title: F27


title: F26

status: Public on Jul 11 2020

type: SRA

city: Chicago

first: Rhonda

middle: D

last: Kineman

state: Illinois

address: 1819 West Polk St

department: Medicine

country: USA

institute: University of Illinois at Chicago

description:
Kd_FvsC_F_DEG.txt
Kd_I_FvsKd_F_DEG.txt
Kd_FvsKd_M_DEG.txt

library_source: transcriptomic

data_processing:
Illumina CASAVA used for base recognition (Base Calling)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mouse reference genome sequence (GRCm38/mm10) using STAR v2.5
HTSeq v0.6.1 to count the read numbers mapped of each gene and then, FPKM (Reads Per Kilobase of exon model per Million mapped reads) of each gene was calculated based on the length of the gene and reads mapped to the gene (Mortazavi et al., 2008).
Differential expression analysis between groups was done using the DESeq2 R package (2_1.6.3) (Anders and Huber, 2010). The resulting p-values were adjusted using the Benajamini and Hochberg´s method to control the False Discovery Rate (FDR). Genes with an adjusted p-value <0.05 were considered as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: All processed data files are a matrix table with the information of all genes in rows.  Column A: gene ID. Column B-G: normalized readcounts of group A of samples (e.g. Kd_M samples). Column H-M: normalized readcounts of group B of samples (e.g. C_M samples). Column N: log2FoldChange: the result performed by DESeq2 R/EdgeR R package. Column O: pvalue. Column P: padj, corrected pvalue. Column Q: gene name. Column R: name of chromosome in which the gene is located. Column S: Strand, the chain information of the gene. Column T: the start position of the gene at the chromosome. Column U: the end position of the gene at the chromosome. Column V: gene length. Column W: gene type. Column X:  gene function description. Column Y-AJ: readcounts of all samples. Column AK-AV:  fpkm of all samples.

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol: All Ghrfl/fl mice were housed in a specific pathogen-free barrier facility maintained at 22-24C with a 12h light/12h dark cycle and were fed standard chow diet.

extract_protocol:
Livers were weighed and snap-frozen in liquid nitrogen and stored at -80C.  Total RNA from male and female livers (6 mice/sex), from GHR-intact controls, aHepGHRkd and aHepGHRkd+2.0*1011 AAV8-TBGp-rIGF1 mice were extracted using Rneasy Plus Mini Kit (Cat# 74134; Qiagen). Total RNA was quality checked (RIN>7) using the Agilent Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq (RNA libraries and analysis performed by Novogene (https://en.novogene.com/).

treatment_protocol: aHepGHRkd were generated by treating 10-12 week-old male and female Ghrfl/fl littermates with a single lateral tail vein injection of 1.5*1011 genome copies (GC) of an adeno-associated virus serotype 8 (AAV8) vector bearing a hepatocyte-specific thyroxine-binding globulin promoter (TBGp) driving a Cre recombinase transgene [AAV8-TBGp-Cre; Cat # 107787-AAV8, AAV.TBG.PI.Cre.rBG (AAV8), Addgene, Watertown, MA, diluted in 100ul sterile PBS)]. To reconstitute hepatocyte IGF1 expression in aHepGHRkd, a  subset of mice were co-injected with AAV8-TBGp-Cre (1.5*1011 GC) + AAV8-TBGp-rIGF1 (2.0*1011 or 1.0*1011 GC AAV8.TBG.PI.ratIGF1.WPRE.bGH).  Injection of an AAV8-TBGp-Null (Cat # 105536-AAV8, pAAV8.TBG.PI.Null.bGH, Addgene) was used to generate control mice and to equalize the total amount of AAV8 injected in each mouse (3.5*1011 GC).

tag: strain

tag: Sex

value: Female

tag: cell type

value: Hepatocyte

tag: genotype

value: aHepGHRkd (Kd)

tag: age of aav-injection

value: 10-12 weeks-old

tag: experiment duration

value: 8 months after AAV-injection

tag: diet

value: Chow diet (Teklad LM-485)


title: F25

description:
Kd_FvsC_F_DEG.txt
Kd_I_FvsC_F_DEG.txt
C_FvsC_M_DEG.txt

value: Control (C )


title: F21


title: F23


title: F24


title: F22

description:
Kd_I_FvsC_F_DEG.txt
Kd_I_FvsKd_F_DEG.txt
Kd_I_FvsKd_I_M_DEG.txt

value: aHepGHRkd + rIGF1 2.0 (Kd_I)


title: F36


title: M18

description:
Kd_MvsC_M_DEG.txt
Kd_I_MvsKd_M_DEG.txt
Kd_FvsKd_M_DEG.txt

value: Male


title: M17

description:
Kd_MvsC_M_DEG.txt
Kd_I_MvsC_M_DEG.txt
C_FvsC_M_DEG.txt


title: M16

description:
Kd_I_MvsC_M_DEG.txt
Kd_I_MvsKd_M_DEG.txt
Kd_I_FvsKd_I_M_DEG.txt


title: M15


title: M13


title: F29


title: M14


title: M12


title: M11


title: M10


title: M9


title: M5


title: M8


title: F20


title: M3


title: M4


title: F19


title: SC_SMA_ko_p10_M250_LCM225

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

description:
LCM225
rpkms_SMA_LCMseq.txt

data_processing:
RNAseq reads were mapped simultaneously to the mm10 mouse genome assembly and the genomic sequence of human SMN2 (including introns) from the hg19 assembly using STAR (version 2.4.1c)
Expression levels were determined using the rpkmforgenes.py software (available at http://sandberg.cmb.ki.se/rnaseq).
Genome_build: mm10 + human SMN2 sequence (hg19 assembly)
Supplementary_files_format_and_content: text file with RPKM

molecule: polyA RNA

source_name: Lumbar spinal cord motor neurons

extract_protocol:
Brains and spinal cords were quickly dissected and snap frozen in 2-Methylbutane on dry ice. Tissues were sectioned in a cryostat and mounted onto PEN membrane glass slides (Zeiss). Quick staining with Histogene (Arcturus/LifeTechnologies) followed by dehydration in rising EtOH concentrations was performed immediately prior to LCM. Individual cells were isolated using a Leica LMD7000 system. Approximately 150 cells were collected into one tube and lysis buffer was added (0.2% triton-X 100 with 2U/ul RNase inhibitor, Clontech) before snap freezing the samples on dry ice. (Nichterwitz et al. 2016)
Smart-seq2 combined with Tn5 tagmentation

tag: tissue

value: Lumbar spinal cord motor neurons

value: SMA

tag: age (days)

tag: group

tag: mouse id


title: SC_SMA_ko_p10_M258_LCM259

description:
LCM259
rpkms_SMA_LCMseq.txt


title: SC_SMA_ko_p10_M249_LCM224

description:
LCM224
rpkms_SMA_LCMseq.txt


title: M2


title: M1


title: SC_SMA_ko_p5_M77_LCM122

description:
LCM122
rpkms_SMA_LCMseq.txt


title: SC_SMA_wt_p10_M253_LCM246

description:
LCM246
rpkms_SMA_LCMseq.txt

value: control


title: SC_SMA_wt_p10_M247_LCM223

description:
LCM223
rpkms_SMA_LCMseq.txt


title: SC_SMA_wt_p10_M252_LCM240

description:
LCM240
rpkms_SMA_LCMseq.txt


title: SC_SMA_wt_p10_M254_LCM258

description:
LCM258
rpkms_SMA_LCMseq.txt


title: Treatment with Enterococcus EME343 rep 3

status: Public on Jul 12 2020

type: RNA

city: Jout-en-Josas

first: Elliot

last: Mathieu

address: Domaine de Vilvert

department: MICALIS

country: France

institute: INRAE

description: 6 hours incubation of BEAS-2B cells with Streptococcus EMS321 for the treatment/ 6 hours incubation BEAS-2B cells non treated for the control

hyb_protocol: Cy3 and Cy5 labelled cDNA were mixed and hybridized at 50oC for 18h on the Agilent Whole Human 4x44K microarrays (Agilent Technologies Inc., Ref#G2519F)

scan_protocol: Each array was scanned at 10µm with a ScanArray 5000 instrument (Perkin Elmer, Waltham, MA) and acquired images were quantified with QuantArray software (Perkin Elmer).

data_processing: The signal intensity of all spots was quantified and normalized (Global LOWESS) using ImaGene version 9.0 (BioDiscovery). Statistical analysis was done with MultiExperiment Viewer (MeV) version 4.8 (TM4 microarray software suite, J. Craig Venter Institute).

organism: Homo sapiens

source_name: Control rep 3

label_protocol: Poly A mRNA were reverse transcribed from 10 µg of total RNA with SuperScript III (Invitrogen) and labelled with either Cy3 or Cy5 (GE Healthcare Life Sciences) before cDNA purification with PCR Purification Kit (Qiagen).

extract_protocol: Total RNA was extracted by TRIzol Reagent (Invitrogen, Ref #15596-026) following manufacturer's protocol and with PhaseLock tubes (Quantabio, Ref #2302830) for nucleic acids separation. Purification was achieved with RNeasy (QIAGEN, RNeasy mini kit, Ref #74104). Quality was assessed by Bioanalyzer (Agilent Technologies). RIN over 8.0 were considered good quality RNA for reverse transcription.

treatment_protocol: BEAS-2B cells were incubated for 6 hours with one of the 7 following bacterial strains: Streptococcus EMS321, Streptococcus EMS383, Streptococcus EMS3101, Enterococcus EME126, Enterococcus EME141, Enterococcus EME343 and Enterococcus EME394.

tag: cell line

value: BEAS-2B cells

value: Bronchial epithelial cells

tag: treatment

value: RPMI

source_name: Enterococcus EME343 rep 1

value: Enterococcus EME343


title: M7


title: gp96 treated-CD4+FoxP3+Treg_rep2 [gp96-67]

city: Beijing

first: Songdong

last: Meng

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: nstitute Of Microbiology Chinese Academy of Sciences

description:
gp96_S21_L008
gp96-67_FPKM

data_processing:
Basecalls performed using CASAVA version 1.8
aligned to the GRCh38 genome assembly using Hisat2（version:2.0.4）
Uniquely mapped reads with mapping quality >=20 were retrieved for downstream analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM and counts

source_name: gp96 treated-CD4+FoxP3+Treg

extract_protocol:
Spleens were removed, CD4+ FoxP3+Tregs cells were sorted from the spleen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: age

value: 11 week

tag: genotype/variation

value: immunized with gp96

value: CD4+FoxP3-GFP+ Tregs


title: pbs treated-CD4+FoxP3+Treg_rep2 [PBS215]

source_name: pbs treated-CD4+FoxP3+Treg

value: Foxp3Cre Myd88fl/fl mice

value: immunized with pbs


title: gp96 treated-CD4+FoxP3+Treg_rep1 [gp96]

description:
gp96_S9_L007
gp96_FPKM


title: pbs treated-CD4+FoxP3+Treg_rep2 [pbs-67]

description:
pbs_S19_L008
pbs-67_FPKM


title: pbs treated-CD4+FoxP3+Treg_rep1 [pbs]

