPE -SPMR -q 0.01 -broad. The "BAMPE" option was used for calculating fragment lengths from the paired end reads, "SPMR" for normalizing read depths to number of fragments per million reads, "broad" for compositing broad regions from nearby peak regions, and the qvalue (FDR) cutoff was set to 0.01. A total of 376 peak regions were called between the IgF sample and the IgG control.
Using the HOMER (v4.7, 8-25-2014) program (http://homer.salk.edu/homer/) we found 15 de novo motifs in pY88-H4 ChIP data
Genome_build: GRCh37
Supplementary_files_format_and_content: SPMR bigwigs

source_name: castration-resistant prostate cancer (CRPC) cell line

growth_protocol: LNCaP-C4-2B cells were grown in DMEM+F12 media supplemented with 10% FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with pY88-H4 or IgG antibody.
Fifty nanograms of immunoprecipitated DNA was fragmented to 300 base pairs using a Covaris M220 Focused-ultrasonicator (Covaris, Inc., Woburn, MA) and then used to generate sequencing libraries using the Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA). The size and quality of the library was evaluated using the Agilent BioAnalzyer, and the library was quantitated with the Kapa Library Quantification Kit.
Each enriched DNA library was then sequenced on an Illumina NextSeq 500 sequencer. The sequencing yield was very good, with over 90 million reads in each sample, of which 82.8 (IgF) and 77.9 million (IgG), respectively, mapped uniquely to the human genome GRCh37.

treatment_protocol: Cells were treated with IGF ligand to activate histone H4 phosphorylation at Tyr88

tag: tissue

value: Prostate, CRPC

value: LNCaP-C4-2B cells

tag: antibody

value: IgG Ab


title: HCC827_DMSO2


title: Lung microbiome of healthy subjects; pooled sample

first: Leopoldo

middle: Nicolas

last: Segal

address: 462 First Avenue NBV 6N5-6N8

department: Medicine

institute: NYU School of Medicine

data_processing:
Reads were demultiplexed and quality filtered with default parameters. Sequences were then clustered into operational taxonomic units (OTUs) using a 97% similarity threshold with UCLUST 4 and the Greengenes 16S reference dataset and taxonomy
The absolute OTU sequence counts were normalized to obtain the relative abundances of the taxa within each sample. These relative abundances at 97% OTU similarity and each of the 5 higher taxonomic levels (phylum, class, order, family, genus) were tested for univariate associations with clinical variables.
Supplementary_files_format_and_content: abundance measurement

organism: human lung metagenome

source_name: pooled samples

extract_protocol:
ion exchange column (Qiagen)
Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25μl reactions with the following reaction conditions: 11μl PCR-grade H2O, 10μl Hot MasterMix (5 Prime Cat# 2200410), 2μl of forward and reversed barcoded primer (5μM) and 2μl template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94°C for 3 min followed by 35 cycles of denaturation at 94°C for 45 seconds, annealing at 58°C for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72°C. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions

tag: cohort

value: NYU; Ohio; LHMP (Lung Human Microbiome Project)

tag: sample type

value: BAL, Upper.Airway or BKG (pooled)

tag: barcode sequence

value: provided in the 'complete_metadata.txt' for each sample

tag: linker primersequence

value: CCGGACTACHVGGGTWTCTAAT


title: HCC4006_Gef1

tag: cell type


title: Rep2_MM_WT_Total mRNA

tag: growth phase

value: Exponentially growing S. aureus

tag: media

value: wildtype

value: total fragmented mRNA


title: REF6-REF6-GFP ab290 #2

status: Public on Mar 28 2016

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

country: China

institute: shenzhen university

data_processing:
Basecalls and quality control and pre-aligned (eland) were performed using Illumina Genome analyzer pipeline
ChIP-seq reads were aligned to the Arabidopsis genome (TAIR10) using BOWTIE2 version 2.2.5.
The program MACS v1.4 was used to identify ChIP-enriched domains (peaks).
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: Young seedlings

growth_protocol: Plants were grown in 1/2MS media with 22 degree in 16h light/8h dark

extract_protocol:
Lysates were clarified from sonicated protein-DNA complexes were isolated with GFP antibody.
Ten ng of ChIP DNA immuoprecipitated by anti-GFP antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Hiseq 2000 was used for high-throughput sequencing of the ChIP-seq library.

