title: 09A018.09B9170_003

description:
09B9170_IonXpressRNA_003
processed data file: A1AT-BAL_gradsids_added.tsv
09A018:09B9170_003_FPKM


title: WYK3340 Patient UC Sample

status: Public on Nov 03 2020

type: SRA

city: Chapel Hill

first: Kim Lab

last: UNC

state: NC

address: 450 West Drive, Room 21-209

country: USA

institute: UNC-CH LCCC

library_source: transcriptomic

data_processing:
Sequence reads were aligned to the human reference genome hg38 using MapSplice v2.2.1
Gene-level counts were quantified using RSEM v.1.3.0 and normalized for variations in read counts
Normalized read counts were log2 transformed
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Urothelial cancer FFPE tissue

extract_protocol:
RNA was isolated from 10uM FFPE slides from all patient samples using the Roche High Pure RNA Paraffin Kit according to manufacturer’s protocol, a minimum of 2 µg of total RNA was isolated from FFPE tissues
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: Female

tag: race

value: White

tag: age

tag: smoking status

value: Current

tag: pathology stage

tag: rnaseq base47 classification

value: Basal

tag: nanostring base47 classification

value: Luminal

tag: overall survival status

tag: overall survival months


title: AF2_21

city: Cambridge

first: Alastair

last: Crisp

address: Francis Crick Avenue

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

data_processing:
Reads aligned to a modified mouse genome (addition of the reporters found in the mouse) using the Salmon pseudoaligner (v0.8.2)
Pseudocounts analysis with the scater library (v1.6.3) (McCarthy et al., 2017), scran library (v1.6.9) (Lun et al., 2016), and sva library (sva: Surrogate Variable Analysis. R package v3.26.0).
Cells with pseudocounts below 3 median-absolute-deviations away from the median were removed. Genes with an average count across all remaining cells of less than 1 were removed.
Size factors were calculated with the scran library (based on the gene counts) and the data normalised by them.
Batch effects were removed using the ComBat empirical Bayes framework from the sva library
Genome_build: GRCm38.68
Supplementary_files_format_and_content: RDS of R SCE object containing metadata and gene expression generated using R,scater,scran and sva; tab-separated normalised gene expression from the SCE object

organism: Mus musculus

source_name: Sample 1A_embryonic thymus

extract_protocol:
Individual cells were flow cytometrically purified on a 96 well format into 0.2% Triton X-100 containing RNase inhibitor, dNTPs and oligo-dT primers and stored at -80oC.
On thawing, lysates were heated to 72 oC for 3 minutes and subject to reverse transcription, PCR preamplification (26 cycles) and PCR purification.  cDNA library quality was assessed for all samples by qualitative PCR using primers for 18s RNA with an additional check by Bioanalyzer using an Agilent high sensitivity DNA chip on a small subset of libraries. A subset of libraries was quantified using the Qubit dsDNA HS assay kit and an average value used to calculate library dilution to 100-150 pg/ml. cDNA library tagmentation and amplification was performed using the Illumina Nextera XT DNA Library Preparation Kit according to manufacturer’s instructions except that all volumes were reduced 4-fold and tagmentation performed at 55oC for 20 minutes. Nextera index and Illumina adapter sequences were incorporated at the amplification stage (N7xx and S5xx). Amplified and indexed libraries were pooled and purified using Agencourt AMPure XP beads at a ratio of 1:0.9 library to beads and washed with 70% ethanol. Two rounds of purification were performed before a final elution in 1.25x total library volume of Nextera Resuspension buffer

tag: mouse id

value: Sample 1A

tag: strain

value: 5x polychromILC mice

tag: tissue

value: Embryonic Thymus


title: 09A009.09B9174_003

city: New Haven

first: Jen-hwa

last: Chu

state: CT

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale University School of Medicine

description:
09B9174_IonXpressRNA_003
processed data file: A1AT-BAL_gradsids_added.tsv
09A009:09B9174_003_FPKM

data_processing:
Basecalls using Torrent Suite Software Version 5.0.5
mRNA-seq reads were aligned to hg19 using a two stage mapping strategy. In the first stage, tophat version 2.0.12 was used with annotation and the --b2-very-sensitive option. In the second stage, bowtie 2.0.5 was used with local alignment and the --very-sensitive option.
Data were filtered using principal component analysis to remove outleirs.
Genome_build: hg19
Supplementary_files_format_and_content: text files that contain the  Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were generated using cufflinks 2.2.0

source_name: BAL_PiZZ on Augmenation Therapy

extract_protocol:
Total RNA was extracted from BALF\ and PBMC samples using Qiazol following Qiagen’s miRNeasy protocol (Qiagen 217004) and using QiaCube
cDNA libraries were made from 1ug of total RNA that had RNA Integrity Number (RINe) over 6.5 upon Poly-A selection using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Ambion 61021) and fragmentation using the AB Library Builder™ System (Life Technologies 4463592) with the Ion Total RNA-Seq Kit for AB Library Builder™ System (Life Technologies 4482416).

tag: subject status

value: Alpha-1 Antitrypsin Deficiency patients

tag: genotype

value: PiZZ on Augmenation Therapy

value: bronchoalveolar lavage (BAL)


title: 04A032.04B9400_001

description:
04B9400_IonXpressRNA_001
processed data file: A1AT-BAL_gradsids_added.tsv
04A032:04B9400_001_FPKM


title: WYK3341 Patient UC Sample

value: Male

value: Former


title: 04A013.04B9249_016

description:
04B9249_IonXpressRNA_016
processed data file: A1AT-BAL_gradsids_added.tsv
04A013:04B9249_016_FPKM


title: AF2_20


title: 03A044.03B9455_011

description:
03B9455_IonXpressRNA_011
processed data file: A1AT-BAL_gradsids_added.tsv
03A044:03B9455_011_FPKM


title: AF2_2


title: 03A022.03B9335_004

description:
03B9335_IonXpressRNA_004
processed data file: A1AT-BAL_gradsids_added.tsv
03A022:03B9335_004_FPKM


title: 03A023.03B9337_004

description:
03B9337_IonXpressRNA_004
processed data file: A1AT-BAL_gradsids_added.tsv
03A023:03B9337_004_FPKM


title: 09A002.09B9172_012

description:
09B9172_IonXpressRNA_012
processed data file: A1AT-BAL_gradsids_added.tsv
09A002:09B9172_012_FPKM


title: WYK3336 Patient UC Sample


title: 03A019.03B9326_016

description:
03B9326_IonXpressRNA_016
processed data file: A1AT-BAL_gradsids_added.tsv
03A019:03B9326_016_FPKM


title: 03A014.03B9214_010

description:
03B9214_IonXpressRNA_010
processed data file: A1AT-BAL_gradsids_added.tsv
03A014:03B9214_010_FPKM


title: AF2_19


title: 05A011.05B9113_014

description:
05B9113_IonXpressRNA_014
processed data file: A1AT-BAL_gradsids_added.tsv
05A011:05B9113_014_FPKM


title: WYK3333 Patient UC Sample


title: 05A005.05B9108_004

description:
05B9108_IonXpressRNA_004
processed data file: A1AT-BAL_gradsids_added.tsv
05A005:05B9108_004_FPKM


title: 05A003.05B9107_010

description:
05B9107_IonXpressRNA_010
processed data file: A1AT-BAL_gradsids_added.tsv
05A003:05B9107_010_FPKM


title: 03A013.03B9211_006

description:
03B9211_IonXpressRNA_006
processed data file: A1AT-BAL_gradsids_added.tsv
03A013:03B9211_006_FPKM


title: WYK3331 Patient UC Sample


title: AF2_18


title: 04A034.04B9401_007

description:
04B9401_IonXpressRNA_007
processed data file: A1AT-BAL_gradsids_added.tsv
04A034:04B9401_007_FPKM


title: 03A012.03B9208_005

description:
03B9208_IonXpressRNA_005
processed data file: A1AT-BAL_gradsids_added.tsv
03A012:03B9208_005_FPKM


title: 10A026.10B9371_002

description:
10B9371_IonXpressRNA_002
processed data file: A1AT-BAL_gradsids_added.tsv
10A026:10B9371_002_FPKM

source_name: BAL_PiZZ Not on Augmenation Therapy

value: PiZZ Not on Augmenation Therapy


title: 10A032.10B9368_004

description:
10B9368_IonXpressRNA_004
processed data file: A1AT-BAL_gradsids_added.tsv
10A032:10B9368_004_FPKM


title: WYK3329 Patient UC Sample


title: WYK3339 Patient UC Sample


title: AF2_17


title: 10A017.10B9195_008

description:
10B9195_IonXpressRNA_008
processed data file: A1AT-BAL_gradsids_added.tsv
10A017:10B9195_008_FPKM


title: 10A010.10B9196_001

description:
10B9196_IonXpressRNA_001
processed data file: A1AT-BAL_gradsids_added.tsv
10A010:10B9196_001_FPKM


title: WYK3325 Patient UC Sample


title: AF2_16


title: AF2_15


title: WYK3320 Patient UC Sample


title: 10A003.10B9187_010

description:
10B9187_IonXpressRNA_010
processed data file: A1AT-BAL_gradsids_added.tsv
10A003:10B9187_010_FPKM


title: 10A001.10B9188_011

description:
10B9188_IonXpressRNA_011
processed data file: A1AT-BAL_gradsids_added.tsv
10A001:10B9188_011_FPKM


title: 10A007.10B9189_012

description:
10B9189_IonXpressRNA_012
processed data file: A1AT-BAL_gradsids_added.tsv
10A007:10B9189_012_FPKM


title: 10A004.10B9183_008

description:
10B9183_IonXpressRNA_008
processed data file: A1AT-BAL_gradsids_added.tsv
10A004:10B9183_008_FPKM


title: WYK3314 Patient UC Sample

value: Never


title: AF2_14


title: 09A023.09B9177_003RUN87

description:
09B9177_IonXpressRNA_003RUN87
processed data file: A1AT-BAL_gradsids_added.tsv
09A023:09B9177_003RUN87_FPKM


title: WYK3313 Patient UC Sample


title: 08A005.08B9140_016

description:
08B9140_IonXpressRNA_016
processed data file: A1AT-BAL_gradsids_added.tsv
08A005:08B9140_016_FPKM


title: AF2_13


title: 10A002.10B9181_012

description:
10B9181_IonXpressRNA_012
processed data file: A1AT-BAL_gradsids_added.tsv
10A002:10B9181_012_FPKM


title: 05A012.05B9340_007

description:
05B9340_IonXpressRNA_007
processed data file: A1AT-BAL_gradsids_added.tsv
05A012:05B9340_007_FPKM


title: AF2_12


title: AF2_11


title: 04A017.04B9251_007

description:
04B9251_IonXpressRNA_007
processed data file: A1AT-BAL_gradsids_added.tsv
04A017:04B9251_007_FPKM


title: WYK3308 Patient UC Sample


title: 05A002.05B9106_004

description:
05B9106_IonXpressRNA_004
processed data file: A1AT-BAL_gradsids_added.tsv
05A002:05B9106_004_FPKM


title: 04A014.04B9097_003

description:
04B9097_IonXpressRNA_003
processed data file: A1AT-BAL_gradsids_added.tsv
04A014:04B9097_003_FPKM


title: 04A007.04B9095_011

description:
04B9095_IonXpressRNA_011
processed data file: A1AT-BAL_gradsids_added.tsv
04A007:04B9095_011_FPKM


title: 03A026.03B9381_005

description:
03B9381_IonXpressRNA_005
processed data file: A1AT-BAL_gradsids_added.tsv
03A026:03B9381_005_FPKM


title: WYK3307 Patient UC Sample


title: WYK3305 Patient UC Sample


title: AF2_10


title: 03A024.03B9336_015

description:
03B9336_IonXpressRNA_015
processed data file: A1AT-BAL_gradsids_added.tsv
03A024:03B9336_015_FPKM


title: AF2_1


title: 03A025.03B9339_014

description:
03B9339_IonXpressRNA_014
processed data file: A1AT-BAL_gradsids_added.tsv
03A025:03B9339_014_FPKM


title: AF1_95


title: 03A010.03B9210_001

description:
03B9210_IonXpressRNA_001
processed data file: A1AT-BAL_gradsids_added.tsv
03A010:03B9210_001_FPKM