description:
pbs_S8_L007
pbs_FPKM


title: SC_SMA_ko_p5_M76_LCM126

description:
LCM126
rpkms_SMA_LCMseq.txt


title: SC_SMA_ko_p5_M46_LCM120

description:
LCM120
rpkms_SMA_LCMseq.txt


title: SC_SMA_ko_p5_M61_LCM121

description:
LCM121
rpkms_SMA_LCMseq.txt


title: pbs treated-CD4+FoxP3+Treg_rep1 [PBS-2-15]


title: M6

value: Hepatocyte

value: 10-12 weeks-old

value: 8 months after AAV-injection


title: SC_SMA_ko_p10_M196_LCM200

description:
LCM200
rpkms_SMA_LCMseq.txt


title: SC_SMA_ko_p10_M199_LCM201

description:
LCM201
rpkms_SMA_LCMseq.txt


title: gp96 treated-CD4+FoxP3+Treg_rep2 [X96215]


title: SC_SMA_ko_p5_M31_LCM124

description:
LCM124
rpkms_SMA_LCMseq.txt


title: SC_SMA_wt_p5_M75_LCM123

description:
This sample includes analysis of GSM2027339/SRX1516144 as well as an independent additional raw data file. The samples were pooled during the mapping procedure.
LCM123
rpkms_SMA_LCMseq.txt


title: gp96 treated-CD4+FoxP3+Treg_rep1 [96-2-15]


title: SC_SMA_wt_p5_M71_LCM119

description:
This sample includes analysis of GSM2027338/SRX1516143 as well as an independent additional raw data file. The samples were pooled during the mapping procedure.
LCM119
rpkms_SMA_LCMseq.txt


title: TAM_induced_D21_wt_R1-2_RNA-seq [new_D21_WT_m_pos_1948_2]

first: Yi

last: He

address: 30 Shuangqing Rd, Haidian Qu, Beijing Shi, China

institute: Tsinghua university

description:
David-pool6-ss_1948_2_FKDL192550337-1a-AK406-N506
processed data file: TAM_KrasG12D_D21.count.txt

data_processing:
The adapters of paired-end reads were trimmed and quality control check were carried out using trim-galore (version 0.6.0). Reads were aligned to mouse genome reference (GRCm38.p6) from GENCODE using HISAT2 (version 2.1.0). Aligned reads stored in SAM format were manipulated to generate bam files using SAMtools (version 1.9) with parameter is “samtools view –b –h –F 4 –f 3”. featureCounts (version 1.6.3) counted reads stored in BAM format to exon sites of genes included in GTF file from GENCODE. Differential gene expression analysis was processed which used raw counts  as input using R (version 3.5.1) package DESeq2 (version 1.22.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts in each sample

source_name: normal pancreas(recovery)

extract_protocol:
Mouse pancreases were digested into single cell suspensions as previously described (Reichert et al., 2013a)
Library preparation was performed using Smart-seq2 as described (Picelli et al., 2013) Using VAHTS mRNA-seq V3 Library Prep Kit (Vazyme, NR611)

treatment_protocol: Tamoxifen injections were performed 150mg/kg, four times per mouse. Caerulein injections were performed on 6 week-old mice essentially as described (Morris et al., 2010), with 8 hourly injections of caerulein for two consecutive days, modified by using 4 μg of caerulein per injection

value: pancreas


title: SC_SMA_wt_p5_M34_LCM127

description:
This sample includes analysis of GSM2027342/SRX1516147 as well as an independent additional raw data file. The samples were pooled during the mapping procedure.
LCM127
rpkms_SMA_LCMseq.txt


title: TAM_induced_D21_wt_R1-3_RNA-seq [new_D21_WT_m_pos_1948_3]

description:
David-pool6-ss_1948_3_FKDL192550337-1a-AK405-N506
processed data file: TAM_KrasG12D_D21.count.txt


title: TAM_induced_D21_wt_R1-1_RNA-seq [new_D21_WT_m_pos_1948_1]

description:
David-pool6-ss_1948_1_FKDL192550337-1a-AK426-N505
processed data file: TAM_KrasG12D_D21.count.txt


title: SC_SMA_wt_p5_M30_LCM125

description:
This sample includes analysis of GSM2027340/SRX1516145 as well as an independent additional raw data file. The samples were pooled during the mapping procedure.
LCM125
rpkms_SMA_LCMseq.txt


title: SC_SMA_ko_p2_M55_LCM153

description:
LCM153
rpkms_SMA_LCMseq.txt


title: SC_SMA_ko_p2_M41_LCM159

description:
LCM159
rpkms_SMA_LCMseq.txt


title: TAM_induced_Tumor_R2-3_RNA-seq [new_Tumor_Kras_881-T3]

description: David-pool2-881-T3_FKDL192544652-1a-AK405-N507

source_name: KrasG12D,KO_Cdkn2a maintained Tumor

value: mCherry-positive cells


title: TAM_induced_Tumor_R2-1_RNA-seq [new_Tumor_Kras_881-T1]

description: David-pool2-881-T1_FKDL192544653-1a-AK426-N506_H3TVJCCX2_L8


title: SC_SMA_ko_p2_M38_LCM163

description:
LCM163
rpkms_SMA_LCMseq.txt

value: Lumbar spinal cord motor neurons


title: TAM_induced_Tumor_R2-2_RNA-seq [new_Tumor_Kras_881-T2]

description: David-pool2-881-T2_FKDL192544653-1a-AK397-N506_H3TVJCCX2_L8


title: TAM_induced_Tumor_R1-3_RNA-seq [new_Tumor_Kras_1991-3]

description: David-mix1-ss-199T1-3_FKDL190762751-1a-N703-N507_H2YV2CCX2_L5


title: TAM_induced_Tumor_R1-2_RNA-seq [new_Tumor_Kras_1991-2]

description: David-mix1-ss-199T1-2_FKDL190762751-1a-N703-N504_H2YV2CCX2_L5


title: SC_SMA_ko_p2_M206_LCM171

description:
LCM171
rpkms_SMA_LCMseq.txt

value: SMA


title: SC_SMA_ko_p2_M207_LCM178

description:
LCM178
rpkms_SMA_LCMseq.txt


title: TAM_induced_Tumor_R1-1_RNA-seq [new_Tumor_Kras_1991-1]

description: David-mix1-ss-199T1-1_FKDL190762751-1a-N701-N504_H2YV2CCX2_L5


title: TAM_induced_D7_KrasG12D_R1-3_RNA-seq [new_D7_Kras_m_pos_1973-3]

description: David-pool2-1973-3_FKDL192544653-1a-AK663-N504_H3TVJCCX2_L8

source_name: Kras maintained ADM and panIN

value: Klf5-mCherry-CreERT2; LSL-KrasG12D


title: SC_SMA_ko_p2_M206_LCM169

description:
LCM169
rpkms_SMA_LCMseq.txt


title: TAM_induced_D7_KrasG12D_R2-2_RNA-seq [new_D7_Kras_m_pos_1961-2]

description: David-pool2-1961-2_FKDL192544653-1a-AK405-N506_H3TVJCCX2_L8


title: TAM_induced_D7_KrasG12D_R2-3_RNA-seq [new_D7_Kras_m_pos_1961-3]

description: David-pool2-1961-3_FKDL192544653-1a-AK397-N505_H3TVJCCX2_L8


title: TAM_induced_D7_KrasG12D_R2-1_RNA-seq [new_D7_Kras_m_pos_1961-1]

description: David-pool2-1961-1_FKDL192544653-1a-AK663-N505_H3TVJCCX2_L8


title: TAM_induced_D7_KrasG12D_R1-2_RNA-seq [new_D7_Kras_m_pos_1973-2]

description: David-pool2-1973-2_FKDL192544653-1a-AK395-N504_H3TVJCCX2_L8


title: SC_SMA_wt_p2_M244_LCM209

description:
LCM209
rpkms_SMA_LCMseq.txt

value: control


title: TAM_induced_D7_KrasG12D_R1-1_RNA-seq [new_D7_Kras_m_pos_1973-1]

description: David-pool2-1973-1_FKDL192544653-1a-AK397-N504_H3TVJCCX2_L8


title: SC_SMA_wt_p2_M28_LCM164

description:
LCM164
rpkms_SMA_LCMseq.txt


title: SC_SMA_wt_p2_M20_LCM161

description:
LCM161
rpkms_SMA_LCMseq.txt


title: SC_SMA_wt_p2_M240_LCM208

description:
LCM208
rpkms_SMA_LCMseq.txt


title: SC_SMA_wt_p5_M29_LCM128

description:
This sample includes analysis of GSM2027341/SRX1516146 as well as an independent additional raw data file. The samples were pooled during the mapping procedure.
LCM128
rpkms_SMA_LCMseq.txt


title: TAM_induced_D0_KrasG12D_R1-2_RNA-seq [new_D0_Kras_m_pos_681-2]

description: David-pool2-681-2_FKDL192544653-1a-DY0021-N505_H3TVJCCX2_L8

source_name: Kras induced in normal pancreas


title: CN12_SMA_ko_p10_M250_LCM238

description:
LCM238
rpkms_SMA_LCMseq.txt

source_name: Hypoglossal nucleus motor neurons

value: Hypoglossal nucleus motor neurons


title: CN12_SMA_ko_p10_M258_LCM255

description:
LCM255
rpkms_SMA_LCMseq.txt


title: CN12_SMA_ko_p10_M249_LCM220

description:
LCM220
rpkms_SMA_LCMseq.txt


title: TAM_induced_D0_KrasG12D_R1-1_RNA-seq [new_D0_Kras_m_pos_681-1]

description: David-pool2-681-1_FKDL192544653-1a-AK406-N505_H3TVJCCX2_L8


title: Knock_out_Foxa2_in_vivo_R2-3_RNA-seq

description:
pool12-ss-1639-3_FKDL202555768-1a-AK397-N506_H7KC2CCX2_L2
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgFoxa2. Using AAV to activte KrasG12D.YFP;Cas9

treatment_protocol: AAV injections were performed 8 days early before Caerulein injections. Caerulein injections were performed on 4 or 6 week-old mice essentially as described (Morris et al., 2010), with 8 hourly injections of caerulein for two consecutive days, modified by using 4 μg of caerulein per injection.