value: Seedling

tag: developmental stage

value: GFP (ab290, abcam)


title: brm REF6-REF6-GFP ab290


title: ref6 BRM-BRM-GFP ab290 #1


title: BRM-BRM-GFP ab290 #1


title: Rep2_MM_WT_RPF

value: MM

tag: strain

tag: genotype

tag: cdna type

value: Ribosome protected mRNA fragments


title: brm REF6-REF6-GFP  ab290 #2


title: HCC1954 Parental 3 MRM

tag: original cell line

value: established breast cancer cell line

tag: growth condition

value: mitogen-rich media (MRM)


title: ref6 BRM-BRM-GFP Input


title: BRM-BRM-GFP Input


title: REF6-REF6-GFP ab290


title: brm REF6-REF6-GFP input


title: REF6-REF6-GFP input


title: pY88-H4 ChIP-Seq

tag: cell line

value: pY88-H4 monoclonal Ab, Promab


title: REF6GFPInput


title: REF6GFPIP


title: BRMGFPIP


title: clf28 inflorescences replicate 3

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

description: Single-end strand-specific RNA-seq

data_processing:
FastaQ files of each sample were aligned against Arabidopsis Genome TAIR 10 using TopHat.
Mapped sequences were assembled into transcripts using Cufflinks.
Assembled transcripts of each sample were summarized and merged into transcription units using Cuffcompare.
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) of each TU were calculated using cuffdiff.
Genome_build: Arabidopsis Genome Annotation TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample produced by Cufflinks.

growth_protocol: Arabidopsis plant (Col-0 and clf-28) materials were grown under long day conditions at 22℃. Aerial samples (shoots) and roots were collected from two-week old plants that grew on MS plate. Inflorescences and siliques were collected from five-week old plants that grew in soil.

extract_protocol: All samples were harvested and frozen immediately in liquid nitrogen until use. Total RNA was extracted and treated with DNase I using RNeasy Plant mini kit (Qiagen). RNA sequence libraries were prepared with TruSeq strand-specific RNA sample Prep kit according to the instructions (Illumina). Sequences were determined by HiSeq 2000 sequencing system in the genomic center in Rockefeller University.

value: inflorescences

value: clf-28 mutant

tag: age (weeks)


title: clf28 siliques replicate 3

description: Single-end strand-specific RNA-seq

tag: tissue

value: siliques


title: clf28 inflorescences replicate 2

description: Single-end strand-specific RNA-seq


title: clf28 siliques replicate 1

description: Single-end strand-specific RNA-seq


title: BRMGFPInput

tag: antibody


title: clf28 shoots replicate 2

description: Single-end strand-specific RNA-seq

value: shoots


title: clf28 shoots replicate 3

description: Single-end strand-specific RNA-seq


title: clf28 roots replicate 2

description: Single-end strand-specific RNA-seq

value: roots


title: clf28 roots replicate 3

description: Single-end strand-specific RNA-seq


title: clf28 roots replicate 1

description: Single-end strand-specific RNA-seq


title: WT siliques replicate 3

description: Single-end strand-specific RNA-seq

source_name: Arabidopsis thaliana_siliques_Col-0, Wild Type

value: Col-0, Wild Type


title: WT inflorescences replicate 2

description: Single-end strand-specific RNA-seq

source_name: Arabidopsis thaliana_inflorescences_Col-0, Wild Type


title: WT siliques replicate 1

description: Single-end strand-specific RNA-seq


title: WT inflorescences replicate 1

description: Single-end strand-specific RNA-seq


title: WT inflorescences replicate 3

description: Single-end strand-specific RNA-seq


title: WT shoots replicate 3

description: Single-end strand-specific RNA-seq

source_name: Arabidopsis thaliana_shoots_Col-0, Wild Type


title: WT siliques replicate 2

description: Single-end strand-specific RNA-seq


title: WT roots replicate 3

description: Single-end strand-specific RNA-seq

source_name: Arabidopsis thaliana_roots_Col-0, Wild Type


title: WT roots replicate 1

description: Single-end strand-specific RNA-seq


title: WT shoots replicate 1

description: Single-end strand-specific RNA-seq


title: WT shoots replicate 2

description: Single-end strand-specific RNA-seq


title: WT roots replicate 2

description: Single-end strand-specific RNA-seq


title: clf28 inflorescences replicate 1

description: Single-end strand-specific RNA-seq


title: Siliques_Stage3

data_processing:
The Arabidopsis genome sequence (TAIR10) and the annotation files were downloaded from the FTP server of The Arabidopsis Information Resource. After quality control analysis of raw sequencing datasets, RNA-seq sequences were aligned to the Arabidopsis genome using TopHat with TAIR10 annotation as reference. Then the mapped sequences of each sample were assembled by Cufflinks with TAIR10 annotation as the reference. Fragments per kilobase of exon per million fragments mapped of assembled transcripts (FPKM) were calculated and normalized using Cuffcompare and Cuffdiff with global normalization parameters. A custom PERL script was made to pick up the the annotated genes with the CuffDiff status "OK" from the CuffDiff results for further analysis.
Genome_build: The Arabidopsis genome sequence (TAIR10)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all Samples