title: WYK3302 Patient UC Sample


title: 03A015.03B9322_005

description:
03B9322_IonXpressRNA_005
processed data file: A1AT-BAL_gradsids_added.tsv
03A015:03B9322_005_FPKM


title: WYK3301 Patient UC Sample


title: WYK3311 Patient UC Sample


title: 03A009.03B9202_002

description:
03B9202_IonXpressRNA_002
processed data file: A1AT-BAL_gradsids_added.tsv
03A009:03B9202_002_FPKM


title: 03A008.03B9200_012

description:
03B9200_IonXpressRNA_012
processed data file: A1AT-BAL_gradsids_added.tsv
03A008:03B9200_012_FPKM


title: WYK3300 Patient UC Sample


title: 03A004.03B9079_009

description:
03B9079_IonXpressRNA_009
processed data file: A1AT-BAL_gradsids_added.tsv
03A004:03B9079_009_FPKM


title: AF1_93


title: 46C_shMef2c-d0

city: shanghai

first: Mingliang

last: Bai

state: shanghai

address: siping road

country: China

institute: tongji university

description: processed data file: shCtrl&shMef2c D0 DGEs

data_processing:
Firstly, we filter the low quality reads (More than 20% of the bases qualities are lower than 10),  reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads.  Then we map those clean reads onto reference genome, followed with novel gene prediction, SNP  & INDEL calling and gene splicing detection. Finally, we identify DEGs (differentially expressed  genes) between samples and do clustering analysis and functional annotations.
We use internal software SOAPnuke to filter reads, followed as:  1) Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 5%; 3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 20% in a read). After filtering, the remaining reads are called "Clean Reads" and stored in FASTQ format (see FASTQ Format in help page FASTQ Format).  Software information: SOAPnuke:  version：v1.5.2  parameters: -l 15 -q 0.2 -n 0.05  website: https://github.com/BGI-flexlab/SOAPnuke
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping  step. For HISAT which is much faster, sensitive and high accuracy analysis software.  Software information:  HISAT2:  Version: v2.0.4  Parameters: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000  Website: http://www.ccb.jhu.edu/software/hisat
It is important to distinguish differential isoform relative abundance, from differential isoform  expression. Changes in relative abundance of isoforms, regardless of the expression change,  indicate a splicing-related mechanism. On the other hand, there can be measurable changes in the  expression of isoforms across samples, without necessarily changing the relative abundance, which  possibly indicates a transcription-related mechanism. We use rMATS] to detect differentially  splicing gene(that is differential isoform relative abundance between samples), a computational tool  to detect differential alternative splicing events from RNA-Seq data, it calculates the inclusion isoform  and skipping isofrom, shown as Figure6. The statistical model of MATS calculates the P-value and  false discovery rate ( FDR ) that the difference in the isoform ratio of a gene between two conditions,  in our project, gene that with FDR <= 0.05 is defined as significant differentially splicing gene ( DSG  ).  Software information:  rMATS:  Version: v3.2.5  Parameters: -analysis U -t paired -a 8  Website: http://rnaseq-mats.sourceforge.net
We mapped clean reads to reference using Bowtie2, and then calculate gene expression  level with RSEM . RSEM is a software package for estimating gene and isoform expression  levels from RNA-Seq data. Then, wecalculate pearson correlation between all samples using cor,  perform hierarchical clustering between all samples using hclust, and draw the diagrams with  ggplot2 with fuctions of R.  Software information:  Bowtie2 :  Version: v2.2.5  Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X  1000 --no-mixed --no-discordant -p 1 -k 200  Website: http://bowtie-bio.sourceforge.net/ Bowtie2 /index.shtml  RSEM :  Version: v1.2.12  Parameters: default  Website: http://deweylab.biostat.wisc.edu/ RSEM
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample

growth_protocol: mESCs line 46C was cultured on irradiated mouse embryonic fibroblasts (MEFs)  in mESCs medium in Dulbecco’s modified eagle medium (DMEM) medium (Gibco, USA) containing 15% fetal bovine serum (FBS, Gibco), 0.1 mmol/L β-mercaptoethanol (Sigma, USA), 2 mmol/L glutamine (Invitrogen, USA), 2 mmol/L nonessential amino acids (NEAA) (Invitrogen), 1 mmol/L  sodium pyruvate (Invitrogen), and 20 ng/ml homemade leukemia inhibitory factor (LIF) at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25μL~100μL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Change the medium every day.

tag: cell line

value: 46C cells

tag: cell type

value: mESC cell line

tag: genotype/variation


title: WYK3299 Patient UC Sample

tag: gender

value: Female


title: 46C_shCtrl-d0

value: shCtrl


title: AF1_92


title: AF1_91


title: AF1_96


title: 01A004.01B9292_012

description:
01B9292_IonXpressRNA_012
processed data file: A1AT-BAL_gradsids_added.tsv
01A004:01B9292_012_FPKM


title: 46C_KO-d0

description: processed data file: WT&KO D0 DGEs


title: 01A003.01B9290_001

description:
01B9290_IonXpressRNA_001
processed data file: A1AT-BAL_gradsids_added.tsv
01A003:01B9290_001_FPKM


title: AF1_90


title: 03A017.03B9323_004RUN87

description:
03B9323_IonXpressRNA_004RUN87
processed data file: A1AT-BAL_gradsids_added.tsv
03A017:03B9323_004RUN87_FPKM


title: 01A002.01B9289_012

description:
01B9289_IonXpressRNA_012
processed data file: A1AT-BAL_gradsids_added.tsv
01A002:01B9289_012_FPKM


title: 03A001.03B9060_011

description:
03B9060_IonXpressRNA_011
processed data file: A1AT-BAL_gradsids_added.tsv
03A001:03B9060_011_FPKM


title: SKBR3_MED1_siNT_24h_DMSO_24h

city: Indianapolis

first: Steven

middle: P

last: Angus

state: IN

address: 1044 W Walnut St

department: Pediatrics

institute: Indiana University School of Medicine

description: SKBR-3-BRD4-MED1-siNontargeting-siFOXA1-Lapatinib.xlsx

library_source: genomic

data_processing:
Reads were aligned to hg19 using Bowtie v1.1.2 with parameters -v 2 -m 1.
Genome_build: hg19
Supplementary_files_format_and_content: The following processing steps were performed to generate peakclassification files:  Calculating read density: The density of reads in each region was normalized to the total number of million mapped reads producing read density in units of reads per million mapped reads (rpm).  The read density of the input chromatin was subtracted from the ChIP read density for normalization.  Peak calling: We used a combination of two algorithms, MACS v1.4.2 and HMCan v1.21, to define enriched regions.  We used HMCan to call peaks in regions of high CNV, defined as regions of size > 50 kb where no MACS peaks are called, and have read coverage that is >3 times the average read coverage.   Peaks within 12.5 kb of each other were stitched as described in Loven et al. 2013 Cell 153.  We used default settings for MACS, and HMCan was run with narrow peak calling configuration file with no blacklisted regions.  Peak genic classification:  A peak region was classified on the basis of its location with respect to GRCh37/hg19 gene annotations.  If the region was +/- 5 kb of any transcription start site, it was classified as a promoter peak.   If it was within -5kb to -200kb of any transcriptional start site, it was classified as a 5' enhancer peak.  If the peak overlapped the gene boundary, and was not classified as a promoter or enhancer peak, it was classified as either a genebody_exon or genebody_intron peak.  If the peak resided within 0 to +200kb from the 3'-most exon, and did not fulfill the criteria for the above classifications, it was classified as a 3' enhancer.   All remaining peaks were designated as "other".

molecule: genomic DNA

source_name: SKBR-3 HER2+ breast carcinoma cell line

extract_protocol:
Whole cell lysates were sonicated resulting in an average chromatin fragment size of ~300 bp and immunoprecipiated with the indicated antibodies.
All libraries were constructed using KAPA Hyper Prep kits with Illumina TruSeq adapters, 18 cycles of amplification and dual SPRI size selection post-amplification

tag: culture media

value: RPMI supplemented with 10% FBS

tag: library preparation kit

value: KAPA Hyper Prep

tag: treatment

value: non-targeting (NT) siRNA control pool  for 48h, then treated with DMSO for 24h

tag: chip antibody

value: MED1/CRSP1/TRAP220 Bethyl Laboratories A300-793A100


title: AF1_9

value: Sample 1A

value: 5x polychromILC mice


title: 46C_WT-d0

description: processed data file: WT&KO D0 DGEs

value: wild type (WT)


title: 10A041.10B9378_006

description:
10B9378_IonXpressRNA_006
processed data file: A1AT-BAL_gradsids_added.tsv
10A041:10B9378_006_FPKM

value: Alpha-1 Antitrypsin Deficiency patients

value: PiMZ


title: AF1_94

value: Embryonic Thymus


title: SKBR3_MED1_siNT_24h_300nM_lapatinib_24h

value: non-targeting (NT) siRNA control pool  for 48h, then treated with 300nM lapatinib for 24h


title: SKBR3_MED1_siFOXA1_24h_DMSO_24h

value: FOXA1 siRNA pool  for 48h, then treated with DMSO for 24h


title: shMef2c

description: shCtrl-VS-shMef2c.PossionDis_Method.GeneDiffExpFilter

data_processing:
Firstly, we filter the low quality reads (More than 20% of the bases qualities are lower than 10),  reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads.  Then we map those clean reads onto reference genome, followed with novel gene prediction, SNP  & INDEL calling and gene splicing detection. Finally, we identify DEGs (differentially expressed  genes) between samples and do clustering analysis and functional annotations.
We use internal software SOAPnuke to filter reads, followed as:  1) Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 5%; 3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 20% in a read). After filtering, the remaining reads are called "Clean Reads" and stored in FASTQ format (see FASTQ Format in help page FASTQ Format).  Software information: SOAPnuke:  version：v1.5.2  parameters: -l 15 -q 0.2 -n 0.05  website: https://github.com/BGI-flexlab/SOAPnuke
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping  step. For HISAT which is much faster, sensitive and high accuracy analysis software.  Software information:  HISAT2:  Version: v2.0.4  Parameters: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000  Website: http://www.ccb.jhu.edu/software/hisat
It is important to distinguish differential isoform relative abundance, from differential isoform  expression. Changes in relative abundance of isoforms, regardless of the expression change,  indicate a splicing-related mechanism. On the other hand, there can be measurable changes in the  expression of isoforms across samples, without necessarily changing the relative abundance, which  possibly indicates a transcription-related mechanism. We use rMATS] to detect differentially  splicing gene(that is differential isoform relative abundance between samples), a computational tool  to detect differential alternative splicing events from RNA-Seq data, it calculates the inclusion isoform  and skipping isofrom, shown as Figure6. The statistical model of MATS calculates the P-value and  false discovery rate ( FDR ) that the difference in the isoform ratio of a gene between two conditions,  in our project, gene that with FDR <= 0.05 is defined as significant differentially splicing gene ( DSG  ).  Software information:  rMATS:  Version: v3.2.5  Parameters: -analysis U -t paired -a 8  Website: http://rnaseq-mats.sourceforge.net
We mapped clean reads to reference using Bowtie2, and then calculate gene expression  level with RSEM . RSEM is a software package for estimating gene and isoform expression  levels from RNA-Seq data. Then, wecalculate pearson correlation between all samples using cor,  perform hierarchical clustering between all samples using hclust, and draw the diagrams with  ggplot2 with fuctions of R.  Software information:  Bowtie2 :  Version: v2.2.5  Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X  1000 --no-mixed --no-discordant -p 1 -k 200  Website: http://bowtie-bio.sourceforge.net/ Bowtie2 /index.shtml  RSEM :  Version: v1.2.12  Parameters: default  Website: http://deweylab.biostat.wisc.edu/ RSEM
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample

source_name: Neural progenitor cells

growth_protocol: ES cells were dissociated to single cells in 0.25% trypsin-EDTA (Invitrogen) and quickly re-aggregated in the differentiation medium ((5 ± 1) ×103 cells/mL) using low-cell-adhesion 6cm dishes and cultured in G-MEM (Gibco) supplemented with 8% knockout serum replacement (KOSR, Gibco), 0.1mmol/L β-mercaptoethanol, 2 mmol/L  glutamine, 2 mmol/L nonessential amino acids, 1 mmol/L sodium pyruvate.