value: eGFP-positive cells


title: SC_SMA_ko_p2_M211_LCM177

description:
LCM177
rpkms_SMA_LCMseq.txt


title: SC_SMA_ko_p2_M209_LCM189

description:
LCM189
rpkms_SMA_LCMseq.txt


title: Knock_out_Foxa2_in_vivo_R2-1_RNA-seq

description:
pool12-ss-1639-1_FKDL202555768-1a-AK395-N506_H7KC2CCX2_L2
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgFoxa2. Using AAV to activte KrasG12D.YFP;Cas9


title: CN12_SMA_wt_p10_M254_LCM249

description:
LCM249
rpkms_SMA_LCMseq.txt


title: CN12_SMA_ko_p10_M196_LCM190

description:
LCM190
rpkms_SMA_LCMseq.txt


title: CN12_SMA_wt_p10_M253_LCM243

description:
LCM243
rpkms_SMA_LCMseq.txt


title: Knock_out_Foxa2_in_vivo_R1-3_RNA-seq

description:
pool12-ss-482-3_FKDL202555768-1a-5UDI212-N506
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgFoxa2. Using AAV to activte KrasG12D.YFP;Cas9


title: Knock_out_Foxa2_in_vivo_R1-2_RNA-seq

description:
pool12-ss-482-2_FKDL202555768-1a-AK426-N506_H7KC2CCX2_L2
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgFoxa2. Using AAV to activte KrasG12D.YFP;Cas9


title: CN12_SMA_wt_p10_M252_LCM229

description:
LCM229
rpkms_SMA_LCMseq.txt


title: Knock_out_Klf5_in_vivo_R2-3_RNA-seq

description:
pool12-ss-1642-3_FKDL202555768-1a-DY0021-N507
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgKlf5. Using AAV to activte KrasG12D.YFP;Cas9


title: Knock_out_Foxa2_in_vivo_R1-1_RNA-seq

description:
pool12-ss-482-1_FKDL202555768-1a-AK663-N506
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgFoxa2. Using AAV to activte KrasG12D.YFP;Cas9


title: CN12_SMA_wt_p10_M247_LCM213

description:
LCM213
rpkms_SMA_LCMseq.txt


title: Knock_out_Klf5_in_vivo_R2-2_RNA-seq

description:
pool12-ss-1642-2_FKDL202555768-1a-AK409-N507
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgKlf5. Using AAV to activte KrasG12D.YFP;Cas9


title: CN12_SMA_ko_p5_M77_LCM72

description:
LCM72
rpkms_SMA_LCMseq.txt


title: CN12_SMA_ko_p5_M61_LCM94

description:
LCM94
rpkms_SMA_LCMseq.txt


title: CN12_SMA_ko_p5_M46_LCM89

description:
LCM89
rpkms_SMA_LCMseq.txt


title: CN12_SMA_ko_p5_M31_LCM33

description:
LCM33
rpkms_SMA_LCMseq.txt


title: TAM_induced_D0_KrasG12D_R1-3_RNA-seq [new_D0_Kras_m_pos_681-3]

description: David-pool2-681-3_FKDL192544653-1a-AK395-N505_H3TVJCCX2_L8


title: Knock_out_Klf5_in_vivo_R1-3_RNA-seq

description:
pool11-ss-484-3_FKDL202555767-1a-AK405-N506
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgKlf5. Using AAV to activte KrasG12D.YFP;Cas9


title: Knock_out_Klf5_in_vivo_R1-2_RNA-seq

description:
pool11-ss-484-2_FKDL202555767-1a-AK406-N506_H7KC2CCX2_L4
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgKlf5. Using AAV to activte KrasG12D.YFP;Cas9


title: CN12_SMA_wt_p5_M71_LCM52

description:
LCM52
rpkms_SMA_LCMseq.txt


title: Knock_out_Klf5_in_vivo_R1-1_RNA-seq

description:
pool11-ss-484-1_FKDL202555767-1a-DY0021-N506
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgKlf5. Using AAV to activte KrasG12D.YFP;Cas9


title: CN12_SMA_wt_p5_M75_LCM56

description:
LCM56
rpkms_SMA_LCMseq.txt


title: CN12_SMA_ko_p10_M199_LCM196

description:
LCM196
rpkms_SMA_LCMseq.txt


title: Knock_out_Foxa2_in_vivo_R2-2_RNA-seq

description:
pool12-ss-1639-2_FKDL202555768-1a-AK396-N506
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgFoxa2. Using AAV to activte KrasG12D.YFP;Cas9


title: CN12_SMA_wt_p5_M29_LCM44

description:
LCM44
rpkms_SMA_LCMseq.txt


title: Knock_out_Rosa_in_vivo_R2-3_RNA-seq

description:
pool12-ss-1637-3_FKDL202555768-1a-5UDI212-N507
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgRosa. Using AAV to activte KrasG12D.YFP;Cas9


title: CN12_SMA_wt_p5_M34_LCM65

description:
LCM65
rpkms_SMA_LCMseq.txt


title: Knock_out_Rosa_in_vivo_R2-1_RNA-seq

description:
pool12-ss-1637-1_FKDL202555768-1a-AK663-N507_H7KC2CCX2_L2
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgRosa. Using AAV to activte KrasG12D.YFP;Cas9


title: CN12_SMA_ko_p2_M211_LCM179

description:
LCM179
rpkms_SMA_LCMseq.txt


title: CN12_SMA_ko_p2_M209_LCM184

description:
LCM184
rpkms_SMA_LCMseq.txt


title: Knock_out_Rosa_in_vivo_R1-3_RNA-seq

description:
pool12-ss-481-3_FKDL202555768-1a-DY0021-N506
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgRosa. Using AAV to activte KrasG12D.YFP;Cas9


title: CN12_SMA_ko_p2_M207_LCM174

description:
LCM174
rpkms_SMA_LCMseq.txt


title: CN12_SMA_ko_p2_M206_LCM165

description:
LCM165
rpkms_SMA_LCMseq.txt


title: Knock_out_Fosl1_in_vivo_R2-3_RNA-seq

description:
pool11-ss-1634-3_FKDL202555767-1a-AK405-N508_H7KC2CCX2_L4
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgFosl1. Using AAV to activte KrasG12D.YFP;Cas9


title: Knock_out_Klf5_in_vivo_R2-1_RNA-seq

description:
pool12-ss-1642-1_FKDL202555768-1a-AK408-N507_H7KC2CCX2_L2
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgKlf5. Using AAV to activte KrasG12D.YFP;Cas9


title: CN12_SMA_wt_p2_M28_LCM99

description:
LCM99
rpkms_SMA_LCMseq.txt


title: Knock_out_Fosl1_in_vivo_R2-2_RNA-seq

description:
pool11-ss-1634-2_FKDL202555767-1a-AK406-N508_H7KC2CCX2_L4
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgFosl1. Using AAV to activte KrasG12D.YFP;Cas9


title: CN12_SMA_ko_p2_M18_LCM116

description:
LCM116
rpkms_SMA_LCMseq.txt


title: Knock_out_Fosl1_in_vivo_R2-1_RNA-seq

description:
pool12-ss-1634-1_FKDL202555768-1a-AK426-N507_H7KC2CCX2_L2
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgFosl1. Using AAV to activte KrasG12D.YFP;Cas9


title: CN12_SMA_wt_p2_M26_LCM86

description:
LCM86
rpkms_SMA_LCMseq.txt


title: CN12_SMA_wt_p2_M244_LCM205

description:
LCM205
rpkms_SMA_LCMseq.txt


title: Knock_out_Fosl1_in_vivo_R1-3_RNA-seq

description:
pool11-ss-1640-3_FKDL202555767-1a-AK409-N508_H7KC2CCX2_L4
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgFosl1. Using AAV to activte KrasG12D.YFP;Cas9


title: Knock_out_Rosa_in_vivo_R2-2_RNA-seq

description:
pool12-ss-1637-2_FKDL202555768-1a-AK397-N507_H7KC2CCX2_L2
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgRosa. Using AAV to activte KrasG12D.YFP;Cas9


title: CN12_SMA_wt_p2_M240_LCM202

description:
LCM202
rpkms_SMA_LCMseq.txt


title: Knock_out_Junb_in_vivo_R2-1_RNA-seq

description:
pool12-ss-1644-1_FKDL202555768-1a-AK404-N507_H7KC2CCX2_L2
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgJunb. Using AAV to activte KrasG12D.YFP;Cas9


title: Knock_out_Junb_in_vivo_R2-3_RNA-seq

description:
pool12-ss-1644-3_FKDL202555768-1a-AK396-N507
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgJunb. Using AAV to activte KrasG12D.YFP;Cas9


title: Knock_out_Fosl1_in_vivo_R1-1_RNA-seq

description:
pool11-ss-1640-1_FKDL202555767-1a-DY0021-N508_H7KC2CCX2_L4
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgFosl1. Using AAV to activte KrasG12D.YFP;Cas9


title: CN10_SMA_ko_p10_M258_LCM260

description:
LCM260
rpkms_SMA_LCMseq.txt

source_name: Vagus nucleus motor neurons

value: Vagus nucleus motor neurons


title: Knock_out_Junb_in_vivo_R1-3_RNA-seq

description:
pool12-ss-477-3_FKDL202555768-1a-AK406-N507_H7KC2CCX2_L2
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgJunb. Using AAV to activte KrasG12D.YFP;Cas9


title: Knock_out_Rosa_in_vivo_R1-2_RNA-seq

description:
pool12-ss-481-2_FKDL202555768-1a-AK405-N506
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgRosa. Using AAV to activte KrasG12D.YFP;Cas9


title: CN10_SMA_ko_p10_M250_LCM237

description:
LCM237
rpkms_SMA_LCMseq.txt


title: Knock_out_Fosl1_in_vivo_R1-2_RNA-seq

description:
pool11-ss-1640-2_FKDL202555767-1a-AK408-N508_H7KC2CCX2_L4
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgFosl1. Using AAV to activte KrasG12D.YFP;Cas9


title: CN10_SMA_ko_p10_M249_LCM221

description:
LCM221
rpkms_SMA_LCMseq.txt


title: Knock_out_Junb_in_vivo_R2-2_RNA-seq

description:
pool12-ss-1644-2_FKDL202555768-1a-AK395-N507
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgJunb. Using AAV to activte KrasG12D.YFP;Cas9


title: Knock_out_Rosa_in_vivo_R1-1_RNA-seq

description:
pool12-ss-481_1_FKDL202555768-1a-AK406-N506_H7KC2CCX2_L2
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgRosa. Using AAV to activte KrasG12D.YFP;Cas9


title: CN10_SMA_ko_p10_M199_LCM199

description:
LCM199
rpkms_SMA_LCMseq.txt


title: CN10_SMA_wt_p10_M253_LCM244

description:
LCM244
rpkms_SMA_LCMseq.txt


title: Knock_out_Kras_in_vivo_R2-2_RNA-seq

description:
pool11-ss-1643-2_FKDL202555767-1a-AK395-N508_H7KC2CCX2_L4
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgKras. Using AAV to activte KrasG12D.YFP;Cas9


title: CN12_SMA_ko_p2_M16_LCM111

description:
LCM111
rpkms_SMA_LCMseq.txt


title: Knock_out_Junb_in_vivo_R1-1_RNA-seq

description:
pool12-ss-477-1_FKDL202555768-1a-AK405-N507
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgJunb. Using AAV to activte KrasG12D.YFP;Cas9


title: Knock_out_Kras_in_vivo_R2-1_RNA-seq

description:
pool11-ss-1643-1_FKDL202555767-1a-AK396-N508_H7KC2CCX2_L4
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgKras. Using AAV to activte KrasG12D.YFP;Cas9


title: Knock_out_Junb_in_vivo_R1-2_RNA-seq

description:
pool11-ss-477-2_FKDL202555767-1a-AK408-N506_H7KC2CCX2_L4
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgJunb. Using AAV to activte KrasG12D.YFP;Cas9


title: Knock_out_Kras_in_vivo_R2-3_RNA-seq

description:
pool11-ss-1643-3_FKDL202555767-1a-AK404-N508_H7KC2CCX2_L4
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgKras. Using AAV to activte KrasG12D.YFP;Cas9