source_name: siliques (11-15 day post-anthesis)

growth_protocol: Col-0 plants of Arabidopsis thaliana were grown under long day conditions (22°C, 16/8 h photoperiod cycles). Stage-specific siliques were derived from 4 stages of silique, which were defined as stage 1 (1-5 days post-anthesis), stage 2 (6-10 days post-anthesis), stage 2 (11-15 days post-anthesis) and stage 4 (6-10 days post-anthesis). All samples were harvested and frozen immediately in liquid nitrogen until use.

extract_protocol:
Total RNAs were extracted using Trizol reagent (Invitrogen, USA). Total RNA was treated with TURBO DNase I (Ambion, USA) for 30 min and purified using RNeasy® Plant Mini Kit (QIAGEN, Germany).
RNA sequence libraries were prepared with TruSeq RNA sample Prep V2 kit according to the instructions (Illumina). The quality and size of cDNA libraries for sequencing were checked using the Agilent 2200 TapeStation system (Agilent Inc.).We sequenced the samples using HiSeq 2000 sequencing system (illumine Inc.) with 100-cycle paired-end sequencing protocol.

value: 11-15 day post-anthesis

value: silique

tag: ecotype


title: clf28 shoots replicate 1

description: Single-end strand-specific RNA-seq


title: Siliques_Stage1

source_name: siliques (0-5 day post-anthesis)

value: 0-5 day post-anthesis


title: RBFOX2 Shearing 293T Condition80U

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: library strategy: eCLIP-seq

data_processing:
Takes output from raw files.  Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6  -m 18  -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT  AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards  --times 1  -e 0.1  -O 5  --quality-cutoff 6  -m 18  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.  Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove  --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within  --outFilterMultimapNmax 30  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All  --readFilesCommand zcat  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep.  Maps unique reads to the human genome.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir  /path/to/STAR_database_file --genomeLoad LoadAndRemove  --readFilesIn  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2  --outSAMunmapped Within  --outFilterMultimapNmax 1  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --outSAMattributes All  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam
takes output from STAR genome mapping.  Custom random-mer-aware script for PCR duplicate removal. Command: barcode_collapse_pe.py  --bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --out_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  --metrics_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.metrics
Takes output from barcode collapse PE.  Sorts resulting bam file for use downstream.  Command: java  -Xmx2048m  -XX:+UseParallelOldGC  -XX:ParallelGCThreads=4  -XX:GCTimeLimit=50  -XX:GCHeapFreeLimit=10  -Djava.io.tmpdir=/full/path/to/files/.queue/tmp  -cp /path/to/gatk/dist/Queue.jar  net.sf.picard.sam.SortSam  INPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  TMP_DIR=/full/path/to/files/.queue/tmp  OUTPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  VALIDATION_STRINGENCY=SILENT  SO=coordinate  CREATE_INDEX=true
Takes output from sortSam, makes bam index for use downstream.  Command: samtools index  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam.bai
Takes inputs from multiple final bam files.  Merges the two technical replicates for further downstream analysis.  Command: samtools  merge  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.D08.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam
Takes output from sortSam, makes bam index for use downstream.  Command: samtools  index  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/CombinedID.merged.bam.bai
Takes output from sortSam.  Only outputs the second read in each pair for use with single stranded peak caller.  This is the final bam file to perform analysis on.  Command: samtools view -hb -f 128  /full/path/to/files/CombinedID.merged.bam  >  /full/path/to/files/CombinedID.merged.r2.bam
Takes results from samtools view.  Calls peaks on those files.  Command: clipper  -b /full/path/to/files/CombinedID.merged.r2.bam  -s hg19  -o /full/path/to/files/CombinedID.merged.r2.peaks.bed  --bonferroni  --superlocal  --threshold-method binomial  --save-pickle
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, bigBed, bed (col1: chrom, col2: chromStart, col3: chromEnd, col4: -log10 pvalue, col5: log2 fold enrichment above input, col6: strand) format, contains clusters of predicted RBP binding

source_name: RBFOX2 Shearing 293T Condition80U

growth_protocol: 293T cells were grown under standard conditions (DMEM + 10% FBS + Pen/Strep (100U / mL)