treatment_protocol: Change the medium every other day.

value: ES-derived neural progenitor cells


title: 10A038.10B9377_009

description:
10B9377_IonXpressRNA_009
processed data file: A1AT-BAL_gradsids_added.tsv
10A038:10B9377_009_FPKM

value: bronchoalveolar lavage (BAL)


title: AF1_88


title: AF1_89


title: shCtrl


title: LincNDIME_KO

description: WT-VS-LincNDIME_KO.PossionDis_Method.GeneDiffExpFilter


title: 10A037.10B9376_002

description:
10B9376_IonXpressRNA_002
processed data file: A1AT-BAL_gradsids_added.tsv
10A037:10B9376_002_FPKM


title: BT474m1_input_for_BRD4_MED1_DMSO

source_name: BT474m1 HER2+ breast carcinoma cell line

value: treated with DMSO for 24h

value: no antibody


title: SKBR3_input_siNT_24h_DMSO_24h


title: AF1_87


title: WT


title: AF1_86


title: 10A036.10B9372_001

description:
10B9372_IonXpressRNA_001
processed data file: A1AT-BAL_gradsids_added.tsv
10A036:10B9372_001_FPKM


title: SKBR3_input_siFOXA1_24h_DMSO_24h


title: SKBR3_BRD4_siNT_24h_DMSO_24h

value: BRD4 Bethyl Laboratories A301-985A100


title: 4_13_30 [JA30_S3]

city: Guangzhou

first: Niu

last: Yu

address: Number 682, Guangshan Yi Road, Longdong

institute: Research Institute of Tropical Forestry, Chinese Academy of Forestry

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep
De novo assembly of the clean reads was carried out using the Trinity platform
The CDS prediction was performed by blast into NR and Swissprot protein database
Supplementary_files_format_and_content: excel files include FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files with CDS sequences for each unigene

organism: Sindora glabra

source_name: Treated with meJA for 30 days_stem

extract_protocol:
Total RNA was extracted from each sample using the TRIzol Reagent (Invitrogen, USA).
paired-end library was sequenced with Illumina HiSeq X Ten (2×150 bp read length)

value: Treated with meJA for 30 days

value: stem


title: 10A028.10B9370_001

description:
10B9370_IonXpressRNA_001
processed data file: A1AT-BAL_gradsids_added.tsv
10A028:10B9370_001_FPKM


title: AF1_85


title: SKBR3_BRD4_siNT_24h_300nM_lapatinib_24h

value: RPMI supplemented with 10% FBS

value: KAPA Hyper Prep


title: AF1_84

value: Sample 1A


title: 4_13_10 [JA10_S3]

source_name: Treated with meJA for 10 days_stem

value: Treated with meJA for 10 days


title: SKBR3_BRD4_siFOXA1_24h_DMSO_24h


title: 10A029.10B9367_014

description:
10B9367_IonXpressRNA_014
processed data file: A1AT-BAL_gradsids_added.tsv
10A029:10B9367_014_FPKM


title: SKBR3_MED1_siFOXA1_24h_300nM_lapatinib_24h

value: FOXA1 siRNA pool  for 48h, then treated with 300nM lapatinib for 24h

value: MED1/CRSP1/TRAP220 Bethyl Laboratories A300-793A100


title: 4_13_20 [JA20_S3]

source_name: Treated with meJA for 20 days_stem

value: Treated with meJA for 20 days


title: AF1_83

value: 5x polychromILC mice

value: Embryonic Thymus


title: AF1_82


title: 10A033.10B9366_008

description:
10B9366_IonXpressRNA_008
processed data file: A1AT-BAL_gradsids_added.tsv
10A033:10B9366_008_FPKM

value: Alpha-1 Antitrypsin Deficiency patients

value: PiMZ


title: 3_13_30 [JA30_S2]


title: 10A040.10B9364_015

description:
10B9364_IonXpressRNA_015
processed data file: A1AT-BAL_gradsids_added.tsv
10A040:10B9364_015_FPKM

value: bronchoalveolar lavage (BAL)


title: SKBR3_FOXA1_300nM_lapatinib_300nM_JQ1_24h

description: SKBR-3-BRD4-MED1-H3K27Ac-FOXA1-Lapatinib-JQ1.xlsx

value: treated with 300nM lapatinib and 300nM JQ1 for 24h

value: FOXA1 Abcam ab5089 (ChIP Grade)


title: AF1_81

source_name: Sample 1B_embryonic thymus

value: Sample 1B


title: SKBR3_BRD4_siFOXA1_24h_300nM_lapatinib_24h

value: BRD4 Bethyl Laboratories A301-985A100


title: 3_13_20 [JA20_S2]

value: stem


title: 10A018.10B9197_003

description:
10B9197_IonXpressRNA_003
processed data file: A1AT-BAL_gradsids_added.tsv
10A018:10B9197_003_FPKM


title: 3_13_10 [JA10_S2]


title: AF1_80


title: SKBR3_FOXA1_300nM_lapatinib_24h

value: RPMI supplemented with 10% FBS

value: treated with 300nM lapatinib for 24h


title: AF1_8


title: SKBR3_FOXA1_300nM_JQ1_24h

value: KAPA Hyper Prep

value: treated with 300nM JQ1 for 24h


title: 3_13 [JAc_S2]

value: Untreated


title: 10A027.10B9369_010

description:
10B9369_IonXpressRNA_010
processed data file: A1AT-BAL_gradsids_added.tsv
10A027:10B9369_010_FPKM


title: AF1_79


title: SKBR3_FOXA1_DMSO_24h

value: treated with DMSO for 24h


title: 4_13 [JAc_S3]


title: 2_13_30 [JA30_S1]

value: Treated with meJA for 30 days


title: AF1_78

value: 5x polychromILC mice


title: 2_13_20 [JA20_S1]

value: Treated with meJA for 20 days


title: SKBR3_input_for_FOXA1_DMSO_24h

value: no antibody


title: 10A015.10B9180_006

description:
10B9180_IonXpressRNA_006
processed data file: A1AT-BAL_gradsids_added.tsv
10A015:10B9180_006_FPKM

value: Alpha-1 Antitrypsin Deficiency patients

value: PiMZ


title: BT474m1_MED1_300nM_lapatinib_300nM_JQ1_24h

description: BT474m1-BRD4-MED1-H3K27Ac-Lapatinib-JQ1.xlsx

value: treated with 300nM lapatinib and 300nM JQ1 for 24h

value: MED1/CRSP1/TRAP220 Bethyl Laboratories A300-793A100


title: AF1_77

value: Sample 1B

value: Embryonic Thymus


title: 2_13_10 [JA10_S1]

value: Treated with meJA for 10 days

value: stem


title: AF1_76


title: BT474m1_MED1_300nM_lapatinib_24h

value: RPMI supplemented with 10% FBS

value: treated with 300nM lapatinib for 24h


title: 2_13 [JAc_S1]


title: BT474m1_MED1_300nM_JQ1_24h

value: KAPA Hyper Prep

value: treated with 300nM JQ1 for 24h


title: AF1_75


title: 10A024.10B9193_004

description:
10B9193_IonXpressRNA_004
processed data file: A1AT-BAL_gradsids_added.tsv
10A024:10B9193_004_FPKM

value: bronchoalveolar lavage (BAL)


title: 10A013.10B9184_004

description:
10B9184_IonXpressRNA_004
processed data file: A1AT-BAL_gradsids_added.tsv
10A013:10B9184_004_FPKM


title: BT474m1_MED1_DMSO_24h

value: treated with DMSO for 24h


title: BIN_UQFortes_7T_small

city: Brisbane

first: Marina

last: Fortes

state: Queensland

address: SCMB, room 454 bld 76

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

description: small RNA

data_processing: libraries were multiplex per lane and paried-end sequenced, with Illumina HiSeq 2000 analyzer

organism: Bos indicus

source_name: Adult testicular tissue parenchyma section, animal 7, small RNA preparation

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

value: testis

tag: tissue subsection

value: parenchyma

tag: developmental stage

value: adult

tag: age

value: 2 years

tag: animal id


title: BIN_UQFortes_7CT_small

description: small RNA

source_name: Adult testicular tissue caput epididymis section, animal 7, small RNA preparation

value: caput epididymis


title: AF1_74

tag: mouse id

value: 5x polychromILC mice


title: BIN_UQFortes_7CD_small

description: small RNA

source_name: Adult testicular tissue cauda epididymis section, animal 7, small RNA preparation

value: cauda epididymis


title: 09A036.09B9166_002

description:
09B9166_IonXpressRNA_002
processed data file: A1AT-BAL_gradsids_added.tsv
09A036:09B9166_002_FPKM

value: Alpha-1 Antitrypsin Deficiency patients

value: PiMZ


title: BT474m1_input_for_H3K27Ac_DMSO_24h

value: no antibody


title: 10A006.10B9182_009

description:
10B9182_IonXpressRNA_009
processed data file: A1AT-BAL_gradsids_added.tsv
10A006:10B9182_009_FPKM


title: AF1_73

value: Sample 1B

tag: strain

value: Embryonic Thymus


title: 09A029.09B9163_002

description:
09B9163_IonXpressRNA_002
processed data file: A1AT-BAL_gradsids_added.tsv
09A029:09B9163_002_FPKM

tag: tissue


title: AF1_72


title: BIN_UQFortes_6FT_small

description: small RNA

source_name: Foetal testis, animal 6, small RNA preparation

value: fetus

value: 7 months


title: 05A017.05B9353_003RUN413

description:
05B9353_IonXpressRNA_003RUN413
processed data file: A1AT-BAL_gradsids_added.tsv
05A017:05B9353_003RUN413_FPKM

tag: subject status


title: AF1_71


title: BT474m1_H3K27Ac_300nM_lapatinib_24h

value: RPMI supplemented with 10% FBS

value: KAPA Hyper Prep

value: treated with 300nM lapatinib for 24h

value: Histone H3K27ac Active Motif 39133


title: BIN_UQFortes_5FT_small

description: small RNA

source_name: Foetal testis, animal 5, small RNA preparation

value: testis


title: WYK3338 Patient UC Sample

value: Male

tag: race

tag: smoking status

value: Never

tag: pathology stage

tag: rnaseq base47 classification

value: Luminal

tag: nanostring base47 classification

tag: overall survival status

tag: overall survival months


title: 09A033.09B9420_003

description:
09B9420_IonXpressRNA_003
processed data file: A1AT-BAL_gradsids_added.tsv
09A033:09B9420_003_FPKM

tag: genotype

value: bronchoalveolar lavage (BAL)


title: 09A028.09B9167_007

description:
09B9167_IonXpressRNA_007
processed data file: A1AT-BAL_gradsids_added.tsv
09A028:09B9167_007_FPKM


title: BIN_UQFortes_4FT_small

description: small RNA

source_name: Foetal testis, animal 4, small RNA preparation


title: AF1_70

value: 5x polychromILC mice


title: AF1_7


title: 05A015.05B9345_010

description:
05B9345_IonXpressRNA_010
processed data file: A1AT-BAL_gradsids_added.tsv
05A015:05B9345_010_FPKM

value: Alpha-1 Antitrypsin Deficiency patients


title: BIN_UQFortes_3T_small

description: small RNA

source_name: Adult testicular tissue parenchyma section, animal 3, small RNA preparation

value: parenchyma

value: adult

value: 2 years


title: BT474m1_H3K27Ac_DMSO_24h

tag: culture media

tag: library preparation kit

tag: treatment

value: treated with DMSO for 24h

tag: chip antibody


title: 04A039.04B9462_006

description:
04B9462_IonXpressRNA_006
processed data file: A1AT-BAL_gradsids_added.tsv
04A039:04B9462_006_FPKM