title: CN10_SMA_wt_p10_M254_LCM250

description:
LCM250
rpkms_SMA_LCMseq.txt


title: CN10_SMA_ko_p10_M196_LCM195

description:
LCM195
rpkms_SMA_LCMseq.txt


title: CN10_SMA_wt_p10_M252_LCM232

description:
LCM232
rpkms_SMA_LCMseq.txt


title: Knock_out_Kras_in_vivo_R1-2_RNA-seq

description:
pool12-ss-485-2_FKDL202555768-1a-AK409-N506
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgKras. Using AAV to activte KrasG12D.YFP;Cas9


title: CN10_SMA_wt_p10_M247_LCM214

description:
LCM214
rpkms_SMA_LCMseq.txt


title: CN10_SMA_ko_p5_M77_LCM74

description:
LCM74
rpkms_SMA_LCMseq.txt


title: CN10_SMA_ko_p5_M31_LCM35

description:
LCM35
rpkms_SMA_LCMseq.txt


title: Knock_out_Kras_in_vivo_R1-1_RNA-seq

description:
pool12-ss-485-1_FKDL202555768-1a-AK408-N506
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgKras. Using AAV to activte KrasG12D.YFP;Cas9


title: TAM_induced_Tumor_R1_ATAC-seq

description: David-mix1-A-199T1_FKDL190762751-1a-N710-N504_H2YV2CCX2_L5

library_source: genomic

data_processing:
The adapters of paired-end reads were trimmed and a quality control check was carried out using trim-galore (version 0.6.0). Trimmed reads were aligned to mouse genome reference (GRCm38.p6) from GENCODE using bowtie2 (version 2.3.4.3) of which the parameter is “–very-sensitive –X 2000”. Aligned reads stored in SAM format were manipulated to generate bam files using samtools (version 1.9) with the parameter “samtools view –b –h –F 1028 –f 3”. ATAC-seq peaks were called using MACS2 (version 2.1.2) using the parameter “macs2 callpeak --verbose 3 -g mm -B -q 0.01 -f BAMPE --nolambda”. Raw counts of peaks in each sample were counted by featureCounts (version 1.6.3). Analysis of differential peak intensity and size factor for29  each sample were both obtained using DESeq2 (version 1.22.1). Normalized bigwig files were generated with 1/size factor using bamCoverage (version 3.2.0).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bedtools

molecule: genomic DNA

extract_protocol:
Mouse pancreases were digested into single cell suspensions as previously described (Reichert et al., 2013a)
TAM_induced* samples: Mouse pancreases were digested into single cell suspensions as previously described (Reichert et al., 2013a)
Libraries were prepared according to TruePrepTM DNA Library Prep Kit V2 for Illumina(Vazyme,TD502). ATAC-seq was performed using 3000 cells isolated from each mouse as described (Wu et al., 2016)

treatment_protocol:
AAV injections were performed 8 days early before Caerulein injections. Caerulein injections were performed on 4 or 6 week-old mice essentially as described (Morris et al., 2010), with 8 hourly injections of caerulein for two consecutive days, modified by using 4 μg of caerulein per injection.
TAM_induced* samples: Tamoxifen injections were performed 150mg/kg, four times per mouse. Caerulein injections were performed on 6 week-old mice essentially as described (Morris et al., 2010), with 8 hourly injections of caerulein for two consecutive days, modified by using 4 μg of caerulein per injection


title: CN10_SMA_wt_p5_M30_LCM83

description:
LCM83
rpkms_SMA_LCMseq.txt


title: CN10_SMA_wt_p5_M34_LCM66

description:
LCM66
rpkms_SMA_LCMseq.txt


title: TAM_induced_D7_KrasG12D_R1_ATAC-seq

description: David-pool4-A-1973_FKDL192548552-1a-AK409-N501


title: Knock_out_Foxa2_in_vivo_R1_ATAC-seq

description: pool11-A-482_FKDL202555767-1a-AK409-N501_H7KC2CCX2_L4


title: TAM_induced_D7_KrasG12D_R2_ATAC-seq


title: CN10_SMA_ko_p5_M61_LCM95

description:
LCM95
rpkms_SMA_LCMseq.txt


title: Knock_out_Foxa2_in_vivo_R2_ATAC-seq

description: pool11-A-1639_FKDL202555767-1a-AK426-N501


title: CN10_SMA_wt_p5_M71_LCM51

description:
LCM51
rpkms_SMA_LCMseq.txt


title: CR

city: Haikou

first: Guo

last: Panyang

address: Renmin road NO.58

institute: Hainan University

description: 150214_I709_FCC6NENACXX_L1_WHBANfysRAAARAAPEI-15

data_processing:
The messenger ribonucleic acid (mRNA) was enriched using oligo (dT) magnetic beads (Invitrogen) according to the manufacturer’s protocol.
After mixing with fragmentation buffer, the mRNA was fragmented into short fragments. The first-strand complementary DNA (cDNA) was synthesized using a random hexamer primer and the second-strand cDNA was synthesized by adding buffer, dNTPs, RNase H, and DNA polymerase I.The double-stranded cDNA was purified using magnetic beads.
The sequencing adaptors were ligated to the fragments. Finally,The fragments were enriched by polymerase chain reaction (PCR) amplification.
The original image data was transferred into sequence data via base calling, which is defined as raw data or raw reads and saved as a fastq file [25]. Those FASTQ files include the detailed read sequences and the read quality information. In addition, the filtering of raw data is needed to decrease the data noise. After filtering, the remaining reads are called “clean reads” and used form downstream bioinformatics analysis.
Clean data were obtained and stored as FASTQ format after filtering by detecting the content of each base to measure the stability of the library and sequencing eligibility.After data quality statistics, clean reads were mapped to reference sequences using Burrows-Wheeler Alignment (BWA) tool [26] and to gene reference using Bowtie.
Genome_build: Reference genome(https://banana-genome-hub.southgreen.fr)
Supplementary_files_format_and_content: Tab-delimited text files include all up regulated and down regulated unigenes.

organism: Musa acuminata AAA Group

source_name: normal -nitrogen roots

growth_protocol: They had been fixed with clean sands and put into growth chamber with a temperature 28-35°C,  in the natural conduction of Hainan province.

extract_protocol:
Tissues (100 mg) were placed into a precooled mortar to be ground into a powder with liquid nitrogen. The powder was collected into a precooled 2 mL Eppendorf tube with 2 mL RNase-free cetyltrimethylammonium bromide (CTAB) extracting solution, which contained 0.1% diethyl pyrocarbonate (DEPC), 2.5% CTAB, 1.4 M NaCl, 20 mM EDTA, 100 mM Tris-HCl (pH 8.0), and 4% polyvinylpyrrolidone (PVP). The tubes were then placed in a water bath at 65 °C for 30 min to induce cell lysis, and centrifuged at 13,000 rpm for 5 min at 25-28 °C. The residue was discarded, and the supernatant solution was transferred into a clean 2 mL Eppendorf tube. Trichloromethane (1 mL) was added to the supernatant solution, blended lightly, and centrifuged at 13 000 rpm for 15 min at 4 °C. The supernatant was transferred into a clean 2 mL Eppendorf tube, and this procedure was repeated once more. Subsequently, 8 M lithium chloride was added with RNase-free water to 0.6 volume of the supernatant and left overnight. The mixture was centrifuged for 30 min at 13 000 rpm and 4 °C to obtain the RNA precipitate. RNase-free ethyl alcohol (75%) was used to wash the RNA precipitate twice. Finally, RNA was dissolved in RNase-free ddH2O and stored at -80 °C until further use.
Poly (A) mRNA from the total RNA was enriched by poly-T oligo-attached magnetic beads (Invitrogen), according to the manufacturer’s protocol. Purified mRNA was then divided into short fragments by mixing with fragmentation buffer. The first strand cDNA was synthesized using a random hexamer primer. The buffer, dNTPs, RNase H, and DNA polymerase I were then added to the fragmented mRNA templates to synthesize the second-strand cDNA. The double-stranded cDNA was purified using magnetic beads. End repair and the addition of 3′-end single nucleotide A (adenine) were then performed. Finally, sequencing adaptors were ligated to the fragments, which were enriched by PCR amplification. During the quality control step, a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA) and a StepOnePlus Real-Time PCR System (Applied Biosystems Inc., Foster City, CA, USA) were used to qualify and quantify sequences for the sample libraries. The constructed library products were prepared for sequencing using a HiSeq 2000 system (Illumina, San Diego, CA, USA) at the Beijing Genomics Institute (BGI).

treatment_protocol: Normal group were adopted Hoagland complete culture solution, treated group were planted in low-nitrogen culture solution (low nitrogen group, LN)

tag: cultivar

value: cv. Cavendish

value: normal group without  low-nitrogen treatment.

value: root


title: CN10_SMA_ko_p2_M211_LCM180

description:
LCM180
rpkms_SMA_LCMseq.txt


title: CN10_SMA_wt_p5_M29_LCM45

description:
LCM45
rpkms_SMA_LCMseq.txt


title: NL

description: 150214_I709_FCC6NENACXX_L1_WHBANfysRAAGRAAPEI-21

source_name: low - nitrogen leaves

value: treated group with low-nitrogen treatment.

value: leaves


title: NR

description: 150214_I709_FCC6NENACXX_L1_WHBANfysRAACRAAPEI-17

source_name: low - nitrogen roots

value: treated group with  low-nitrogen treatment.