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps - see Supplementary Fig. 2A). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

treatment_protocol: While plated, cells were crosslinked with UV (254 nm, 400 mJ/cm2). Cells were then isolated with cell scrapers, pelleted at 200g, and snap frozen.

tag: rip antibody

tag: antibody manufacturer

value: Bethyl

tag: antibody catalog#

tag: antibody lot#

tag: rnase i fragmentation condition


title: RBFOX2 Shearing 293T Condition40U Rep2

description: library strategy: eCLIP-seq

source_name: RBFOX2 Shearing 293T Condition40U


title: clf28 siliques replicate 2

description: Single-end strand-specific RNA-seq


title: RBFOX2 Shearing 293T Condition10U

description: library strategy: eCLIP-seq

source_name: RBFOX2 Shearing 293T Condition10U


title: Siliques_Stage2

source_name: siliques (6-10 day post-anthesis)

value: 6-10 day post-anthesis


title: RBFOX2 Shearing 293T Condition40U Rep1

description: library strategy: eCLIP-seq


title: RBFOX2 Shearing 293T Condition0U

description: library strategy: eCLIP-seq

source_name: RBFOX2 Shearing 293T Condition0U

value: 0 U


title: SLBP 293T Rep4 Input

description: library strategy: eCLIP-seq

source_name: SLBP 293T  Input

value: none (input)

value: 5 U


title: RBFOX2 Shearing 293T Condition5U Rep1

description: library strategy: eCLIP-seq

source_name: RBFOX2 Shearing 293T Condition5U


title: RBFOX2 Shearing 293T Condition400U

description: library strategy: eCLIP-seq

source_name: RBFOX2 Shearing 293T Condition400U


title: RBFOX2 Shearing 293T Condition5U Rep2

description: library strategy: eCLIP-seq


title: Siliques_Stage4

source_name: siliques (16-20 day post-anthesis)

value: 16-20 day post-anthesis


title: SLBP 293T Rep3 Input

description: library strategy: eCLIP-seq


title: RBFOX2 Shearing 293T Condition20U

description: library strategy: eCLIP-seq

source_name: RBFOX2 Shearing 293T Condition20U


title: SLBP 293T Rep3

description: library strategy: eCLIP-seq

source_name: SLBP 293T

value: SLBP

value: MBL


title: SLBP 293T Rep4

description: library strategy: eCLIP-seq


title: SLBP 293T Rep1 Input

description: library strategy: eCLIP-seq


title: SLBP 293T Rep2 Input

description: library strategy: eCLIP-seq


title: IgG 293T Rep1 Input

description: library strategy: eCLIP-seq

source_name: IgG 293T  Input


title: SLBP 293T Rep2

description: library strategy: eCLIP-seq


title: RBFOX2 293T Rep2 Input

description: library strategy: eCLIP-seq

source_name: RBFOX2 293T  Input


title: RBFOX2 iCLIP Rep1

description: library strategy: iCLIP-seq

data_processing:
Sequencing reads from CLIP-seq libraries were first trimmed of polyA tails, adapters, and low quality ends using cutadapt with parameters --match-read-wildcards --times 2 -e 0 -O 5 --quality-cutoff' 6 -m 18 -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b TGGAATTCTCGGGTGCCAAGG -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT.
Reads were then mapped against a database of repetitive elements derived from RepBase18.05. Bowtie version 1.0.0 with parameters -S -q -p 16 -e 100 -l 20 was used to align reads against an index generated from Repbase sequences (Langmead et al., 2009).
Reads not mapped to Repbase sequences were aligned to the hg19 human genome (UCSC assembly) using STAR (Dobin et al., 2013) version 2.3.0e with parameters --outSAMunmapped Within –outFilterMultimapNmax 1 –outFilterMultimapScoreRange 1.
Reads that were PCR replicates were removed from each CLIP-seq library using a custom script. Briefly one read with a unique barcode was kept at each nucleotide position when more than one with the same barcode was mapped to the same location
Clusters were then assigned using the CLIPper software with parameters --bonferroni --superlocal --threshold- software (Lovci et al., 2013).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, bigBed format, contains clusters of predicted RBFOX2 binding

source_name: RBFOX2 iCLIP

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.
RNA libraries were prepared for sequencing using published protocol at: http://www.jove.com/video/2638/iclip-transcriptome-wide-mapping-protein-rna-interactions-with