value: PiMZ


title: BT474m1_BRD4_300nM_lapatinib_300nM_JQ1_24h

value: treated with 300nM lapatinib and 300nM JQ1 for 24h

value: BRD4 Bethyl Laboratories A301-985A100


title: BT474m1_H3K27Ac_300nM_JQ1_24h

value: RPMI supplemented with 10% FBS

value: KAPA Hyper Prep

value: treated with 300nM JQ1 for 24h


title: BT474m1_BRD4_300nM_lapatinib_24h

value: treated with 300nM lapatinib for 24h


title: BIN_UQFortes_3FT_small

description: small RNA

source_name: Foetal testis, animal 3, small RNA preparation

value: testis

tag: developmental stage

value: fetus

tag: age

value: 7 months

tag: animal id


title: 04A024.04B9413_004

description:
04B9413_IonXpressRNA_004
processed data file: A1AT-BAL_gradsids_added.tsv
04A024:04B9413_004_FPKM

tag: tissue

value: bronchoalveolar lavage (BAL)


title: 04A025.04B9411_011

description:
04B9411_IonXpressRNA_011
processed data file: A1AT-BAL_gradsids_added.tsv
04A025:04B9411_011_FPKM

tag: subject status


title: AF1_67

tag: mouse id

value: Sample 1B

tag: strain

value: 5x polychromILC mice

value: Embryonic Thymus


title: AF1_69


title: 04A030.04B9415_006

description:
04B9415_IonXpressRNA_006
processed data file: A1AT-BAL_gradsids_added.tsv
04A030:04B9415_006_FPKM

value: Alpha-1 Antitrypsin Deficiency patients


title: BIN_UQFortes_3CT_small

description: small RNA

source_name: Adult testicular tissue caput epididymis section, animal 3, small RNA preparation

tag: tissue subsection

value: caput epididymis

value: adult

value: 2 years


title: 09A031.09B9165_007

description:
09B9165_IonXpressRNA_007
processed data file: A1AT-BAL_gradsids_added.tsv
09A031:09B9165_007_FPKM

value: PiMZ


title: BIN_UQFortes_3CD_small

description: small RNA

source_name: Adult testicular tissue cauda epididymis section, animal 3, small RNA preparation

value: cauda epididymis


title: AF1_68


title: 04A035.04B9402_009

description:
04B9402_IonXpressRNA_009
processed data file: A1AT-BAL_gradsids_added.tsv
04A035:04B9402_009_FPKM


title: SKBR3_MED1_300nM_lapatinib_300nM_JQ1_24h

description: SKBR-3-BRD4-MED1-H3K27Ac-FOXA1-Lapatinib-JQ1.xlsx

source_name: SKBR-3 HER2+ breast carcinoma cell line

value: RPMI supplemented with 10% FBS

value: treated with 300nM lapatinib and 300nM JQ1 for 24h

value: MED1/CRSP1/TRAP220 Bethyl Laboratories A300-793A100


title: AF1_66


title: BT474m1_H3K27Ac_300nM_lapatinib_300nM_JQ1_24h

description: BT474m1-BRD4-MED1-H3K27Ac-Lapatinib-JQ1.xlsx

value: KAPA Hyper Prep

value: Histone H3K27ac Active Motif 39133


title: BT474m1_BRD4_DMSO_24h

value: treated with DMSO for 24h

value: BRD4 Bethyl Laboratories A301-985A100


title: BIN_UQFortes_2T_small

description: small RNA

source_name: Adult testicular tissue parenchyma section, animal 2, small RNA preparation

value: testis

value: parenchyma


title: BT474m1_BRD4_300nM_JQ1_24h

source_name: BT474m1 HER2+ breast carcinoma cell line

value: treated with 300nM JQ1 for 24h


title: 04A004.04B9087_014

description:
04B9087_IonXpressRNA_014
processed data file: A1AT-BAL_gradsids_added.tsv
04A004:04B9087_014_FPKM

value: bronchoalveolar lavage (BAL)


title: BIN_UQFortes_2FT_small

description: small RNA

source_name: Foetal testis, animal 2, small RNA preparation

value: fetus

value: 7 months


title: BIN_UQFortes_2CT_small

description: small RNA

source_name: Adult testicular tissue caput epididymis section, animal 2, small RNA preparation

value: caput epididymis

value: adult


title: SKBR3_MED1_300nM_JQ1_24h


title: 03A043.03B9456_006

description:
03B9456_IonXpressRNA_006
processed data file: A1AT-BAL_gradsids_added.tsv
03A043:03B9456_006_FPKM

value: Alpha-1 Antitrypsin Deficiency patients

value: PiMZ


title: AF1_65

value: Sample 1B

value: 5x polychromILC mice

value: Embryonic Thymus


title: SKBR3_MED1_300nM_lapatinib_24h

value: RPMI supplemented with 10% FBS

value: KAPA Hyper Prep

value: treated with 300nM lapatinib for 24h

value: MED1/CRSP1/TRAP220 Bethyl Laboratories A300-793A100


title: 03A041.03B9449_010

description:
03B9449_IonXpressRNA_010
processed data file: A1AT-BAL_gradsids_added.tsv
03A041:03B9449_010_FPKM


title: AF1_64


title: AF1_63


title: BIN_UQFortes_2CD_small

description: small RNA

source_name: Adult testicular tissue cauda epididymis section, animal 2, small RNA preparation

value: testis

value: cauda epididymis

value: 2 years


title: SKBR3_MED1_DMSO_24h

value: treated with DMSO for 24h


title: BIN_UQFortes_26L_small

description: small RNA

source_name: liver, animal 26, small RNA preparation

value: liver


title: 03A040.03B9448_004RUN413

description:
03B9448_IonXpressRNA_004RUN413
processed data file: A1AT-BAL_gradsids_added.tsv
03A040:03B9448_004RUN413_FPKM

value: bronchoalveolar lavage (BAL)


title: 03A039.03B9446_015

description:
03B9446_IonXpressRNA_015
processed data file: A1AT-BAL_gradsids_added.tsv
03A039:03B9446_015_FPKM


title: AF1_61

source_name: Sample 1B_embryonic thymus


title: BIN_UQFortes_24L_small

description: small RNA

source_name: liver, animal 24, small RNA preparation


title: 03A038.03B9445_009

description:
03B9445_IonXpressRNA_009
processed data file: A1AT-BAL_gradsids_added.tsv
03A038:03B9445_009_FPKM


title: BIN_UQFortes_25L_small

description: small RNA

source_name: liver, animal 25, small RNA preparation


title: AF1_60


title: SKBR3_H3K27Ac_300nM_lapatinib_300nM_JQ1_24h

value: treated with 300nM lapatinib and 300nM JQ1 for 24h

value: Histone H3K27ac Active Motif 39133


title: SKBR3_H3K27Ac_300nM_lapatinib_24h


title: AF1_62


title: BIN_UQFortes_23L_small

description: small RNA

source_name: liver, animal 23, small RNA preparation

value: adult


title: AF1_6


title: SKBR3_H3K27Ac_300nM_JQ1_24h

value: treated with 300nM JQ1 for 24h


title: 03A034.03B9392_009

description:
03B9392_IonXpressRNA_009
processed data file: A1AT-BAL_gradsids_added.tsv
03A034:03B9392_009_FPKM

value: Alpha-1 Antitrypsin Deficiency patients

value: PiMZ


title: SKBR3_input_for_BRD4_H3K27Ac_and_MED1_DMSO

value: no antibody


title: AF1_59

value: Sample 1B

value: 5x polychromILC mice

value: Embryonic Thymus


title: 03A035.03B9394_008

description:
03B9394_IonXpressRNA_008
processed data file: A1AT-BAL_gradsids_added.tsv
03A035:03B9394_008_FPKM


title: SKBR3_H3K27Ac_DMSO_24h

value: RPMI supplemented with 10% FBS

value: KAPA Hyper Prep


title: 03A029.03B9390_013

description:
03B9390_IonXpressRNA_013
processed data file: A1AT-BAL_gradsids_added.tsv
03A029:03B9390_013_FPKM


title: AF1_57


title: BIN_UQFortes_13T_small

description: small RNA

source_name: Adult testicular tissue parenchyma section, animal 13, small RNA preparation

value: testis

value: parenchyma


title: SKBR3_BRD4_300nM_lapatinib_300nM_JQ1_24h

value: BRD4 Bethyl Laboratories A301-985A100


title: 03A027.03B9382_015

description:
03B9382_IonXpressRNA_015
processed data file: A1AT-BAL_gradsids_added.tsv
03A027:03B9382_015_FPKM


title: AF1_58


title: BIN_UQFortes_13CT_small

description: small RNA

source_name: Adult testicular tissue caput epididymis section, animal 13, small RNA preparation

value: caput epididymis

value: 2 years


title: 03A021.03B9333_005

description:
03B9333_IonXpressRNA_005
processed data file: A1AT-BAL_gradsids_added.tsv
03A021:03B9333_005_FPKM

value: bronchoalveolar lavage (BAL)


title: BIN_UQFortes_13CD_small

description: small RNA

source_name: Adult testicular tissue cauda epididymis section, animal 13, small RNA preparation

value: cauda epididymis


title: SKBR3_BRD4_300nM_JQ1_24h


title: BIN_UQFortes_12T_small

description: small RNA

source_name: Adult testicular tissue parenchyma section, animal 12, small RNA preparation

value: adult


title: SKBR3_BRD4_DMSO_24h

value: treated with DMSO for 24h


title: Cortex Trisomy rep2 RNA-Seq

city: Zhengzhou

first: Weili

last: Shi

state: Henan

address: 7 Weiwu Road

department: Medical Genetics Institute of Henan Province

institute: Henan Provincial People's Hospital

data_processing:
Basecalls was performed using CASAVA
Raw reads of each sample were trimmed to remove adaptor sequences and low quality bases, then were aligned to the human genome GRCh37 reference with HISAT2
The reads of RNA-seq were normalized using Cufflinks
Differential expressed genes were identified by cuffdiff with the following setting: fold change greater than 2 and adjusted p value less than 0.05
Genome_build: Human GRCh37
Supplementary_files_format_and_content: Matrix table with gene counts for every gene in two groups

source_name: Cerebral cortex

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen). Poly (A) RNA purification was performed via GenElute mRNA miniprep kit (Sigma).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Down syndrome

tag: gestational weeks

value: Cerebral cortex


title: Cortex Trisomy rep3 RNA-Seq


title: AF1_53


title: AF1_55


title: BIN_UQFortes_12CD_small

description: small RNA

source_name: Adult testicular tissue cauda epididymis section, animal 12, small RNA preparation


title: AF1_56


title: 03A016.03B9327_008

description:
03B9327_IonXpressRNA_008
processed data file: A1AT-BAL_gradsids_added.tsv
03A016:03B9327_008_FPKM

value: Alpha-1 Antitrypsin Deficiency patients

value: PiMZ


title: BIN_UQFortes_22L_small

description: small RNA

source_name: Liver, animal 22, small RNA preparation

value: liver


title: BIN_UQFortes_12CT_small

description: small RNA

source_name: Adult testicular tissue caput epididymis section, animal 12, small RNA preparation


title: RNAs from seed coat 26°C stage2 (17dap) [R26SC-17-2]

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

country: France

institute: INRAE

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
SOAPnuke: version：v1.5.2, parameters: -l 15 -q 0.5 -n 0.1, website: https://github.com/BGI-flexlab/SOAPnuke
Genome mapping against Medicago genome version 5 was performed using Salmon algorithm
Clean reads were mapped to the reference genome Medicago version 5 and quantified using Salmon algorithm to calculate gene expression level in counts
Genome_build: Medciago truncatula genome version 5 (https://medicago.toulouse.inra.fr/MtrunA17r5.0-ANR/)
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

organism: Medicago truncatula

source_name: RNAs from seed coat 26°C stage2 (17dap)

growth_protocol: Plants were grown in a culture room in trays containing a sterile  soil at 20°C/18°C, with a 16 h light photoperiod at 200 μmol photons m -²s-².