title: CL

description: 150214_I709_FCC6NENACXX_L1_WHBANfysRAABRAAPEI-16

source_name: normal -nitrogen leaves


title: CN10_SMA_ko_p2_M209_LCM186

description:
LCM186
rpkms_SMA_LCMseq.txt


title: Knock_out_Klf5_in_vivo_R2_ATAC-seq

description: pool11-A-1642_FKDL202555767-1a-AK404-N501_H7KC2CCX2_L4


title: Knock_out_Klf5_in_vivo_R1_ATAC-seq

description: pool11-A-484_FKDL202555767-1a-5UDI212-N501


title: TAM_induced_Tumor_R2_ATAC-seq

description: David-pool1-A-881T_FKDL192544652-1a-AK663-N501


title: Knock_out_Rosa_in_vivo_R2_ATAC-seq

description: pool11-A-1637_FKDL202555767-1a-AK396-N501


title: SL58814

city: Southampton

first: Ana

last: Garcia

address: Tremona Road

country: United Kingdom

institute: University of Southampton

data_processing:
CASAVA software version 1.9 was used for demultiplexing and producing FASTQ sequence files.
Raw FASTQ sequence files generated using CASAVA version 1.9 software were transferred to a dedicated Linux-based computing cluster for further processing.
Low quality sequences were filtered out.
FASTX application was used to trim adapter sequences from the 30 end of the sequence read, discard any sequence of less than 17 nucleotides after trimming, and collapse identical reads into Non-coding RNA 2019, 5, 51 4 of 12 single entries while retaining the read count for each unique sequence.
Non-redundant sequences were then aligned to genomic and mRNA sequence using bowtie 2
The mapped sequences were aligned to common and abundant non-coding RNAs (tRNAs, rRNAs, and snoRNAs), again using bowtie 2.
The genome-mapped sequences were further aligned to both mature microRNA and primary microRNA databases (miRBase 20.0), using OMAP# alignment software developed at ORB
Alignment result files were parsed by a custom Perl script to generate FASTA files containing the read count for each unique sequence and information about the target from the database (e.g., microRNA name and ID).
The FASTA files were tabulated using an additional custom OMAP Perl script in order to determine the raw sequence read count for each target database entry
The raw reads were converted to reads per million mapped reads (RPM).
The RPM values were filtered to retain a list of small RNAs with a minimum of 10 mapped reads (detection threshold) in 25% of samples
Missing values were replaced with the average RPM value equivalent to one read
Genome_build: hg19
Genome_build: Sequence reads were then mapped to rRNA, tRNA and snoRNA databases.
Genome_build: Reads mapped to genome were then aligned to precursor and mature microRNAs in miRBase 20.0 and piRNAs from piRNA database.
Supplementary_files_format_and_content: Processed every alignment counts.xlsx
Supplementary_files_format_and_content: Matrix for all samples. The sequence reads that aligned to the genome with up to one mismatch, were aligned to the Ensembl human cDNA sequence database version 70. The raw read counts for perfectly matched transcript are reported in this tab. The data was supported in descending order based on the mean read count.
Supplementary_files_format_and_content: Processed miRNA counts.xlsx
Supplementary_files_format_and_content: Matrix for all samples. The candidate microRNA sequences were aligned to human microRNAs in miRBase20.0 and normalized read counts for perfectly matched target mature microRNAs were reported in this tab.
Supplementary_files_format_and_content: Values on this tab are given as microRNA-specific reads in the form of RPM (Reads per Million mapped reads).  The RPM of 10 reads was defined as the Detection Threshold, which was calculated from the formula: (10 reads )/ (total mapped reads/1M).  0 was replaced by average of 1 read RPM across all samples.  Anova P and FDR values were obtained using NIA Array Analysis Software.
Supplementary_files_format_and_content: An aditional Anova was calculated for 13 samples which had > 5% of the total reads mapped to genome  designated as microRNA reads. (Percentage of microRNA Mapped over Genome Mapped (%))
Supplementary_files_format_and_content: Data is sorted in ascending order based on the Anova P value (All samples)

source_name: Bronchoalveolar Lavage

growth_protocol: Bronchoalveolar Lavage was extracted from severe asthmatic patients or healthy controls

extract_protocol:
Nanovesicle RNA was extracted from twenty millilitres of bronchoalveolar lavage using the ExoMir kit (Biooscientific, Austin, TX, USA) following manufacturer’s instructions. BAL was loaded into a 20-mL syringe and passed through a sequence of two filters. The pore size of the top filter was 0.2 µm whereas the bottom filter’s pore size was 0.02 µm. RNA from each of the filters was harvested separately using 1 ml of Bioopure reagent. RNA extraction was then performed according to the manufacturer’s instructions. Extracts from the bottom filter were used for small RNA-sequencing
Template DNA molecules suitable for cluster generation were prepared from the re-purified RNA samples using the NEBNext Small RNA-Seq Library Preparation Kit (New England BioLabs, Ipswich, MA, USA) according to the manufacturer’s instructions, with an additional step following the RNA linker ligation after cDNA synthesis. cDNA fragments were fractionated using a 12% acrylamide-urea gel and 58–88 nt fragments, corresponding to inserts of 11–41 nt, were excised and purified to ensure a minimum size range of 17–35 nt inserts was recovered for each sample. Libraries were electrophoresed through a freshly cast 6% native polyacrylamide gel and the library fragments of an appropriate size (~130–160 nt) were purified and recovered by agitation of the fragments overnight at 37 ◦C at 200 rpm in elution buffer, passage of the eluate through a 0.45-µm filter, and ethanol precipitation. The quality and size distribution of the amplified libraries were determined utilizing an Agilent High Sensitivity DNA Bioanalyzer microfluidic chip. Libraries were quantified using the KAPA Library Quantification Kit (KK4824, Kapa Biosystems, Boston, MA, USA). Libraries were pooled at equimolar concentrations and diluted prior to loading onto the flow cell of the cBot cluster station (Illumina Inc., San Diego, CA, USA). The libraries were extended and bridge amplified to create single sequence clusters using the TruSeq SR Cluster Kit version 3—HS (Illumina Inc., San Diego, CA, USA). The flow cell carrying amplified clusters was loaded on the HiSeq 2000 sequencing system (Illumina Inc., San Diego, CA, USA) and sequenced with 50 bp single-end reads using the TruSeq SBS Kit version 3—HS (Illumina Inc., San Diego, CA, USA)

treatment_protocol: BAL fluid was filtered using a 100-µm nylon filter and then centrifuged at 400 rcf for 10 min at 4 ◦C. The supernatant was removed, aliquoted, and stored at −80 ◦C.

tag: disease state

value: severe asthmatic


title: SL58815


title: SL58813


title: SL58812


title: SL58811


title: CN10_SMA_ko_p2_M206_LCM166

description:
LCM166
rpkms_SMA_LCMseq.txt


title: SL58810


title: CN10_SMA_ko_p2_M18_LCM118

description:
LCM118
rpkms_SMA_LCMseq.txt


title: Knock_out_Fosl1_in_vivo_R2_ATAC-seq

description: pool11-A-1634_FKDL202555767-1a-AK405-N501


title: Knock_out_Fosl1_in_vivo_R1_ATAC-seq

description: pool11-A-1640_FKDL202555767-1a-AK406-N501


title: SL58807


title: CN10_SMA_ko_p2_M16_LCM113

description:
LCM113
rpkms_SMA_LCMseq.txt


title: CN10_SMA_wt_p2_M26_LCM90

description:
LCM90
rpkms_SMA_LCMseq.txt


title: Knock_out_Rosa_in_vivo_R1_ATAC-seq

description: pool11-A-481_FKDL202555767-1a-AK395-N501_H7KC2CCX2_L4


title: SL58803

value: Healthy


title: SL58805


title: SL58804


title: CN10_SMA_ko_p2_M207_LCM175

description:
LCM175
rpkms_SMA_LCMseq.txt


title: CN10_SMA_wt_p2_M244_LCM206

description:
LCM206
rpkms_SMA_LCMseq.txt


title: Knock_out_Junb_in_vivo_R2_ATAC-seq

description: pool11-A-1644_FKDL202555767-1a-AK663-N501_H7KC2CCX2_L4

value: pancreas


title: SL58802


title: CN10_SMA_wt_p2_M240_LCM203

description:
LCM203
rpkms_SMA_LCMseq.txt


title: SL58800


title: SL46261


title: SL58809


title: SL46260


title: CN7_SMA_ko_p10_M258_LCM256

description:
LCM256
rpkms_SMA_LCMseq.txt

source_name: Facial nucleus motor neurons

value: Facial nucleus motor neurons


title: SL58801


title: Knock_out_Kras_in_vivo_R2_ATAC-seq

description: pool11-A-1643_FKDL202555767-1a-DY0021-N501_H7KC2CCX2_L4


title: Foxa2-OE_Junb_and_Fosl1+KrasG12D_ChIP

description: pool12-Foxa2-3-4-J-F-dox_FKDL202555768-1a-3

data_processing:
The adapters of paired-end reads were trimmed and quality control checks were carried out using trim-galore (version 0.6.0). Trimmed reads were aligned to mouse genome reference (GRCm38.p6) from GENCODE using bowtie2 (version 2.3.4.3) of which the parameter is “–very-sensitive –X 2000”. Aligned reads stored in SAM format were manipulated to generate bam files using samtools (version 1.9) with parameter is “samtools view –b –h –F 1028 –f 3”. Peaks of ChIP-seq were called using MACS2 (version 2.1.2) using the parameter “macs2 callpeak --verbose 3 -g mm -B -q 1e-3 -f BEDPE”. Analysis of differential peaks intensity was processed using MAnorm (version 1.1.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deeptools

source_name: pancreatic adenocarcinoma

growth_protocol:
KPCS and KP cell line: DMEM+10%FBS+1%P/S.
To KrasG12D cell line: DMEM+10%FBS+1%P/S+1ug/ml Doxycycline; PDA cell line:DMEM+10%FBS+1%P/S

extract_protocol:
Briefly, cells were crosslinked at room temperature for 10 min with 1% formaldehyde,  washed twice with PBS and sonicated in lysis buffer (50 mM HEPES/KOH pH 7.5, 140  mM NaCl, 0.1% Na-Deoxycholate, 1% Triton X-100, 1 mM EDTA, complete protease  inhibitor cocktail). Samples were immunoprecipitated at 4 ºC overnight and washed six  times with ChIP wash buffer (20 mM Tris, pH 7.9, 500 mM NaCl, 2 mM EDTA, 1% Triton  X-100, 0.1% SDS) and once with TE buffer. Bound DNA was eluted in 1% SDS buffer  and reverse-crosslinked for 6 h at 65 ºC
DNA samples were treated sequentially with  RNase A and Protease K and then purified with ChIP DNA Clean & Concentrator-5  (Zymo Research, D4014)

treatment_protocol:
KPCS and KP cell line were treated by Refametinib,PD0325901,MK-2206 2HCl or DMSO for 12h.
To KrasG12D cell line: +KrasG12D means treatment with Dox;-KrasG12D  means No Dox add.PDA cell line:+KrasG12D means endogenous KrasG12D expression.

value: pancreatic adenocarcinoma cancer Tet-on KrasG12D cell line

tag: chip antibody

value: anti-Foxa2 (Cell Signaling, #8186)


title: CN7_SMA_ko_p10_M249_LCM222

description:
LCM222
rpkms_SMA_LCMseq.txt

value: SMA


title: Knock_out_Kras_in_vivo_R1_ATAC-seq

description: pool11-A-485_FKDL202555767-1a-AK397-N501_H7KC2CCX2_L4

tag: cell type


title: SL58808


title: SL46262


title: SL58806


title: SL46259


title: PAX6D KO Rep3

city: Nanjing

first: Yunlong

last: Tao

state: Jiangsu

address: 163 Xianlin Road

department: School of life sciences

institute: Nanjing University

description:
cuffnorm normalized gene FPKM.txt
DKO_2

data_processing:
Aligment: HISAT2, Galaxy Version 2.1.0+galaxy3
Generation of normalized abundance: Cufflinks
Differentially expressed genes: Cuffdiff
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: retinal progenitor cells

growth_protocol: retinal progenitor cells generated from human pluripotent stem cells.hESCs were passaged to Vitronectin-coated plates and cultured to 60-70% confluency. On day 0 of retinal differentiation, cells were enzymatically detached by dispase (1mg/ml) and cultured in suspension with E8 medium to form embryoid bodies (EB). EBs were gradually transitioned into neural induction medium (NIM) containing DMEM/F12 (1:1), 1% N2 and 1x NEAA by replacing the medium with a 3:1 ratio of E8/NIM on day 1, 1:1 on day 2, and 100% NIM on day 3. On day 7, EBs were seeded onto plates with NIM containing 5% FBS. The medium was changed to NIM one day later and fed with NIM every other day. On day 16 the medium was changed to RDM (retinal differentiation medium) containing DMEM/F12 (3:1) supplemented with 2% B27 (without vitamin A) and1x NEAA with daily medium change.