value: Abcam


title: SLBP 293T Rep1

description: library strategy: eCLIP-seq


title: RBFOX2 293T Rep1 Input

description: library strategy: eCLIP-seq


title: RBFOX2 293T Rep2

description: library strategy: eCLIP-seq

source_name: RBFOX2 293T


title: RBFOX2 Shearing 293T Condition2000U

description: library strategy: eCLIP-seq

source_name: RBFOX2 Shearing 293T Condition2000U


title: RBFOX2 293T Rep1

description: library strategy: eCLIP-seq


title: S46.H5

city: SAN FRANCISCO

first: John

state: California

address: 35 Medical Center Way

institute: UCSF

description:
polyA RNA
single cell

data_processing:
Bulk RNA-seq: Strand-specific reads were aligned to the human reference genome, Ensembl GRCh37/hg19 release 75, using TopHat v2.0.10 with the flags (--library-type fr-firststrand –microexon-search). De novo transcriptome assembly was performed separately on rRNA depletion total RNA-seq alignments, and on polyA selection RNA-seq alignments, using Cufflinks v2.2.1 with the flags (-M ensembl_75_mtRNA_rRNA.gtf -b genome.fa -u --library-type fr-firststrand --max-multiread-fraction 0.25 --3-overhang-tolerance 2000). Transcriptome assemblies at all developmental stages and replicates were merged, separately for rRNA depletion total RNA-seq and polyA selection RNA-seq, with the Ensembl 75/GENCODE 19 reference transcriptome, using Cuffmerge. To identify transcripts novel compared to Ensembl, we utilized Cuffcompare class codes and extracted those assembled transcripts classified as: i – novel intronic, u – novel intergenic, x – novel antisense. All novel transcripts under 200 nt in length were removed. Of the remaining transcripts, we determined minimal read coverage thresholds based on whether Cufflinks classified previously annotated transcripts as having “full_read_support.” By analyzing the true positive rate vs. false positive rate of classifying known genes as obtaining “full_read_support” at various coverage thresholds, we determined the minimum coverage to be 1.4 for polyA and 1.67 for total RNA-seq (at FDR = 0.05). Starting with just the polyA RNA-seq data, transcripts with read coverage above 1.4 in both biological replicates of at least one developmental stage were included in the reference and considered to be expressed in the neocortex. Due to limited availability of early fetal tissue, the GW14.5 sample was treated as the biological duplicate of the GW13 sample. Novel transcripts that were predicted to have protein coding capability by one or more of the following methods were classified as transcripts of uncertain coding potential (TUCP): CPAT, threshold = 0.364; CPC, threshold = 0; Pfam. For comparing to the Pfam database, the longest potential open reading frame (ORF) of each novel transcript was obtained, and any putative ORF that had a significant match for a protein domain annotated in Pfam A or Pfam B resulted in the parent transcript being classified as a TUCP. All remaining novel lncRNAs and TUCPs were then named according to recently proposed nomenclature standards, for instance LINC-[nearest mRNA] for intergenic lncRNAs and [nearest mRNA]-AS for antisense lncRNAs, and were then merged to the Ensembl 75 reference transcriptome, resulting in the polyA Full reference transcriptome. The polyA Stringent reference transcriptome was produced by removing all novel single-exon lncRNAs and TUCPs. Known lncRNAs from Ensembl were obtained by identifying transcripts with one of the following biotype classifications: “3prime_overlapping_ncrna,” “antisense,” “lincRNA,” “processed_transcript,” “sense_intronic,” and “sense_overlapping.” The same pipeline, with the coverage threshold of 1.67, was performed for reads derived from the total RNA-seq. Gene-level fragment counts for each polyA and total RNA sample were quantified using featureCounts v1.4.6, using the flags: -p -s 2 -B -C -t exon -g gene_id. Count tables were normalized to TPM (Transcripts per Million) for internal comparisons and visualizations of bulk RNA-seq. To identify differentially expressed genes, we used DESeq2 on gene-level fragment counts derived from the polyA samples and polyA Full reference transcriptome. Pairwise negative binomial significance tests were performed between developmental stages using biological duplicates, and the union of genes that were significant at FDR < 0.01 were classified as differentially expressed.
Single Cell RNA-seq: Paired end 100 reads from single cell cDNA libraries were quality trimmed using Trim Galore with the flags: -q 20 --nextera --length 20. Trimmed reads were aligned to the human reference genome, Ensembl GRCh37/hg19 release 75, augmented with the 92 ERCC Spike-In Control sequences, using TopHat v2.0.10 with the flags: --transcriptome-index=polya_stringent_reference.gtf --prefilter-multihits. The polyA Stringent reference transcriptome, derived from whole tissue RNA-seq as described above, was used as a transcriptome guide. Gene-level fragment counts were quantified using featureCounts v1.4.6 with the flags: -p -B -C. Counts were normalized by transcriptome size factors according to DESeq. 50 additional single cell libraries were also included, which were deposited in SRP041736.