extract_protocol:
Total RNAs were extracted from the frozen grinded tissues lots using the Macherey-Nagel NucleoSpin RNA Plus kit (Macherey-Nagel, GmbH & Co. KG, Germany) following manufacturer’s instructions
Samples were sent to BGI, Hong Kong, for library preparation. Libraries were constructed following a custom protocol from samples that passed quality controls (mass > 2µg, concentration>80ng/microl, OD260/280 ~= 2.00, OD260/230 ~= 2.20, RIN>6.5, 28S/18S<1.0, baseline smooth). After mRNA enrichment, RNA was fragmented and reverse transcribed to double-strand cDNA (dscDNA) by N6 random primer. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer, splint oligo and DNA ligase, followed by sequencing on BGISEQ-500 platform, generating an average 24M reads of 50bp per sample

treatment_protocol: After flowering, control plants were grown at the same temperature condition 20°C/19°C but stressed plants were transferred to another culture room with same growing condition except temperature 26°C/14°C

tag: cultivar

value: Stage 2

tag: condition

value: stress 26°C

value: seed coat


title: RNAs from seed coat 26°C stage2 (17dap) [R26SC-17-1]


title: BIN_UQFortes_7T

description: Total (large) RNA

source_name: Adult testicular tissue parenchyma section, animal 7

value: testis


title: RNAs from seed coat 26°C stage1 (14dap) [R26SC-14-2]

source_name: RNAs from seed coat 26°C stage1 (14dap)

value: Stage 1


title: AF1_52

value: Sample 1B

value: 5x polychromILC mice

value: Embryonic Thymus


title: Cortex Control rep2 RNA-Seq

value: Diploid  control


title: AF1_51


title: BIN_UQFortes_7CT

description: Total (large) RNA

source_name: Adult testicular tissue caput epididymis section, animal 7

value: caput epididymis

value: 2 years


title: RNAs from seed coat 26°C stage1 (14dap) [R26SC-14-1]


title: SKBR3_BRD4_300nM_lapatinib_24h

source_name: SKBR-3 HER2+ breast carcinoma cell line

value: RPMI supplemented with 10% FBS

value: KAPA Hyper Prep

value: treated with 300nM lapatinib for 24h

value: BRD4 Bethyl Laboratories A301-985A100


title: Cortex Control rep1 RNA-Seq

value: Cerebral cortex


title: AF1_50

source_name: Sample 1B_embryonic thymus


title: AF1_54


title: Cortex Trisomy rep3 Input

data_processing:
Library strategy: MeRIP-Seq
Basecalls was performed using CASAVA
Raw data of each sample were trimmed by the Trimmomatic software to remove adaptor and low quality bases. Then the reads greater than 50 bp were aligned to the human genome GRCh37 reference using BWA
m6A peaks were called by MACS2 with the corresponding input sample worked as control.
The motifs enriched in m6A peaks were analyzed by HOMER.
Genome_build: Human GRCh37
Supplementary_files_format_and_content: Peak text file in two groups

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen). Polyadenylated RNA was isolated by Sigma GenElute mRNA miniprep kit. Purified mRNA was randomly fragmented via RNA fragmentation Reagents (Millipore). m6A antibody (Synaptic Systems) was incubated with Magnetic Beads A/G Blend (Millipore). Afterwards, fragmented mRNA was added to m6A antibody-beads mixture. The eluted RNA was extracted with Acid Phenol followed by standard ethanol precipitation.
The TruSeq Stranded mRNA Sample Prep Kit (Illumina) was used for library preparation both on m6A IP and input samples, and then the library was deeply sequenced on an Illumina HiSeq platform.


title: RNAs from endosperm 26°C stage 4 (28dap) [R26Eo-28-2]

value: Stage 4

value: endosperm


title: BIN_UQFortes_7CD

description: Total (large) RNA

source_name: Adult testicular tissue cauda epididymis section, animal 7

value: cauda epididymis

value: adult


title: BIN_UQFortes_6FT

description: Total (large) RNA

source_name: Foetal testis, animal 6

value: testis

value: fetus

value: 7 months


title: AF1_49

value: Sample 1B

value: 5x polychromILC mice


title: Cortex Trisomy rep1 RNA-Seq

value: Down syndrome


title: RNAs from endosperm 26°C stage 4 (28dap) [R26Eo-28-1]

value: stress 26°C


title: RNAs from endosperm 26°C stage3 (22dap) [R26Eo-22-2]

source_name: RNAs from endosperm 26°C stage3 (22dap)

value: Stage 3


title: BIN_UQFortes_4FT

description: Total (large) RNA

source_name: Foetal testis, animal 4

value: caput epididymis


title: Cortex Trisomy rep2 Input

value: Diploid  control


title: BIN_UQFortes_5FT

description: Total (large) RNA

source_name: Foetal testis, animal 5


title: Cortex Trisomy rep2 MeRIP-Seq


title: AF1_48

value: Embryonic Thymus


title: Cortex Trisomy rep3 MeRIP-Seq


title: BIN_UQFortes_3T

description: Total (large) RNA

source_name: Adult testicular tissue parenchyma section, animal 3

value: 2 years


title: AF1_47


title: RNAs from endosperm 26°C stage3 (22dap) [R26Eo-22-1]


title: RNAs from endosperm 26°C stage2 (17dap) [R26Eo-17-2]

source_name: RNAs from endosperm 26°C stage2 (17dap)

value: Stage 2


title: AF1_46


title: Cortex Trisomy rep1 Input

source_name: Cerebral cortex

value: Cerebral cortex


title: RNAs from endosperm 26°C stage2 (17dap) [R26Eo-17-1]

value: endosperm


title: BIN_UQFortes_3FT

description: Total (large) RNA

source_name: Foetal testis, animal 3


title: Cortex Trisomy rep1 MeRIP-Seq


title: BIN_UQFortes_3CT

description: Total (large) RNA

source_name: Adult testicular tissue caput epididymis section, animal 3


title: RNAs from endosperm 26°C stage1 (14dap) [R26Eo-14-2]

source_name: RNAs from endosperm 26°C stage1 (14dap)

value: Stage 1


title: Cortex Control rep2 Input


title: AF1_44


title: AF1_5


title: RNAs from endosperm 26°C stage1 (14dap) [R26Eo-14-1]


title: AF1_43


title: Cortex Control rep2 MeRIP-Seq


title: BIN_UQFortes_3CD

description: Total (large) RNA

source_name: Adult testicular tissue cauda epididymis section, animal 3

value: cauda epididymis

value: adult


title: BIN_UQFortes_2T

description: Total (large) RNA

source_name: Adult testicular tissue parenchyma section, animal 2

value: testis

value: parenchyma


title: RNAs from embryo 26°C stage 4 (28dap) [R26E-28-3]

source_name: RNAs from embryo 26°C stage 4 (28dap)

value: Stage 4

value: embryo


title: Cortex Control rep1 Input


title: AF1_42

value: Sample 1B

value: 5x polychromILC mice


title: BIN_UQFortes_2CT

description: Total (large) RNA

source_name: Adult testicular tissue caput epididymis section, animal 2


title: RNAs from embryo 26°C stage4 (28dap) [R26E-28-1]

source_name: RNAs from embryo 26°C stage4 (28dap)

value: stress 26°C


title: AF1_40

source_name: Sample 1B_embryonic thymus


title: patient 3_TGFb1+DSE, rep2

first: Viviana

last: Cremasco

state: MA

address: 250 Massachusetts Avenue

institute: Novartis Institutes for BioMedical Research

data_processing:
Sequence intensity files were generated using the Illumina Real Time Analysis
Intensity files were demultiplexed and then aligned to the transcriptome using the 10x Genomics Cellranger software package (v3.1)
bam files were generated and sorted using 10x Genomics Cellranger software
Count matrices were generated using 10x Genomics Cellranger software
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix csv files contains cell by gene matrix for all samples, cell barcodes are appended by library id, metadata.csv file contains all the related metadata including patient ID, treatment condition and library ID.

source_name: Dissociated colorectal cancer tumor

growth_protocol: Dissociated human colorectal cancer tumor samples were thawed and cultured in vitro

extract_protocol:
All cells were harvested as input for 10x Genomics Chromium Single Cell platform
Libraries were prepared according to 10x Genomics Chromium Single Cell platform

treatment_protocol: The cells were treated by isotype control or TGFb blockade (DSE or NIS) for 24hr

value: Dissociated colorectal cancer tumor

tag: timepoint

value: 24 hr

tag: individual

value: patient 3

tag: library id


title: BIN_UQFortes_2FT

description: Total (large) RNA

source_name: Foetal testis, animal 2

value: fetus

value: 7 months


title: BIN_UQFortes_2CD

description: Total (large) RNA

source_name: Adult testicular tissue cauda epididymis section, animal 2

value: 2 years


title: RNAs from embryo 26°C stage4 (28dap) [R26E-28-2]


title: AF1_4

value: Embryonic Thymus


title: BIN_UQFortes_26L

description: Total (large) RNA

source_name: liver, animal 26

value: liver


title: RNAs from embryo 26°C stage3 (22dap) [R26E-22-3]

source_name: RNAs from embryo 26°C stage3 (22dap)

value: Stage 3


title: AF1_45


title: patient 3_NIS793+TGFb1, rep2

tag: treatment


title: RNAs from embryo 26°C stage3 (22dap) [R26E-22-2]


title: BIN_UQFortes_25L

description: Total (large) RNA

source_name: liver, animal 25

value: adult


title: RNAs from embryo 26°C stage3 (22dap) [R26E-22-1]


title: patient 3_NIS793+TGFb1, rep1


title: BIN_UQFortes_24L

description: Total (large) RNA

source_name: liver, animal 24


title: RNAs from embryo 26°C stage2 (17dap) [R26E-17-3]

source_name: RNAs from embryo 26°C stage2 (17dap)

value: Stage 2


title: patient 3_IgG2+TGFb1, rep2


title: BIN_UQFortes_23L

description: Total (large) RNA

source_name: liver, animal 23


title: RNAs from embryo 26°C stage2 (17dap) [R26E-17-2]


title: AF1_41


title: Cortex Control rep1 MeRIP-Seq

source_name: Cerebral cortex

value: Diploid  control

value: Cerebral cortex


title: patient 3_TGFb1+DSE, rep1


title: RNAs from embryo 26°C stage2 (17dap) [R26E-17-1]

value: embryo


title: RNAs from embryo 26°C stage1 (14dap) [R26E-14-3]

source_name: RNAs from embryo 26°C stage1 (14dap)

value: Stage 1


title: BIN_UQFortes_13CT

description: Total (large) RNA

source_name: Adult testicular tissue caput epididymis section, animal 13

value: testis

value: caput epididymis


title: AF1_36

value: Sample 1B

value: 5x polychromILC mice


title: AF1_34


title: RNAs from embryo 26°C stage1 (14dap) [R26E-14-2]

value: stress 26°C


title: HepG2 cells, nosg+shglinc+shc-myc

city: Beijing

first: Fengyang

last: Jing

address: xueyuan road #38

institute: Peking university

description:
fpkm_lncRNA.txt
fpkm_mRNA.txt
Sample_Z_8

data_processing:
Basecalls performed using CASAVA version 1.8
Raw reads were processed using fastp version 0.20.0. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference of human mRNAs and lncRNAs using bowtie2(version 2.3.1) with parameters -k30 -t -p 20.
FPKM value and read counts of each transcript were obtained by eXpress(version 1.5.1) with parameters --no-update-check --rf-stranded.
DEGs were identified using the edgeR library . P value < 0.05 and absolute value of foldchange >=2 was set as the threshold for significantly differential expression.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: liver carcinoma cells

growth_protocol: Briefly, the culture medium containing lentivirus particles were used for infection human liver carcinoma HepG2 cells. RNA-seq analyses confirmed that the ten lncRNAs were likewise reduced by c-Myc stable knockdown in human liver carcinoma HepG2 cells.

extract_protocol:
Total RNA was extracted by Trizol.
Firstly, ribosomal RNA was removed by kits, RNA fragmentation and short RNA strands were carried out by NEBNext First Strand Synthesis Reaction Buffer under elevated temperature. Subsequently，First cDNA strand was synthesized using random hexamer primers and RNA fragments as template. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair、 add poly(A)and adapter were implemented. In order to select cDNA fragments of preferentially 300bp in length, the library fragments were purified with agarose gel electrophoresis and the UNG enzyme was used to digest second strand of cDNA. PCR was performed, aimed products were retrieved by agarose gel electrophoresis, and the library was completed.