extract_protocol:
Total RNA was isolated with the RNeasy Plus Mini Kit according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: retinal progenitor cells derived from embryonic stem cell

value: day 20

tag: genotype

value: PAX6D -/-


title: CN7_SMA_ko_p10_M199_LCM257

description:
LCM257
rpkms_SMA_LCMseq.txt


title: PAX6D KO Rep2

description:
cuffnorm normalized gene FPKM.txt
DKO_1


title: PAX6D KO Rep1

description:
cuffnorm normalized gene FPKM.txt
DKO_0


title: Foxa2-OE_Junb_and_Fosl1-KrasG12D_ChIP

description: pool12-Foxa2-3-4-J-F-no-dox_FKDL202555768-1a-7


title: Knock_out_Junb_in_vivo_R1_ATAC-seq

description: pool11-A-477_FKDL202555767-1a-AK408-N501_H7KC2CCX2_L4

value: eGFP-positive cells


title: CN7_SMA_ko_p10_M196_LCM191

description:
LCM191
rpkms_SMA_LCMseq.txt


title: PAX6 KO Rep2

description:
cuffnorm normalized gene FPKM.txt
KO_1


title: CN7_SMA_wt_p10_M254_LCM251

description:
LCM251
rpkms_SMA_LCMseq.txt

value: control


title: PAX6 KO Rep3

description:
cuffnorm normalized gene FPKM.txt
KO_2


title: PAX6 KO Rep1

description:
cuffnorm normalized gene FPKM.txt
KO_0


title: WT Rep3

description:
cuffnorm normalized gene FPKM.txt
WT_2

value: wildtype


title: Foxa2-OE_Vector-KrasG12D_ChIP

description: pool12-Foxa2-3-4-V-no-dox_FKDL202555768-1a-1


title: CN7_SMA_wt_p10_M253_LCM245

description:
LCM245
rpkms_SMA_LCMseq.txt


title: WT Rep1

description:
cuffnorm normalized gene FPKM.txt
WT_0


title: Klf5-OE_Junb_and_Fosl1+KrasG12D_ChIP

description: pool12-Klf5-3-4-J-F-dox_FKDL202555768-1a-6

value: anti-Klf5 (Abcam, ab137676)


title: PAX6D INPUT2

data_processing:
reads trimmed by Trimmomatic (Galaxy)
Aligment: Map with BWA (Galaxy)
MACS2 callpeak (Galaxy)
Genome_build: hg38
Supplementary_files_format_and_content: bed files with regional information

source_name: Neuroepithelilal cells

growth_protocol: human embryonic stem cells are differentiated to neuroepithelial cells first. We use DOX to turn on PAX6A and PAX6D in two different cell lines.

extract_protocol:
the cultures were digested with TrypLE to become single cells and then were crosslinked using 1% formaldehyde provided by the kit.  The cells were incubated at room temperature for 10 mins in a chemical fume hood. After incubation, the cells were treated with glycine solution for 5 mins at room temperature. After washing with cold PBS twice, the cells were lysed with the lysis buffer in the presence of protease inhibitors and MNase (provided by the kit to digest DNA). They were then sonicated (three 20-second pulses at 3 watts power) to yield DNA fragments of about 150bp to 1000bp. After taking 10 µl samples as an INPUT the rest samples were incubated with 1 µg FLAG antibody in 100 µl IP buffer provided by the kit overnight at 2-8 °C. The pull-downs were harvested by ChIP Grade Protein A/G Magnetic Beads. The DNAs were recovered from the INPUTs and IPs
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neuroepithelilal cells

value: day 10


title: CN7_SMA_wt_p10_M252_LCM228

description:
LCM228
rpkms_SMA_LCMseq.txt


title: Klf5-OE_Junb_and_Fosl1-KrasG12D_ChIP

description: pool12-Klf5_3-4_JF_no_dox_FKDL202555768-1a-4_H7KC2CCX2_L2


title: CN7_SMA_wt_p10_M247_LCM215

description:
LCM215
rpkms_SMA_LCMseq.txt


title: PAX6D INPUT1


title: PAX6D IP1

value: Monoclonal ANTI-FLAG M2 antibody from Sigma (F3165)


title: PAX6D IP2


title: CN7_SMA_ko_p5_M77_LCM73

description:
LCM73
rpkms_SMA_LCMseq.txt


title: PAX6A INPUT2


title: Klf5-OE_Vector-KrasG12D_ChIP

description: pool12-Klf5-3-4-V-no-dox_FKDL202555768-1a-2


title: PAX6A IP2


title: 3MK35

city: Xi’an

first: Fan

middle: Fan

last: Gao

state: Shaanxi

address: West Yanta Road 277

department: Dialysis Department of Nephrology Hospital

institute: the First Affiliated Hospital of Xi’an Jiaotong University

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using TopHat2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion and CIRCExplorer2. All samples were generated unique circular RNAs.
Genome_build: Mus_musculus Ensembl relaese-88
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each isoforms

source_name: kidney

growth_protocol: The mice were housed at 25°C and fed standard rodent chow and tap water.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA removal kit (Illumina, San Diego, USA).Then the left RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the Truseq Stranded Total RNA HT Sample Prep Kit (Illumina, San Diego, USA).

tag: strain

value: kidney

tag: Sex

value: male

value: 24 month old


title: CN7_SMA_ko_p5_M31_LCM34

description:
LCM34
rpkms_SMA_LCMseq.txt

value: Facial nucleus motor neurons


title: CN7_SMA_ko_p5_M61_LCM96

description:
LCM96
rpkms_SMA_LCMseq.txt


title: 3MK34


title: 3MK33


title: PAX6A IP1


title: PAX6A INPUT1


title: Foxa2-OE_Vector+KrasG12D_ChIP

description: pool12-Foxa2-3-4-V-dox_FKDL202555768-1a-12

value: pancreatic adenocarcinoma cancer Tet-on KrasG12D cell line


title: KP_H3K27ac+KrasG12D_ChIP_MK-2206 2HCl_treatment

value: KP

value: pancreatic adenocarcinoma cancer cell line

value: anti-H3K27ac (Abcam ab4729)


title: Input_KP_H3K27ac+KrasG12D_ChIP_MK-2206 2HCl_treatment

description: David-pool3-Input-KPC-AKTi_FKDL192545724-1a-11


title: CN7_SMA_wt_p5_M75_LCM57

description:
LCM57
rpkms_SMA_LCMseq.txt


title: KP_H3K27ac+KrasG12D_ChIP_DMSO_treatment


title: PT_RNA_rep2

city: Guangzhou

first: Zhicheng

last: Dong

state: Guangdong

address: 230 Wai Huan Xi Road,Guangzhou Higher Education Mega Center

department: School of Life Sciences

institute: Guangzhou University

data_processing:
After removing adaptor sequences and low-quality data. The sequences were aligned to Arabidopsis genome using STAR, and the mapped reads in each gene were quantified using HOMER.
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: The Arabidopsis (Col-0 ecotype) seeds were germinated and grown in soil for 14 days at 21°C under 16 hour light/8 hour dark, and then plants got heat treatment for 1.5 h at 37 °C each day for one week.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Thermo Fisher), followed by DNase I treatment
Poly(A) RNA were purified using Dynabeads® Oligo (dT)25 (Thermo Fisher) . RNA-seq libraries were prepared using a NEBNext Ultra RNA Library Prep Kit (New England BioLabs) according to the manua

treatment_protocol: leaf tissue was collected after a heat shock at 45 °C for 5min

value: leaf

value: 3 weeks

tag: molecule

value: polyA RNA


title: WT Rep2

description:
cuffnorm normalized gene FPKM.txt
WT_1

value: retinal progenitor cells derived from embryonic stem cell

value: day 20


title: CN7_SMA_wt_p5_M71_LCM53

description:
LCM53
rpkms_SMA_LCMseq.txt

tag: tissue

value: control


title: CN7_SMA_wt_p5_M34_LCM64

description:
LCM64
rpkms_SMA_LCMseq.txt

tag: age (days)


title: KP_H3K27ac+KrasG12D_ChIP_Refametinib_treatment

description: David-pool3-KPC-Ra-MEKi_FKDL192545724-1a-1


title: Klf5-OE_Vector+KrasG12D_ChIP

description: pool12-Klf5-3-4-V-dox_FKDL202555768-1a-5

value: anti-Klf5 (Abcam, ab137676)


title: PT_RNA_rep1


title: CN7_SMA_wt_p5_M29_LCM46

description:
LCM46
rpkms_SMA_LCMseq.txt

tag: group


title: KP_H3K27ac+KrasG12D_ChIP_PD0325901_treatment

description: David-pool3-KPC-PD-MEKi_FKDL192545724-1a-12


title: 3MK21

value: 12 month old


title: KPCS_H3K27ac+KrasG12D_ChIP_DMSO_treatment

value: KPCS


title: 3MK20

value: kidney


title: 3MK31

value: male


title: P_RNA_rep2


title: P_RNA_rep1


title: CN7_SMA_ko_p2_M38_LCM156

description:
LCM156
rpkms_SMA_LCMseq.txt

value: SMA

tag: mouse id


title: CN7_SMA_ko_p2_M211_LCM182

description:
LCM182
rpkms_SMA_LCMseq.txt

value: Facial nucleus motor neurons


title: KPCS_H3K27ac+KrasG12D_ChIP_Refametinib_treatment

description: David-pool3-806-Ra-MEKi_FKDL192545724-1a-5

tag: cell line


title: T_RNA_rep2

growth_protocol: The Arabidopsis (Col-0 ecotype) seeds were germinated and grown in soil for 21 days at 21°C under 16 hour light/8 hour dark.


title: 3MK19


title: 3MK18


title: CN7_SMA_ko_p2_M209_LCM185

description:
LCM185
rpkms_SMA_LCMseq.txt


title: 3MK32

value: 24 month old


title: CN7_SMA_ko_p2_M207_LCM176

description:
LCM176
rpkms_SMA_LCMseq.txt


title: N_RNA_rep2


title: 3MK17


title: KPCS_H3K27ac+KrasG12D_ChIP_MK-2206 2HCl_treatment


title: T_RNA_rep1


title: KPCS_H3K27ac+KrasG12D_ChIP_PD0325901_treatment

description: David-pool3-806-PD-MEKi_FKDL192545724-1a-4


title: 3MK9

value: 3 month old


title: CN7_SMA_ko_p2_M206_LCM170

description:
LCM170
rpkms_SMA_LCMseq.txt


title: D7_WT_R3-3_RNA-seq

source_name: pancreatic "normal' duct cell

treatment_protocol: Caerulein injections were performed on 6 week-old mice essentially as described (Morris et al., 2010), with 8 hourly injections of caerulein for two consecutive days, modified by using 4 μg of caerulein per injection


title: N_RNA_rep1


title: 3MK8


title: CN7_SMA_ko_p2_M18_LCM117

description:
LCM117
rpkms_SMA_LCMseq.txt


title: PT_GRO_rep2

data_processing:
Library strategy: GRO-seq
After trimming of adapter and filtering of low quality data by Cutadapt v1.2.1, reads originating from rRNA were filtered by aligning against an index consisting of the 45S and 5S transcripts using STAR v2.5.3a and unmapped reads were subsequently aligned to the Arabidopsis genome TAIR10. Only uniquely mapped reads were retained, and the 5’ coordinate of each read was used as the position of engaged polymerase.
Genome_build: TAIR10