source_name: Cerebral Cortex

extract_protocol:
Single-cell capture and cell lysis using Fluidigm C1.
RT and whole transcriptome amplifcation on the Fluidigm C1 IFC; library indexed  by illumina Nextera DNA Sample Prep Kit

value: Cerebral Cortex


title: S46.H9

description:
polyA RNA
single cell


title: S46.H7

description:
polyA RNA
single cell


title: S46.H8

description:
polyA RNA
single cell


title: S46.H3

description:
polyA RNA
single cell


title: S46.H2

description:
polyA RNA
single cell


title: S46.H10

description:
polyA RNA
single cell


title: S46.G7

description:
polyA RNA
single cell


title: S46.G9

description:
polyA RNA
single cell


title: S46.G6

description:
polyA RNA
single cell


title: S46.G4

description:
polyA RNA
single cell


title: S46.G2

description:
polyA RNA
single cell


title: S46.G5

description:
polyA RNA
single cell


title: IgG 293T Rep1

description: library strategy: eCLIP-seq

source_name: IgG 293T

value: IgG isotype control

value: Thermo Fisher


title: S46.G1

description:
polyA RNA
single cell


title: S46.G11

description:
polyA RNA
single cell


title: S46.F6

description:
polyA RNA
single cell


title: S46.F4

description:
polyA RNA
single cell


title: S46.F8

description:
polyA RNA
single cell


title: S46.F7

description:
polyA RNA
single cell


title: S46.F11

description:
polyA RNA
single cell


title: S46.F1

description:
polyA RNA
single cell


title: S46.F12

description:
polyA RNA
single cell


title: S46.F2

description:
polyA RNA
single cell


title: S46.F9

description:
polyA RNA
single cell


title: S46.E7

description:
polyA RNA
single cell


title: S46.F5

description:
polyA RNA
single cell


title: S46.E8

description:
polyA RNA
single cell


title: S46.E2

description:
polyA RNA
single cell


title: S46.E1

description:
polyA RNA
single cell


title: S46.E11

description:
polyA RNA
single cell


title: S46.E12

description:
polyA RNA
single cell


title: S46.E4

description:
polyA RNA
single cell


title: S46.D9

description:
polyA RNA
single cell


title: S46.D8

description:
polyA RNA
single cell


title: S46.D7

description:
polyA RNA
single cell


title: S46.D2

description:
polyA RNA
single cell


title: S46.D5

description:
polyA RNA
single cell


title: S46.D12

description:
polyA RNA
single cell


title: S46.D3

description:
polyA RNA
single cell


title: S46.D6

description:
polyA RNA
single cell


title: S46.D1

description:
polyA RNA
single cell


title: S46.D10

description:
polyA RNA
single cell


title: S46.F10

description:
polyA RNA
single cell


title: S46.C9

description:
polyA RNA
single cell


title: S46.C5

description:
polyA RNA
single cell


title: S46.C6

description:
polyA RNA
single cell


title: S46.B8

description:
polyA RNA
single cell


title: S46.C4

description:
polyA RNA
single cell


title: S46.B9

description:
polyA RNA
single cell


title: S46.C3

description:
polyA RNA
single cell


title: S46.C7

description:
polyA RNA
single cell


title: S46.B5

description:
polyA RNA
single cell


title: S46.C8

description:
polyA RNA
single cell


title: S46.B2

description:
polyA RNA
single cell


title: S46.B12

description:
polyA RNA
single cell


title: S46.B3

description:
polyA RNA
single cell


title: S46.B7

description:
polyA RNA
single cell


title: S46.B11

description:
polyA RNA
single cell


title: S46.C12

description:
polyA RNA
single cell


title: S46.E3

description:
polyA RNA
single cell


title: S46.C10

description:
polyA RNA
single cell


title: S46.D4

description:
polyA RNA
single cell


title: S46.B4

description:
polyA RNA
single cell


title: S46.B1

description:
polyA RNA
single cell


title: S46.A8

description:
polyA RNA
single cell


title: S46.A7

description:
polyA RNA
single cell


title: S46.A9

description:
polyA RNA
single cell


title: S46.A6

description:
polyA RNA
single cell


title: S46.A5

description:
polyA RNA
single cell


title: S46.A4

description:
polyA RNA
single cell


title: S46.C11

description:
polyA RNA
single cell


title: S46.A2

description:
polyA RNA
single cell


title: S44.H9

description:
polyA RNA
single cell


title: S44.H5

description:
polyA RNA
single cell


title: S46.A10

description:
polyA RNA
single cell


title: S46.A1

description:
polyA RNA
single cell


title: S44.H6

description:
polyA RNA
single cell


title: S44.G9

description:
polyA RNA
single cell


title: S46.A12

description:
polyA RNA
single cell


title: S44.G7

description:
polyA RNA
single cell


title: S46.B10

description:
polyA RNA
single cell


title: S44.G5

description:
polyA RNA
single cell


title: S44.F9

description:
polyA RNA
single cell


title: S44.G10

description:
polyA RNA
single cell


title: S44.G8

description:
polyA RNA
single cell


title: S44.F6

description:
polyA RNA
single cell


title: S44.D9

description:
polyA RNA
single cell


title: S44.E10

description:
polyA RNA
single cell


title: S44.D8

description:
polyA RNA
single cell


title: S44.D10

description:
polyA RNA
single cell


title: S44.C9

description:
polyA RNA
single cell


title: S44.D5

description:
polyA RNA
single cell


title: S44.B9

description:
polyA RNA
single cell


title: S44.B8

description:
polyA RNA
single cell


title: S44.B7

description:
polyA RNA
single cell


title: S44.A8

description:
polyA RNA
single cell


title: S44.B6

description:
polyA RNA
single cell


title: S46.A11

description:
polyA RNA
single cell


title: S44.A11

description:
polyA RNA
single cell


title: S44.A6

description:
polyA RNA
single cell


title: S44.A9

description:
polyA RNA
single cell


title: A2_N712_S508

description:
polyA RNA
single cell


title: S44.A10

description:
polyA RNA
single cell


title: A2_N711_S507

description:
polyA RNA
single cell


title: A2_N712_S507

description:
polyA RNA
single cell


title: A2_N711_S508

description:
polyA RNA
single cell


title: A2_N712_S502

description:
polyA RNA
single cell


title: A2_N711_S504

description:
polyA RNA
single cell


title: A2_N711_S502

description:
polyA RNA
single cell


title: A2_N711_S505

description:
polyA RNA
single cell


title: A2_N711_S501

description:
polyA RNA
single cell


title: A2_N710_S503

description:
polyA RNA
single cell


title: A2_N710_S507

description:
polyA RNA
single cell


title: A2_N710_S508

description:
polyA RNA
single cell


title: S44.F10

description:
polyA RNA
single cell


title: A2_N710_S501

description:
polyA RNA
single cell


title: A2_N710_S502

description:
polyA RNA
single cell


title: A2_N710_S506

description:
polyA RNA
single cell


title: A2_N709_S507

description:
polyA RNA
single cell


title: A2_N709_S508

description:
polyA RNA
single cell


title: A2_N709_S506

description:
polyA RNA
single cell


title: A2_N708_S506

description:
polyA RNA
single cell


title: A2_N709_S503

description:
polyA RNA
single cell


title: A2_N709_S505

description:
polyA RNA
single cell


title: A2_N708_S502

description:
polyA RNA
single cell


title: A2_N707_S508

description:
polyA RNA
single cell


title: R2_-P3_#04

city: Taipei

first: Tzyy-Jen

last: Chiou

address: No. 128, Sec. 2, Academia Road, Nankang

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

description: Pi starvation 3-day

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed by adaptor sequence, and low-quality sequences were eliminated. Sequences were mapped to Arabidopsis thaliana reference (TAIR10) whole genome using CLC Genomics Workbench 7.0.4
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. The number of reads mapping to the exons of a transcript were counted and normalized by the kilobase size of a transcript and by the megabase size of the library.
Genome_build: TAIR10
Supplementary_files_format_and_content: xlsx file includes description, RPKM values and normalized values for each Sample

source_name: plant seedlings

growth_protocol: Seeds were surface sterilized and germinated on agar plates with one-half modified Hoagland nutrient solution containing 250 μM KH2PO4, 1% sucrose, and 1% bactoagar.

extract_protocol:
Total RNA was isolated using RNAzol (Molecular Research Center).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The Pi-sufficient (+Pi) and Pi-deficient (−Pi) media were supplemented with 250 µM for 10-day and 10 µM KH2PO4 for additional 1-day or 3-days, respectively.