tag: cell type

value: HepG2 cells

value: nosg+shglinc+shc-myc

tag: growth condition

value: nosg means the medium does not contain Serine and Glycine


title: HepG2 cells, nosg+shc-myc

description:
fpkm_lncRNA.txt
fpkm_mRNA.txt
Sample_Z_7

value: nosg+shc-myc


title: BIN_UQFortes_13T

description: Total (large) RNA

source_name: Adult testicular tissue parenchyma section, animal 13

value: parenchyma

tag: developmental stage

tag: age

value: 2 years


title: AF1_39

tag: tissue

value: Embryonic Thymus


title: HepG2 cells, nosg+shglinc

description:
fpkm_lncRNA.txt
fpkm_mRNA.txt
Sample_Z_6

value: nosg+shglinc


title: RNAs from embryo 26°C stage1 (14dap) [R26E-14-1]


title: BIN_UQFortes_13CD

description: Total (large) RNA

source_name: Adult testicular tissue cauda epididymis section, animal 13

value: cauda epididymis

value: adult

tag: animal id


title: HepG2 cells, nosg

description:
fpkm_lncRNA.txt
fpkm_mRNA.txt
Sample_Z_5

value: nosg


title: AF1_33

tag: mouse id


title: AF1_38

tag: strain


title: BIN_UQFortes_12T

description: Total (large) RNA

source_name: Adult testicular tissue parenchyma section, animal 12

tag: tissue subsection


title: AF1_32

source_name: Sample 1B_embryonic thymus


title: AF1_37


title: RNAs from seed coat 20°C stage2 (26dap) [R20SC-26-2]

source_name: RNAs from seed coat 20°C stage2 (26dap)

value: Stage 2

value: control 20°C

value: seed coat


title: HepG2 cells, shglinc+shc-myc

description:
fpkm_lncRNA.txt
fpkm_mRNA.txt
Sample_Z_4

value: shglinc+shc-myc

value: control medium


title: AF1_31

value: Sample 1B

value: 5x polychromILC mice


title: BIN_UQFortes_12CT

description: Total (large) RNA

source_name: Adult testicular tissue caput epididymis section, animal 12

value: testis

value: caput epididymis


title: patient 3_IgG2+TGFb1, rep1

source_name: Dissociated colorectal cancer tumor

value: Dissociated colorectal cancer tumor

value: 24 hr

value: patient 3


title: RNAs from seed coat 20°C stage2 (26dap) [R20SC-26-1]


title: BIN_UQFortes_22L

description: Total (large) RNA

source_name: Liver, animal 22

value: liver

value: 2 years


title: AF1_30

value: Embryonic Thymus


title: BIN_UQFortes_12CD

description: Total (large) RNA

source_name: Adult testicular tissue cauda epididymis section, animal 12

value: cauda epididymis

value: adult


title: HepG2 cells, shglinc

description:
fpkm_lncRNA.txt
fpkm_mRNA.txt
Sample_Z_2

value: HepG2 cells

value: shglinc


title: HepG2 cells, shc-myc

description:
fpkm_lncRNA.txt
fpkm_mRNA.txt
Sample_Z_3

value: shc-myc


title: RNAs from seed coat 20°C stage1 (17dap) [R20SC-17-2]

source_name: RNAs from seed coat 20°C stage1 (17dap)

value: Stage 1

value: control 20°C

value: seed coat


title: AF1_3

value: Sample 1B

value: 5x polychromILC mice


title: RNAs from seed coat 20°C stage1 (17dap) [R20SC-17-1]


title: C5_105dB: Cochlea_Very_Loud Rep4

city: Chicago

first: Jeffrey

last: Savas

state: Illinois

address: 303 E. Chicago Avenue, Ward 12-013

department: Neurology

institute: Northwestern University

description: Awake animals are exposed to 30 minutes of noise and RNA is collected immediately after

data_processing:
CASAVA base recognition (Base Calling)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR  mismatch =2
quantiation by FeatureCounts,v1.5.0-p3, using default paramaetrs
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cochlea

extract_protocol:
Cochlea were removed and RNA was harvested using Trizol reagent immediately after noise exposure. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 30-minute exposure to set intensity of noise

value: FVB/NCrl

value: Cochlea

value: post natal day 60


title: HepG2 cells, ctrl

description:
fpkm_lncRNA.txt
fpkm_mRNA.txt
Sample_Z_1

value: ctrl

value: control medium


title: AF1_35


title: AF1_29


title: C4_105dB: Cochlea_Very_Loud Rep3


title: C2_105dB: Cochlea_Very_Loud Rep2


title: RNAs from endosperm 20°C stage4 (44dap) [R20Eo-44-2]

source_name: RNAs from endosperm 20°C stage4 (44dap)

value: Stage 4

value: endosperm


title: AF1_28

value: Embryonic Thymus


title: RNAs from endosperm 20°C stage4 (44dap) [R20Eo-44-1]


title: AF1_27


title: RNAs from endosperm 20°C stage3 (36dap) [R20Eo-36-2]

source_name: RNAs from endosperm 20°C stage3 (36dap)

value: Stage 3


title: AF1_26


title: H18_19086_TB

city: Aachen

first: Ronghui

last: Li

address: Pauwelsstr. 19

country: Germany

institute: RWTH Aachen

data_processing:
The Cell Ranger Software (version 2.1.1) was used for processing sequencing information.
Seurat (version 2.3.4 and 3.1.0) was used to integrate the singlecell RNA-seq data.
Genome_build: hg38
Supplementary_files_format_and_content: matrix: In hdf4 format. The top level of the file contains a single HDF5 group, called matrix, and metadata stored as HDF5 attributes. Within the matrix group are datasets containing the dimensions of the matrix, the matrix entries, as well as the features and cell-barcodes associated with the matrix rows and columns, respectively.
Supplementary_files_format_and_content: Molecule Info : The cellranger pipeline outputs an HDF5 file containing per-molecule information for all molecules that contain a valid barcode and valid UMI and were assigned with high confidence to a gene or Feature Barcode. This HDF5 file contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis.
Supplementary_files_format_and_content: Summary : The cellranger pipeline outputs a summary HTML file named web_summary.html that contains summary metrics and automated secondary analysis results. Rarely, an issue may also be detected during the pipeline run leading to an alert also appearing on this page, and more information about these is provided in the troubleshooting documentation.

molecule: polyA RNA

source_name: Bone marrow

growth_protocol: We isolated non-hematopoietic cells from unprocessed human bone marrow biopsies with and without fibrosis. Biopsies were each around 3-5mm in size. Material was crushed and flushed, bone chips were additionally digested with collagenase 2.

extract_protocol: Single Cell 3′ Reagent Kits (v2) User Guide (manual part no. CG00052, Rev D). All protocols to generate scRNA-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here: https://support.10xgenomics.com/single-cell-gene-expression

treatment_protocol: Whole bone marrow cells were brought into single cell suspension and FACS sorted to isolate CD45-/CD235ab-/CD71-/CD41-/CD61- cells.

value: Human Biopsy

tag: Stage

tag: fibrosis

value: non-fibrotic

tag: details

value: Follicular Lymphoma St1; no bone marrow infiltration

tag: gender

value: male

value: 57 years old


title: H18_19892_TB

value: myelofibrosis

value: PMF; JAK2V617F+

value: 72 years old


title: RNAs from endosperm 20°C stage3 (36dap) [R20Eo-36-1]

tag: cultivar

tag: condition

value: control 20°C


title: RNAs from endosperm 20°C stage2 (26dap) [R20Eo-26-2]

source_name: RNAs from endosperm 20°C stage2 (26dap)

value: Stage 2


title: AF1_25

value: Sample 1B

value: 5x polychromILC mice


title: B3_94dB: Cochlea_Loud Rep3

value: FVB/NCrl

value: Cochlea

value: post natal day 60


title: C1_105dB: Cochlea_Very_Loud Rep1


title: AF1_24

value: Embryonic Thymus


title: ALDHpositive_GSK458_PD901_rep1

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

data_processing:
library strategy: BruSeq
Real Time Analysis (RTA3) software used for basecalling.
Adapter trimming: 151-bp paired-end raw reads were trimmed using BBDuk (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/) using the following options (bbduk.sh -Xmx2g ktrim=r mink=11 hdist=1 k=31 minlength=75 ref=/bbmap/resources/adapters.fa). Only trimmed reads 1 (R1) were used for the susbsequent mapping steps.
Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2 (2.3.3)
Reads that did not align with rRNA, mitochondrial and EBV genomes were subsequently mapped to human genome build hg38/GRCh38 using STAR (v 2.5.3a) and a STAR index created from GENCODE annotation version 27
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Uniquely mapped reads were counted in 1kb genomic bins and bin RPKM values calculated as previously described (Paulsen et. al. 2013)
Genome_build: hg38
Supplementary_files_format_and_content: The columns of the genes.bed files are: (1) chromosome; (2) start; (3) end; (4) name; (5) strand; (6) gene length  (7) read count (8) RPKM

growth_protocol: SU-DIPG XIII cells were maintained under normal culture conditions in Tumor Stem Neurobasal-A medium (Invitrogen) mixed 1:1 with DMEM F-12 (Invitrogen-11330-032) supplemented 1:100 by volume with 1M HEPES (Invitrogen), 100mm Sodium Pyruvate (Invitrogen), Non-essential Amino Acids (Invitrogen), GlutaMAX-I supplement (Invitrogen), and 100X Antibiotic-Antimycotic (Invitrogen); further supplemented with B27(-A) (Invitrogen), human-FGF (20ng/ml, Shenandoah Biotech), human-EGF (20ng/ml, Shenandoah Biotech), human PDGF-AB (20ng/ml, Shenandoah Biotech) and heparin (10ng/ml STEMCELL Technologies).

extract_protocol:
Cells were labeled with 2 mM Bromouridine (Sigma Aldrich) for 30 min, sorted, total RNA isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013 (Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response. Proc. Natl. Acad. Sci. U.S.A. 2013; 110:2240–2245)
To equal amounts of total RNA, a spike cocktail was added, consisting of a mixture of Bru-labeled and unlabeled E. coli, drosophila and synthetic RNAs. To isolate the Bromouridine incorporated RNA (Bru-RNA), total RNA was incubated at 80˚C for 10 minutes, then added to magnetic goat anti-mouse IgG Dynabeads (Invitrogen) conjugated with anti-BrdU antibodies (Becton Dickinson). The RNA and beads were incubated for 1 hour at room temperature with gentle mixing, followed by 3 washes with 0.1% BSA in PBS. The beads were resuspended in 35μl DEPC-treated water, mixed and incubated at 96˚C for 10 min to elute the Bru-RNA. The eluted Bru-RNA was quantitated and used in the preparation of cDNA libraries. Briefly, 300ng of Bru-RNA was fragmented, and rRNA eliminated by mixing with first strand buffer,random primers and FastSelect (Qiagen)and incubated at 85˚C for 10 min. The first strand cDNA was synthesized in the presence of Actinomycin D to result in strand specific libraries and was purified using AMPure RNAclean beads (Beckman Coulter). The second strand cDNA was synthesized, then purified using AMPure XP beads (Beckman Coulter). Subsequently, end repair, adenylation, and adaptor ligation was performed, followed by a size selection. For this, the cDNA was run on a 3% NuSieve 3:1 agarose gel (Lonza) and gel slices excised in the 500bp region. The gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then PCR amplified using dual index primers. Resulting libraries were purified with AmPure XP beads, quantitated and submitted to the University of Michigan Advanced Genomics core for sequencing.

treatment_protocol: SU-DIPG XIII cells were treated with 100 nM of PD0325901 (PD-901), 100 nM of GSK2126458 (GSK-458), 50 nM PD-901 + 50 nM GSK-458 (combination) or equimolar DMSO for a total of 2 hours prior to ALDEFLUOR staining procedure. The first 1.5 hours were treatment only followed by 30 minutes of treatment plus 2 mM Bromouridine.