extract_protocol:
The fine tissue powder was solubilized in 30 ml extraction buffer (2 M hexylene glycol, 20 mM PIPES pH 7.0, 10 mM MgCl2, 5 mM 2-mercaptoethanol) and filtrated through 110 μm and 60 μm nylon mesh. Add triton X-100 into the lysates to the final concentration of 1% and leave on ice for 10 minutes. Cell fractionation was performed using a 30%-80% percoll gradient solution and nuclei were collected at the 30%-80% interface.
Breifly, nascent RNA was treated with T4 PNK (NEB) and followed by acidic phenol/chloroform purification. Phosphorylated nascent RNA was polyA tailed using E. coli Poly(A) Polymerase (NEB) and reverse transcribed by superscript III reverse transcriptase (Invitrogen) with RT primer (GRO-oligo2, synthesized by IDT DNA, 5’-/5Phos/GA TCG TCG GAC TGT AGA ACT CTG AAC /idSp/CC TTG GCA CCC GAG AAT TCC ATT TTT TTT TTT TTT TTT TTT VN-3’). Free RT primer was removed by Exonuclease I (Fermentas) and RNA was eliminated by alkaline hydrolysis. The resulted 1st-strand cDNA was resolved from a 10% TBE-urea polyacrylamide gel. The cDNA with size above120 nt was recovered and self-ligated using CircLigase (Epicentre). The circularized single-stranded cDNA was relinearized by APE 1 (NEB). The linearized cDNA was recovered again by a 10% TBE-urea polyacrylamide gel. The cDNA was PCR amplified by Kapa HiFi polymerase with the illumina compatible primers (Universal primer F 5’GAT CGT CGG ACT GTA GAA CTC TGA ACG TGT AGA TCT CGG TGG TCG CCG TAT CAT T 3’, Reverse Index primer R 5’CAA GCA GAA GAC GGC ATA CGA GAT NNNNNN GTG ACT GGA GTT CCT TGG CAC CCG AGA ATT CCA 3’, NNNNNN: index). The PCR reaction starts with a 30s denaturation at 94˚C, followed by 12-14 cycles of 10s denaturation at 94˚C, 15s annealing at 60˚C and 15s extension at 72˚C. The PCR product was resolved in a non-denaturing 8% TBE polyacrylamide gel and size region 200-330 bp was recovered. cDNA library concentration was determined by Qubit QuantIT (Invitrogen) and kapa quantitative realtime PCR according to the manual.

value: nascent RNA


title: D7_WT_R3-2_RNA-seq


title: CN7_SMA_ko_p2_M16_LCM112

description:
LCM112
rpkms_SMA_LCMseq.txt


title: 3MK7


title: D7_WT_R3-1_RNA-seq


title: D7_WT_R2-3_RNA-seq


title: 3MK6


title: P_GRO_rep2


title: PT_GRO_rep1


title: D7_WT_R2-2_RNA-seq


title: 3MK5


title: P_GRO_rep1


title: D7_WT_R2-1_RNA-seq


title: CN7_SMA_wt_p2_M26_LCM87

description:
LCM87
rpkms_SMA_LCMseq.txt


title: T_GRO_rep2


title: CN7_SMA_wt_p2_M244_LCM207

description:
LCM207
rpkms_SMA_LCMseq.txt


title: D7_WT_R1-3_RNA-seq


title: D7_WT_R1-2_RNA-seq


title: T_GRO_rep1


title: CN7_SMA_wt_p2_M240_LCM204

description:
LCM204
rpkms_SMA_LCMseq.txt


title: CN4_SMA_ko_p10_M196_LCM192

description:
LCM192
rpkms_SMA_LCMseq.txt

source_name: Oculomotor/trochlear nuclei motor neurons


title: D7_KrasG12D_R3-3_RNA-seq

source_name: Kras maintained ADM and panIN

value: Pdx1-cre; Klf5-mCherry-CreERT2; LSL-KrasG12D; R26RLSL-YFP


title: N_GRO_rep2

value: leaf


title: D7_WT_R1-1_RNA-seq


title: 14 month old WT striatum nuclei (BCR3)

city: Baltimore

first: Sonia

last: Malaiya

state: Maryland

address: 209, Roundhouse Ct.

department: Institute of Genome Science

institute: University of Maryland

data_processing:
Base calling was performed using cellranger v3.0.2 to the mm10 transcriptome model
Ambient RNA was reduced using SoupX v0.1.1 at 10% global contamination and nuclei outside the range of 1260-6300 UMIs/nucleus were removed for all samples except BCR1, which used the range 1260-4470 UMIs/nucelus.
Doublets were removed using identification of nuclei expressing mutually exclusive cell type markers by simple scoring. Nuclei with >5% mitochondrial counts were removed using Seurat.
Counts were normalized to log (counts per million) and MNN batch correction was performed for 937 highly variable genes across all the samples using the scran R package.
Counts were imputed using the knn-smoothing method.
Genome_build: mm10
Supplementary_files_format_and_content: Matrices of the batch corrected file after MNN correction
smooth.norm.txt
nuclei.meta.csv

source_name: Striatum

growth_protocol: Raised for 14-15 months under standard conditions

extract_protocol:
Mice were anesthetized using a phenobarbital based euthanasia solution and the straital tissue was dissected on ice. The samples were flash frozen, smashed into a thin layer, suspended in lysis buffer and disaggregated. The solution was filtered and centrifuged. Pellet was resuspended in 50% Iodixanol Solution, filtered again and placed on top of 29% Iodixanol Solution. The density barrier was centrifuged and the pellet was washed with 10 ml of PBS, 2% BSA and 1X RNAse Inhibitor. This was centrifuged again, suspended in 1 ml of PBS, 2% BSA, 1X RNAse Inhibitor and filtered using a 40 micron Flowmi cell strainer. The final solution was adjusted to 5000 nuclei/ml.
Sequencing libraries were generated using the Chromium Single Cell Gene Expression 3’ kit with Version 3 chemistries

value: Male

value: WT

value: Striatum


title: 14 month old HttQ175/+ striatum nuclei (BCR4)


title: 14 month old WT striatum nuclei (BCR6)


title: CN7_SMA_wt_p2_M14_LCM107

description:
LCM107
rpkms_SMA_LCMseq.txt


title: 14 month old WT striatum nuclei (BCR2)


title: CN3_SMA_ko_p10_M258_LCM253

description:
LCM253
rpkms_SMA_LCMseq.txt

value: Oculomotor/trochlear nuclei motor neurons


title: CN7_SMA_wt_p2_M28_LCM100

description:
LCM100
rpkms_SMA_LCMseq.txt

value: control


title: N_GRO_rep1

value: 3 weeks


title: D7_KrasG12D_R3-2_RNA-seq


title: 14 month old HttQ175/+ striatum nuclei (BCR1)


title: CN3_SMA_ko_p10_M196_LCM194

description:
LCM194
rpkms_SMA_LCMseq.txt


title: 14 month old HttQ175/+ striatum nuclei (BCR5)


title: 15 month old HttQ175/+ striatum nuclei (BBY2)


title: D7_KrasG12D_R3-1_RNA-seq


title: miRNA-seq_24MK34

description: Small RNA

data_processing:
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: miRBase 22.0
Supplementary_files_format_and_content: tab-delimited text files include sequence and expression of all miRNAs

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.


title: D7_KrasG12D_R2-3_RNA-seq


title: CN3CN4_SMA_ko_p10_M249_LCM218

description:
LCM218
rpkms_SMA_LCMseq.txt


title: miRNA-seq_24MK32

description: Small RNA


title: D7_KrasG12D_R2-2_RNA-seq


title: keloid tissues 12

city: Suzhou

first: Shuyu

last: Zhang

address: Ren Ai Road 199

institute: Suzhou University

data_processing:
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4)
Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change
Genome_build: Hg19
Supplementary_files_format_and_content: raw count

source_name: keloid tissues

growth_protocol: Keloid-derived primary cells were routinely cultured with DME/F-12 complete medium(include 10% FBS and 5% Penicillin and streptomycin antibody), in 37℃ 5% CO2  environment.

extract_protocol:
Total RNA was isolated using trizol.Total RNA (1 μg) was used for removing the rRNAs using NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA)  following the manufacturer's instructions
RNA libraries were constructed by using rRNA-depleted RNAs with NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
RNA-seq.10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

treatment_protocol: Keloid-derived primary cells that were isolated from patients, and then divided into three groups and each group had four repeats. The first group of cells was treated without radiation, the second group of cells were received 4 Gy delivered in 2-Gy fractions once per day over 2 days and the third group of cells were received 8 Gy delivered in 2-Gy fractions once per day over 4 days.The last two groups of cells were irradiated at a fixed rate of 1.15 Gy/min using an X-ray linear accelerator (Rad Source Technologies Inc., Suwanee, GA, USA). 24 hours post irradiation of the third group of cells, all keloid-derived primary cells were collected and subjected to mRNA expression analysis.