value: root

tag: treatment

value: Pi starvation

tag: time

value: 3 day

tag: plant


title: R2_-P3_WT

description: Pi starvation 3-day


title: R2_-P1_#12

description: Pi starvation 1-day

value: 1 day


title: R2_-P1_WT

description: Pi starvation 1-day


title: A2_N707_S505

description:
polyA RNA
single cell

tag: developmental stage


title: R2_-P3_#12

description: Pi starvation 3-day


title: A2_N707_S507

description:
polyA RNA
single cell


title: R2_-P1_#04

description: Pi starvation 1-day


title: A2_N707_S501

description:
polyA RNA
single cell


title: A2_N707_S504

description:
polyA RNA
single cell


title: R2_+P0_#12

description: Pi sufficiency 10-day

value: Pi sufficiency

value: 10 day


title: R1_-P3_#12

description: Pi starvation 3-day


title: R2_+P0_WT

description: Pi sufficiency 10-day


title: R1_-P3_#04

description: Pi starvation 3-day


title: A2_N706_S504

description:
polyA RNA
single cell


title: A2_N706_S507

description:
polyA RNA
single cell


title: R1_-P3_WT

description: Pi starvation 3-day


title: A2_N706_S506

description:
polyA RNA
single cell


title: A2_N708_S503

description:
polyA RNA
single cell


title: A2_N706_S503

description:
polyA RNA
single cell


title: R1_-P1_#12

description: Pi starvation 1-day


title: R1_-P1_#04

description: Pi starvation 1-day


title: A2_N705_S507

description:
polyA RNA
single cell


title: R1_-P1_WT

description: Pi starvation 1-day


title: A2_N708_S508

description:
polyA RNA
single cell


title: A2_N705_S505

description:
polyA RNA
single cell


title: R1_+P0_#12

description: Pi sufficiency 10-day


title: A2_N706_S508

description:
polyA RNA
single cell


title: R2_+P0_#04

description: Pi sufficiency 10-day


title: A2_N705_S504

description:
polyA RNA
single cell


title: A2_N705_S502

description:
polyA RNA
single cell


title: S2_-P3_#12

description: Pi starvation 3-day

value: shoot


title: A2_N704_S508

description:
polyA RNA
single cell


title: R1_+P0_#04

description: Pi sufficiency 10-day


title: S2_-P1_#12

description: Pi starvation 1-day


title: A2_N704_S501

description:
polyA RNA
single cell


title: S2_-P3_WT

description: Pi starvation 3-day


title: S2_-P3_#04

description: Pi starvation 3-day


title: A2_N704_S503

description:
polyA RNA
single cell


title: A2_N706_S501

description:
polyA RNA
single cell


title: S2_-P1_#04

description: Pi starvation 1-day


title: A2_N703_S503

description:
polyA RNA
single cell


title: A2_N703_S501

description:
polyA RNA
single cell


title: A2_N704_S506

description:
polyA RNA
single cell


title: A2_N703_S508

description:
polyA RNA
single cell


title: A2_N703_S506

description:
polyA RNA
single cell


title: A2_N702_S508

description:
polyA RNA
single cell


title: A2_N702_S507

description:
polyA RNA
single cell


title: S2_+P0_#12

description: Pi sufficiency 10-day


title: S1_-P3_#12

description: Pi starvation 3-day


title: S2_+P0_WT

description: Pi sufficiency 10-day


title: S1_-P3_#04

description: Pi starvation 3-day


title: A2_N702_S506

description:
polyA RNA
single cell


title: R1_+P0_WT

description: Pi sufficiency 10-day


title: S1_-P3_WT

description: Pi starvation 3-day


title: A2_N702_S504

description:
polyA RNA
single cell


title: A2_N702_S501

description:
polyA RNA
single cell


title: A2_N701_S508

description:
polyA RNA
single cell


title: S1_-P1_#12

description: Pi starvation 1-day


title: A2_N701_S507

description:
polyA RNA
single cell


title: S1_-P1_WT

description: Pi starvation 1-day


title: A2_N701_S506

description:
polyA RNA
single cell


title: S1_+P0_#04

description: Pi sufficiency 10-day


title: A2_N701_S502

description:
polyA RNA
single cell


title: S2_-P1_WT

description: Pi starvation 1-day


title: S1_+P0_#12

description: Pi sufficiency 10-day


title: S2_+P0_#04

description: Pi sufficiency 10-day


title: A2_N701_S503

description:
polyA RNA
single cell


title: S1_+P0_WT

description: Pi sufficiency 10-day


title: A1_N712_S507

description:
polyA RNA
single cell