tag: cell line

value: SU-DIPG-XIII

tag: bru labeling time

value: 0.5 hours

tag: assay

value: bruseq

tag: time between end of bru labeling and rna extraction

value: 0 hours

tag: labeling agent

value: Bromouridine (Bru)

tag: sorted cell fraction

value: ALDHpositive

tag: molecule subtype

value: bru-labeled RNA


title: ALDHnegative_GSK458_PD901_rep1

tag: treatment

value: ALDHnegative


title: B4_94dB: Cochlea_Loud Rep4

tag: tissue

tag: age


title: B2_94dB: Cochlea_Loud Rep2

tag: strain


title: RNAs from endosperm 20°C stage2 (26dap) [R20Eo-26-1]

tag: developmental stage

value: endosperm


title: B1_94dB: Cochlea_Loud Rep1


title: RNAs from endosperm 20°C stage1 (17dap) [R20Eo-17-2]

source_name: RNAs from endosperm 20°C stage1 (17dap)

value: Stage 1

value: control 20°C


title: AF1_22

tag: mouse id

value: Sample 1B


title: A4_70dB: Cochlea_Ambient Rep4


title: AF1_23

value: 5x polychromILC mice


title: ALDHnegative_PD901_rep1


title: ALDHpositive_PD901_rep1


title: H18_20186_TB

value: Human Biopsy

tag: Stage

tag: fibrosis

value: non-fibrotic

tag: details

value: CNS Lymphoma; no bone marrow infiltration

value: female

value: 77 years old


title: AF1_21

value: Embryonic Thymus


title: A3_70dB: Cochlea_Ambient Rep3

value: FVB/NCrl

value: Cochlea

value: post natal day 60


title: RNAs from embryo 20°C stage4 (44dap) [R20E-44-3]

source_name: RNAs from embryo 20°C stage4 (44dap)

tag: cultivar

value: Stage 4

tag: condition

value: embryo


title: ALDHpositive_GSK458_rep1

tag: cell line

value: SU-DIPG-XIII

tag: bru labeling time

value: 0.5 hours

value: bruseq

value: 0 hours

value: Bromouridine (Bru)

value: ALDHpositive

value: bru-labeled RNA


title: A2_70dB: Cochlea_Ambient Rep2


title: AF1_20

value: Sample 1B

value: 5x polychromILC mice


title: AF1_2


title: RNAs from embryo 20°C stage4 (44dap) [R20E-44-2]

value: control 20°C


title: ALDHnegative_DMSO_rep1

value: DMSO

tag: assay

tag: time between end of bru labeling and rna extraction

value: ALDHnegative


title: A1_70dB: Cochlea_Ambient Rep1

value: FVB/NCrl


title: ALDHpositive_DMSO_rep1

tag: labeling agent

tag: sorted cell fraction


title: AF1_19

value: Embryonic Thymus


title: Gli

data_processing:
The Cell Ranger Software (version 2.1.1) was used for processing sequencing information.
Seurat (version 2.3.4 and 3.1.0) was used to integrate the singlecell RNA-seq data.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz - cell level barcodes seen in this sample
Supplementary_files_format_and_content: features.tsv.gz - list of quantitated features
Supplementary_files_format_and_content: matrix.mtx.gz - (sparse) matrix of counts for cells and features

source_name: Gli1+tdTom+ cells

growth_protocol: 6-7 week old Gli1CreERt2;Rosa26tdTomato-mice were injected intraperitoneally with 3x10 mg tamoxifen in corn oil / 3% ethanol (Sigma). Mice were sacrificed 2 weeks after the last injection of tamoxifen.

treatment_protocol: Compact bones were crushed and flushed and subjected to red blood cell lysis to obtain the bone marrow fraction. Bone chips were digested with Liberase. Viable Gli1-tdTom+ cells were sorted (Aria II) into DMEM/10% FCS and used for droplet based scRNAseq.

value: bone marrow

tag: cell type

value: Gli1+tdTom+ cells

value: Homeostasis


title: RNAs from embryo 20°C stage3 (36dap) [R20E-36-2]

source_name: RNAs from embryo 20°C stage3 (36dap)

value: Stage 3

tag: tissue

value: embryo


title: RNAs from embryo 20°C stage3 (36dap) [R20E-36-3]


title: WT_JAKV617V_27_2

data_processing:
The Cell Ranger Software (version 2.1.1) was used for processing sequencing information.
Seurat (version 2.3.4 and 3.1.0) was used to integrate the singlecell RNA-seq data.
Genome_build: mm10
Supplementary_files_format_and_content: matrix: In hdf4 format. The top level of the file contains a single HDF5 group, called matrix, and metadata stored as HDF5 attributes. Within the matrix group are datasets containing the dimensions of the matrix, the matrix entries, as well as the features and cell-barcodes associated with the matrix rows and columns, respectively.
Supplementary_files_format_and_content: Molecule Info : The cellranger pipeline outputs an HDF5 file containing per-molecule information for all molecules that contain a valid barcode and valid UMI and were assigned with high confidence to a gene or Feature Barcode. This HDF5 file contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis.
Supplementary_files_format_and_content: Summary : The cellranger pipeline outputs a summary HTML file named web_summary.html that contains summary metrics and automated secondary analysis results. Rarely, an issue may also be detected during the pipeline run leading to an alert also appearing on this page, and more information about these is provided in the troubleshooting documentation.

source_name: bone marrow

growth_protocol: Recipient mice received 4-5x105 cells from 8-week-old WT littermates that had been harvested 48 hours prior to transplantation and transduced with ThPO (GFP+) lentivirus or control empty vector lentivirus (Empty vector-GFP+). For JAK2V617F studies, WT BM cells were transduced with JAK2(V617F) (JAK2) retrovirus or control pMIG retrovirus (control: JAK2 empty vector) and transplanted into 10.5 Gy-irradiated 8-10-week-old female B6.SJL recipients. Mice were randomly assigned to transplant groups. Mice from the early ThPO cohort were sacrificed 5 weeks post-transplant, whilst mice in the late ThPO cohort were sacrificed 10 weeks posttransplant. Mice used in the JAK2 experiment were sacrificed at 28 weeks post-BM transplant, when hemoglobin levels decreased, owing to the varying phenotypic severity of JAK2V617F.

extract_protocol:
All protocols to generate scRNA-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here:https://support.10xgenomics.com/single-cell-gene-expression
Single Cell 3' v2

treatment_protocol: Whole bone marrow was MACS-depleted for CD11b, GR1, NK1.1, TER119, CD4, CD8, B220, CD45, CD71 and CD4 and subsequently FACS-sorted for lineage-, CD45-, CD71-, Ter119- and CD41- negativity.

value: bone marrow stromal cells

value: JAK2 Fibrosis

tag: transduction

value: JAK2(V617F) retrovirus


title: AF1_18

data_processing:
Reads aligned to a modified mouse genome (addition of the reporters found in the mouse) using the Salmon pseudoaligner (v0.8.2)
Pseudocounts analysis with the scater library (v1.6.3) (McCarthy et al., 2017), scran library (v1.6.9) (Lun et al., 2016), and sva library (sva: Surrogate Variable Analysis. R package v3.26.0).
Cells with pseudocounts below 3 median-absolute-deviations away from the median were removed. Genes with an average count across all remaining cells of less than 1 were removed.
Size factors were calculated with the scran library (based on the gene counts) and the data normalised by them.
Batch effects were removed using the ComBat empirical Bayes framework from the sva library
Genome_build: GRCm38.68
Supplementary_files_format_and_content: RDS of R SCE object containing metadata and gene expression generated using R,scater,scran and sva; tab-separated normalised gene expression from the SCE object

source_name: Sample 1B_embryonic thymus

tag: strain


title: RNAs from endosperm 20°C stage1 (17dap) [R20Eo-17-1]

tag: developmental stage

value: Stage 1

value: endosperm


title: ALDHnegative_GSK458_rep1

value: SU-DIPG-XIII

tag: treatment

value: 0.5 hours

value: bruseq

value: 0 hours

value: Bromouridine (Bru)

tag: molecule subtype

value: bru-labeled RNA


title: AF1_16

tag: mouse id

value: Sample 1B

value: 5x polychromILC mice

value: Embryonic Thymus


title: RNAs from embryo 20°C stage2 (26dap) [R20E-26-3]

source_name: RNAs from embryo 20°C stage2 (26dap)

value: Stage 2

value: control 20°C


title: RNAs from embryo 20°C stage3 (36dap) [R20E-36-1]

value: Stage 3

value: embryo


title: AF1_15


title: WT_EV_31_2

value: bone marrow stromal cells

value: bone marrow

tag: Stage

value: JAK2 Fibrosis

value: empty vector


title: AF1_14


title: WT_EV_28_2


title: ThPO_late2

value: ThPO Fibrosis

value: ThPO (GFP+) lentivirus


title: RNAs from embryo 20°C stage2 (26dap) [R20E-26-2]

tag: cultivar


title: AF1_13


title: RNAs from embryo 20°C stage4 (44dap) [R20E-44-1]

value: Stage 4

tag: condition


title: ThPO_late1


title: RNAs from embryo 20°C stage2 (26dap) [R20E-26-1]


title: AF1_12


title: RNAs from embryo 20°C stage1 (17dap) [R20E-17-3]

source_name: RNAs from embryo 20°C stage1 (17dap)

value: Stage 1


title: AF1_11


title: RNAs from embryo 20°C stage1 (17dap) [R20E-17-1]


title: WT_JAKV617V_27_1

value: JAK2(V617F) retrovirus


title: ThPO_early1

value: ThPO Prefibrosis


title: AF1_17

value: Sample 1B


title: RNAs from embryo 20°C stage1 (17dap) [R20E-17-2]


title: AF1_10

value: 5x polychromILC mice


title: ThPO_early2


title: EV_late2


title: Gout patient peripheral blood mononuclear cells_intercritical gout_rep1

type: RNA

city: Nanchong City

first: daifei

last: dai

state: Sichuan Province

address: No. 234, Fujiang Road, Shunqing District

institute: North Sichuan Medical College

description: Patients with gout were in the asymptomatic period after or between gout flares

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed and  fixed.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: Gout patient  peripheral blood mononuclear cells,intercritical gout,replicate 1

label_protocol: MRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA purification was prepared using TRIzol reagent (Invitrogen, Gran Island, NY, USA) according to the manufacturer’s instructions followed by the application of PBMCs to RNeasy spin columns (Qiagen, Venlo, Limburg, Netherlands). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis or Agilent 2100 Bioanalyzer.

treatment_protocol: Peripheral blood anticoagulated with ethelene diamine tetraccetic (EDTA) was obtained from all subjects. Human peripheral blood mononuclear cells (PBMCs) were isolated with Ficoll-Hypaque gradients.

value: peripheral blood mononuclear cells

tag: gender

value: male

tag: age


title: Gout patient peripheral blood mononuclear cells_acute gout_rep1

description: Patients with gout had evident episode of acute inflammation

source_name: Gout patient  peripheral blood mononuclear cells,acute gout,replicate 1


title: Input

city: Linkoping

first: Srivathsa

last: Magadi

address: Campus US, Building 463 Cellbiologen, Entrance 64

department: Department of Biomedical and Clinical Sciences (BKV) Division of Molecular Medicine and Virology (MMV)

country: Sweden

institute: Linkoping University

description: Input chromatin

data_processing:
Fastq reads were mapped to UCSC/dm3 genome (archive-2015-07-17-14-30-40) downloaded from iGenomes using bowtie2 version 2.2.8
Bedgraphs of mapped reads were generated by bedtools genomecov (v2.25.0)
Reads that overlapped with dm3 repeat elements (downloaded from UCSC,) were removed from bam files prior to peak calling using bamtools intersect
Peak calling was performed with macs2 over input (-p 0.05, version 2.1.0.20140616)
Genome wide peak distribution was performed with the pavis tool
Genome_build: dm3
Supplementary_files_format_and_content: Bed file containing overlapping peaks from replicates over input

organism: Drosophila melanogaster

source_name: 3rd instar larval CNS

growth_protocol: Expanded population of NSC like cells were obtained by overexpressing UAS-dpn,UAS-mγ using neural stem cell specific grhGal4 and maintained at 25°C.

extract_protocol:
Chromatin lysate was crosslinked with 1%FA and quenched with Glycine, chromatin was fragmented using bioruptor and immunoprecipitated chromatin was purified using Qiagen PCR purification kit.
Libraries were prepared according to Ion Torrent instructions

treatment_protocol: CNSs from 3rd instar wandering larvae were dissected in ice cold PBS

value: larval brains with neural stem cell hyperplasia

tag: chip antibody

value: Homemade Deapan antibody

tag: genotype

value: grhGal4;UAS-dpn, UAS-m<gamma>


title: AF1_1

extract_protocol:
Individual cells were flow cytometrically purified on a 96 well format into 0.2% Triton X-100 containing RNase inhibitor, dNTPs and oligo-dT primers and stored at -80oC.
On thawing, lysates were heated to 72 oC for 3 minutes and subject to reverse transcription, PCR preamplification (26 cycles) and PCR purification.  cDNA library quality was assessed for all samples by qualitative PCR using primers for 18s RNA with an additional check by Bioanalyzer using an Agilent high sensitivity DNA chip on a small subset of libraries. A subset of libraries was quantified using the Qubit dsDNA HS assay kit and an average value used to calculate library dilution to 100-150 pg/ml. cDNA library tagmentation and amplification was performed using the Illumina Nextera XT DNA Library Preparation Kit according to manufacturer’s instructions except that all volumes were reduced 4-fold and tagmentation performed at 55oC for 20 minutes. Nextera index and Illumina adapter sequences were incorporated at the amplification stage (N7xx and S5xx). Amplified and indexed libraries were pooled and purified using Agencourt AMPure XP beads at a ratio of 1:0.9 library to beads and washed with 70% ethanol. Two rounds of purification were performed before a final elution in 1.25x total library volume of Nextera Resuspension buffer

value: Embryonic Thymus


title: EV_late1

value: bone marrow stromal cells

value: bone marrow


title: Dpn_ChIP_rep2

description:
Genome-wide Deadpan binding replicate 2
BED file with intersection of replicate 1 and replicate 2


title: Healthy control subject peripheral blood mononuclear cells_rep6

description: Healthy controls had no evidence of disease

source_name: Healthy control subject peripheral blood mononuclear cells,replicate 6


title: Gout patient peripheral blood mononuclear cells_intercritical gout_rep3

source_name: Gout patient  peripheral blood mononuclear cells,intercritical gout,replicate 3


title: Gout patient peripheral blood mononuclear cells_acute gout_rep3

source_name: Gout patient  peripheral blood mononuclear cells,acute gout,replicate 3


title: Gout patient peripheral blood mononuclear cells_intercritical gout_rep2

source_name: Gout patient peripheral blood mononuclear cells,intercritical gout,replicate 2


title: Gout patient peripheral blood mononuclear cells_acute gout_rep2

source_name: Gout patient  peripheral blood mononuclear cells,acute gout,replicate 2


title: Healthy control subject peripheral blood mononuclear cells_rep5

source_name: Healthy control subject peripheral blood mononuclear cells,replicate 5


title: EV_early2

value: empty vector


title: Murine TM, fibrous/mucosal

city: San Francisco

first: Aaron

last: Tward

address: 505 Parnassus AVE

institute: UCSF

description: Mice were maintained under approval from the Institutional Animal Care and Use Committee at the University of California, San Francisco. Prior to single cell capture, 38 murine TMs were pooled and incubated in dispase, which allowed the epidermis to be separated from the underlying tissue. The epidermis was dissociated into sungle cells using trypLE, and the fibrous/mucosal fraction was dissociated using collagenase P and DNAse.

data_processing:
10X Genomics Cell Ranger pipeline
See their website for their proprietary steps
the output matrix files are here and are included for postprocessing for R analysis
The web summaries for the experiments are attached as a guide to how the sequencing results turned out.
Genome_build: mm10 for mouse, and hg19 for human

source_name: tympanic membrane

growth_protocol: See tissue dissociation protocol in SAMPLES section

extract_protocol:
Cells were resuspended at 1,000 cells/μL in 0.04% BSA in PBS and loaded onto the Chromium Controller from 10x Genomics for single cell capture.
cDNA library for RNA-seq

value: FVB/NJ wild type

value: tympanic membrane


title: Murine TM, epidermis


title: EV_early1


title: S3 nascent RNA replicate 3

status: Public on Nov 02 2020

city: Oxford

first: Robert

middle: A

last: Beagrie

address: Headley Way

department: Molecular Haematology Unit

institute: MRC Weatherall Institute of Molecular Medicine

data_processing:
Psuedo-aligned with Kallisto 0.43.0 to Ensembl transcriptome reference GRCm38.93 (command: "kallisto quant -i /path/to/index -o /path/to/output /path/to/fastq")
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene by sample counts matrix (comma separated values)

source_name: Primary mouse erythroblasts (Lin-; CD71 high; Ter119 high)

growth_protocol: Fetal livers were freshly isolated at e12.5-e13.5 from C57BL/6 mouse embryos. Primary erythroid progenitors were purified by FACS sorting lineage-negative cells based on their expression of CD71 and Ter119 as previously described (Oudelaar, Beagrie et al. Nat. Comms 2020). FACS-purified cells were rested for six-hours post-sort in erythroid media (IMDM supplemented with 20% FCS and 0.001% β-mercaptoethanol).

extract_protocol:
Cells were  pelleted by centrifugation at 200G for 5 minutes and washed in PBS. The cell pellet was lysed in tri-reagent, and snap frozen on dry ice/ethanol. Total RNA was extracted from tri-reagent using a Direct-zol RNA kit (Zymo). 4sU labelled RNA was purified as previously described (Duffy et al. PMID 27925666). Briefly, 20-100µg of labelled total RNA was added to 50µl MTSEA-biotin-XX (0.1mg/ml in dimethylformamide) and 25μl of 10x Biotinylation buffer (100mM Tris pH 7.4 10mM EDTA) in a 250μl reaction and rotated for 30 minutes at room temperature. 400µl chloroform/isoamylalcohol (24:1) was added to the reaction and incubated for 3m. The aqueous phase was isolated using phase-lock gel tubes and purified by isopropanol precipitation. The RNA pellet was resuspended in 60µl RNase free water, denatured at 65°C for 10 min and cooled on ice for 5 min. RNA was incubated with 60µl µMacs streptavidin magnetic beads (Miltenyi) for 15 minutes at room temperature with rotation, applied to a MACS column in a magnetic stand and washed with 1ml MACS wash buffer (100mM Tris pH 7.5, 10mm EDTA, 1M NaCl, 0.1% Tween20) two times at 65°C and two times at room temperature. RNA was eluted from the column by applying 100 μL of freshly prepared 100 mM dithiothreitol (DTT), followed by a second elution round 5 min later, then purified using a Qiagen RNeasy RNA clean-up kit with on-column DNase digestion, eluting in 20μl of DEPC water.
Libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio) following the manufacturer’s instructions with a fragmentation time of 3 minutes and 14 cycles of PCR amplification.

treatment_protocol: 500μM 4‐thiouridine (4sU) was added to liquid cultures for 45 minutes

value: fetal liver

value: primary erythroblasts

tag: cell markers

value: Lin-; CD71 high; Ter119 high

tag: rna population

value: nascent RNA


title: Lin nascent RNA replicate 3

source_name: Primary mouse erythroblasts (Lin+)

tag: cell type

value: Lin+


title: Healthy control subject peripheral blood mononuclear cells_rep4

source_name: Healthy control subject peripheral blood mononuclear cells,replicate 4

tag: tissue


title: Healthy control subject peripheral blood mononuclear cells_rep3

source_name: Healthy control subject peripheral blood mononuclear cells,replicate 3


title: Healthy control subject peripheral blood mononuclear cells_rep1

source_name: Healthy control subject peripheral blood mononuclear cells,replicate 1


title: S1 nascent RNA replicate 3

source_name: Primary mouse erythroblasts (Lin-; CD71 high; Ter119-)

value: Lin-; CD71 high; Ter119-


title: Dpn_ChIP_rep1

description:
Genome-wide Deadpan binding replicate 1
BED file with intersection of replicate 1 and replicate 2


title: S0_CD71_medium nascent RNA replicate 3

source_name: Primary mouse erythroblasts (Lin-; CD71 medium; Ter119-)

value: Lin-; CD71 medium; Ter119-


title: S3 nascent RNA replicate 2


title: Lin nascent RNA replicate 2


title: S1 nascent RNA replicate 2


title: S0_CD71_medium nascent RNA replicate 2


title: S2 nascent RNA replicate 2

source_name: Primary mouse erythroblasts (Lin-; CD71 high; Ter119 medium)

value: Lin-; CD71 high; Ter119 medium


title: S0_CD71_low nascent RNA replicate 2

source_name: Primary mouse erythroblasts (Lin-; CD71-; Ter119-)


title: Lin nascent RNA replicate 1


title: S2 nascent RNA replicate 3


title: S3 nascent RNA replicate 1


title: Healthy control subject peripheral blood mononuclear cells_rep2

source_name: Healthy control subject peripheral blood mononuclear cells,replicate 2

value: peripheral blood mononuclear cells

value: male


title: S0_CD71_low nascent RNA replicate 3


title: Sorted T cells 34_LDC_(Clariom_S_Human)

city: Essen

first: Rene

last: Scholtysik

address: Virchowstrasse 173

department: IFZ

institute: University Hospital Essen

description:
Sorted T cells
RNA expression profiling

hyb_protocol: Hybridization was performed according to the manufactorers' recommendations (Clariom S, Affymetrix, Santa Clara, CA, USA).

scan_protocol: Scanning was performed according to the manufactorers' recommendations (Clariom S, Affymetrix, Santa Clara, CA, USA).

data_processing: Robust multi-array analysis of background-adjusted, normalized and log-transformed probe-set values were conducted. Threshold settings for significantly regulated genes were ≥ 2- fold difference from DMSO-treated control cells, with p < 0.05.

label: biotin

source_name: Sorted T-PLL cells

label_protocol: One μg of total RNA including miRNA from each sample was labeled with biotin using the FlashTag Biotin HSR Kit (Genisphere, Hatfield, PA).

growth_protocol: FACS sorted T-PLL cells were cultured in serum containing medium (RPMI 1640, 10 % fetal calf serum) for 90 min in the presence (10 µM) or absence (DMSO control) of LDC526.

extract_protocol: Total RNA was extracted with the miRNeasy Mini kit (Qiagen) according to the manufacturer’s instructions.

value: m


title: Sorted T cells 3_DMSO_(Clariom_S_Human)

description:
Sorted T cells
RNA expression profiling


title: Sorted T cells 3_LDC_(Clariom_S_Human)

description:
Sorted T cells
RNA expression profiling


title: S11_MM1S_BioRep3_Pd

city: Salamanca

first: Teresa

last: Paíno Gómez

state: Salamanca

address: Campus Miguel de Unamuno

country: Spain

institute: Centro de Investigación del Cáncer

hyb_protocol: Hybridization was performed on the Affymetrix Clariom S Human array as per the manufacturers protocol.

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing:
Raw data were quantile normalized, background corrected and log2 transformed with the Robust Multi-array Average (RMA) algorithm using the oligo package (v.1.44.0) in R (v.3.5.0).  BrainArray custom CDF files (version 22 Ensembl) at  gene level were used as reference.
ClariomSHuman_Hs_ENSG.cdf

source_name: MM.1S multiple myeloma cell line

label_protocol: As per manufacturer's instructions (Affymetrix)

growth_protocol: MM.1S cells were cultured in RPMI-1640 medium +  10% inactivated FBS.

extract_protocol: RNA and DNA were extracted using AllPrep DNA/RNA Mini Kit (Qiagen). RNA integrity was assessed using Agilent 2100 Bioanalyzer.

treatment_protocol: MM.1S cells were sub-lethally treated (% viability: 74-81%) with:  PIM (PIM447 100 nM, for 24 hours), Pd (pomalidomide 200 nM + dexamethasone 5 nM, for 15 hours) or PIM-Pd (PIM447 100 nM + pomalidomide 200 nM + dexamethasone 5 nM, for 10 hours). Untreated MM.1S cells were used as control.

value: Pomalidomide + Dexamethasone

tag: biological replicate (pairs)


title: S2 nascent RNA replicate 1

tag: strain


title: S8_MM1S_BioRep2_PIM-Pd

value: PIM447 + Pomalidomide + Dexamethasone


title: S0_CD71_medium nascent RNA replicate 1

tag: developmental stage


title: Sorted T cells 10_LDC_(Clariom_S_Human)

description:
Sorted T cells
RNA expression profiling


title: Sorted T cells 34_DMSO_(Clariom_S_Human)

description:
Sorted T cells
RNA expression profiling


title: Sorted T cells 10_DMSO_(Clariom_S_Human)

description:
Sorted T cells
RNA expression profiling