tag: treatment

value: keloid-derived primary cells with 2Gy×4 radiation

value: keloid-derived primary cells


title: keloid tissues 11


title: miRNA-seq_24MK31

description: Small RNA

value: kidney


title: CN3CN4_SMA_ko_p10_M199_LCM197

description:
LCM197
rpkms_SMA_LCMseq.txt


title: keloid tissues 10


title: D7_KrasG12D_R2-1_RNA-seq


title: miRNA-seq_12MK21

description: Small RNA

value: male

value: 12 month old


title: miRNA-seq_24MK35

description: Small RNA


title: CN4_SMA_wt_p10_M254_LCM252

description:
LCM252
rpkms_SMA_LCMseq.txt


title: D7_KrasG12D_R1-3_RNA-seq


title: CN3_SMA_wt_p10_M254_LCM247

description:
LCM247
rpkms_SMA_LCMseq.txt


title: miRNA-seq_12MK20

description: Small RNA


title: D7_KrasG12D_R1-2_RNA-seq


title: miRNA-seq_12MK19

description: Small RNA


title: CN3_SMA_wt_p10_M252_LCM230

description:
LCM230
rpkms_SMA_LCMseq.txt


title: keloid tissues 9


title: keloid tissues 8

value: keloid-derived primary cells with 2Gy×2 radiation


title: CN3CN4_SMA_ko_p10_M250_LCM234

description:
LCM234
rpkms_SMA_LCMseq.txt

value: SMA


title: keloid tissues 7


title: miRNA-seq_24MK33

description: Small RNA

value: 24 month old


title: CN3CN4_SMA_wt_p10_M253_LCM241

description:
LCM241
rpkms_SMA_LCMseq.txt


title: miRNA-seq_12MK18

description: Small RNA


title: D2_WT_R3-3_RNA-seq

source_name: ADM


title: CN3CN4_SMA_wt_p10_M252_LCM227

description:
LCM227
rpkms_SMA_LCMseq.txt


title: D2_WT_R3-2_RNA-seq


title: keloid tissues 5


title: CN3CN4_SMA_wt_p10_M247_LCM217

description:
LCM217
rpkms_SMA_LCMseq.txt


title: miRNA-seq_3MK9

description: Small RNA

value: 3 month old


title: D2_WT_R3-1_RNA-seq


title: keloid tissues 4

value: keloid-derived primary cells without radiation


title: miRNA-seq_3MK8

description: Small RNA


title: D2_WT_R2-3_RNA-seq


title: miRNA-seq_3MK7

description: Small RNA


title: keloid tissues 3


title: D7_KrasG12D_R1-1_RNA-seq


title: CN3CN4_SMA_ko_p5_M76_LCM78

description:
LCM78
rpkms_SMA_LCMseq.txt


title: D2_WT_R2-2_RNA-seq


title: CN3CN4_SMA_ko_p5_M61_LCM97

description:
LCM97
rpkms_SMA_LCMseq.txt


title: keloid tissues 2


title: keloid tissues 1


title: CN3CN4_SMA_ko_p5_M46_LCM93

description:
LCM93
rpkms_SMA_LCMseq.txt


title: miRNA-seq_3MK6

description: Small RNA


title: miRNA-seq_3MK5

description: Small RNA


title: CN3CN4_SMA_ko_p5_M31_LCM37

description:
LCM37
rpkms_SMA_LCMseq.txt


title: D2_WT_R2-1_RNA-seq


title: D2_WT_R1-3_RNA-seq


title: D2_WT_R1-2_RNA-seq


title: keloid tissues 6


title: miRNA-seq_12MK17

description: Small RNA


title: CN3CN4_SMA_ko_p5_M31_LCM36

description:
LCM36
rpkms_SMA_LCMseq.txt


title: D2_WT_R1-1_RNA-seq


title: CN3CN4_SMA_ko_p5_M77_LCM85

description:
LCM85
rpkms_SMA_LCMseq.txt


title: HRP2_KO_rep4

city: Leuven

first: Siska

last: Van Belle

state: Vlaams Brabant

address: Herestraat 49, bus 1023

country: Belgium

institute: KU Leuven

data_processing:
Sequencing of the cDNA library with 75 bp single end reads was performed using an Illumina NextSeq 500 system
Quality control of fastq files was done with FastQC and reads were aligned  using STARv2.42 and gencode as guide gtf
Counts were generated on the fly by STAR using GTF GRCm38 version 91 from Ensembl
Differential expression analysis was performed using DESeq2, which used Wald test statistic for p-value calculation
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed data files contain raw and DESeq2 normalized counts in txt format.

source_name: Hrp2-/- lin- BM cells

growth_protocol: lineage depleted cells from bone marrow

extract_protocol:
Aurum™ Total RNA Mini Kit, Biorad
Total RNA samples (500 ng) were purified using DNAse I kit according to the Rapid out removal DNA kit instructions (Thermoscientific) and converted into cDNA by using QuantSeq 3ʹ mRNA-seq reverse 4 Library Prep Kit (Lexogen) according to manufacturer’s instruction to generate compatible library for Illumina sequencing.

value: KO

value: lin- BM cells

tag: biological replicate


title: HRP2_WT_rep3

source_name: Hrp2+/+ lin- BM cells

value: WT


title: Fibro_KAT5_c.1105T_A

city: Montréal

first: Sophie

last: Ehresmann

state: Quebec

address: 110 Avenue des pins

country: Canada

institute: IRCM

description: Sequencing Strategy: Paired End, 100bp

data_processing:
Sequences were trimmed using Trimmomatic then aligned to GRCh37 using STAR. Duplicate and misaligned reads were discarded using Picard, and raw counts were called using HTSeq. Normalized counts are output from DESeq2 differential analysis.
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel file of normalized read counts

source_name: fibroblast

growth_protocol: Low passage fibroblasts were cultivated in DMEM (ThermoFisher), 10% FBS (VWR), 1mM GlutaMax (ThermoFisher), antibiotics-antimycotics (ThermoFisher).

extract_protocol:
Illumina Truseq V2 mRNA Stranded
RNA was extracted using Qiazol (Qiagen) and RNeasy kits (Qiagen), then subjected to Turbo DNAse treatment (Thermo).

value: fibroblast

tag: kat5 genotype

value: Affected

tag: replicate


title: Fibro_CTL_6

description: Sequencing Strategy: Paired End, 100bp

value: wildtype

value: Healthy


title: Fibro_CTL_5

description: Sequencing Strategy: Paired End, 100bp


title: D2_KrasG12D_R3-3_RNA-seq

value: Pdx1-cre; Klf5-mCherry-CreERT2; LSL-KrasG12D; R26RLSL-YFP


title: HRP2_KO_rep3


title: CN4_SMA_wt_p5_M30_LCM80

description:
LCM80
rpkms_SMA_LCMseq.txt

data_processing:
RNAseq reads were mapped simultaneously to the mm10 mouse genome assembly and the genomic sequence of human SMN2 (including introns) from the hg19 assembly using STAR (version 2.4.1c)
Expression levels were determined using the rpkmforgenes.py software (available at http://sandberg.cmb.ki.se/rnaseq).
Genome_build: mm10 + human SMN2 sequence (hg19 assembly)
Supplementary_files_format_and_content: text file with RPKM

extract_protocol:
Brains and spinal cords were quickly dissected and snap frozen in 2-Methylbutane on dry ice. Tissues were sectioned in a cryostat and mounted onto PEN membrane glass slides (Zeiss). Quick staining with Histogene (Arcturus/LifeTechnologies) followed by dehydration in rising EtOH concentrations was performed immediately prior to LCM. Individual cells were isolated using a Leica LMD7000 system. Approximately 150 cells were collected into one tube and lysis buffer was added (0.2% triton-X 100 with 2U/ul RNase inhibitor, Clontech) before snap freezing the samples on dry ice. (Nichterwitz et al. 2016)
Smart-seq2 combined with Tn5 tagmentation

value: Oculomotor/trochlear nuclei motor neurons

value: control


title: Fibro_CTL_4

description: Sequencing Strategy: Paired End, 100bp


title: Fibro_CTL_3

description: Sequencing Strategy: Paired End, 100bp


title: CN3_SMA_wt_p5_M75_LCM60

description:
LCM60
rpkms_SMA_LCMseq.txt


title: D2_KrasG12D_R3-2_RNA-seq


title: D2_KrasG12D_R3-1_RNA-seq


title: HRP2_KO_rep2


title: HRP2_KO_rep1


title: CN3_SMA_wt_p5_M30_LCM79

description:
LCM79
rpkms_SMA_LCMseq.txt


title: Fibro_KAT5_c.1237T_G_rep2

description: Sequencing Strategy: Single End, 100bp

extract_protocol:
Illumina Truseq RNA V2
RNA was extracted using Qiazol (Qiagen) and RNeasy kits (Qiagen), then subjected to Turbo DNAse treatment (Thermo).


title: HRP2_WT_rep2


title: CN3_SMA_wt_p5_M29_LCM47

description:
LCM47
rpkms_SMA_LCMseq.txt


title: HRP2_WT_rep1


title: Fibro_KAT5_c.1237T_G_rep1

description: Sequencing Strategy: Single End, 100bp


title: Fibro_CTL_2_rep2

description: Sequencing Strategy: Single End, 100bp


title: CN3CN4_SMA_wt_p5_M71_LCM55

description:
LCM55
rpkms_SMA_LCMseq.txt


title: Fibro_CTL_2_rep1

description: Sequencing Strategy: Single End, 100bp


title: D2_KrasG12D_R2-1_RNA-seq

extract_protocol:
Mouse pancreases were digested into single cell suspensions as previously described (Reichert et al., 2013a)
Library preparation was performed using Smart-seq2 as described (Picelli et al., 2013) Using VAHTS mRNA-seq V3 Library Prep Kit (Vazyme, NR611)


title: D2_KrasG12D_R2-2_RNA-seq


title: CN4_SMA_wt_p5_M75_LCM59

description:
LCM59
rpkms_SMA_LCMseq.txt


title: CN3CN4_SMA_ko_p2_M38_LCM157

description:
LCM157
rpkms_SMA_LCMseq.txt


title: D2_KrasG12D_R1-3_RNA-seq


title: D2_KrasG12D_R1-2_RNA-seq


title: Fibro_CTL_1_rep1

description: Sequencing Strategy: Single End, 100bp


title: CN3CN4_SMA_ko_p2_M211_LCM181

description:
LCM181
rpkms_SMA_LCMseq.txt


title: D2_KrasG12D_R1-1_RNA-seq


title: siHDAC9_Poly_IC_S49

city: La Jolla

first: Richard

middle: L

last: Gallo

state: California

address: 9500 Gilman Drive

department: Dermatology

institute: University of California San Diego

description: si HDAC9 Poly:IC

data_processing:
Isolated total RNA was submitted to the UCSD IGM Genomics Center for analysis by a Tapestation bioanalyzer (Agilent, LA Jolla, CA). Samples with RIN values of 9.0 and above were utilized for Illumina library preparation and subsequent RNA-sequencing using a high-output run V4 platform (Illumina, San Diego, USA) with a single read 100 cycle runs. Subsequent analysis was done on Partek flow software (Partek, St. Louis, MO) using the Tophat2 aligner (version 2.0.8) quantifying to the transcriptome using the mm10_RefSeq Transcripts 16_08_01_v2.
Supplementary_files_format_and_content: abundance measurements

source_name: Keratinocytes

growth_protocol: nHEK cells were cultured on uncoated plastic 6-well plate in EpiLife (Thermo Fisher Scientific) supplemented with EpiLife defined growth factor (Thermo Fisher Scientific).

extract_protocol:
HDAC8 and HDAC9 in nHEK were knocked down using Silencer Select siRNA (Thermo Fisher Scientific). After siRNA treatment for 16 hours, siRNA-treated was recovered for 48 to 72 hours before further experiments.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 24 hours after Poly:IC stimulation

tag: tag

value: Keratinocytes

tag: sirna

value: si HDAC9

tag: agent


title: CN3CN4_SMA_ko_p2_M207_LCM172

description:
LCM172
rpkms_SMA_LCMseq.txt


title: D0_WT_R2-3_RNA-seq

data_processing:
The adapters of paired-end reads were trimmed and quality control check were carried out using trim-galore (version 0.6.0). Reads were aligned to mouse genome reference (GRCm38.p6) from GENCODE using HISAT2 (version 2.1.0). Aligned reads stored in SAM format were manipulated to generate bam files using SAMtools (version 1.9) with parameter is “samtools view –b –h –F 4 –f 3”. featureCounts (version 1.6.3) counted reads stored in BAM format to exon sites of genes included in GTF file from GENCODE. Differential gene expression analysis was processed which used raw counts  as input using R (version 3.5.1) package DESeq2 (version 1.22.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts in each sample

source_name: pancreatic normal duct cell


title: siHDAC8_Poly_IC_S48

description: si HDAC8 Poly:IC

value: si HDAC8


title: CN3CN4_SMA_ko_p2_M206_LCM167

description:
LCM167
rpkms_SMA_LCMseq.txt

value: SMA


title: D2_KrasG12D_R2-3_RNA-seq


title: CN3CN4_SMA_ko_p2_M16_LCM115

description:
LCM115
rpkms_SMA_LCMseq.txt


title: siHDAC9_S46

description: si HDAC9


title: JQ-1_Rep3

city: Chiba

first: Yoshitoshi

last: Kasuya

address: 1-8-1 Inohana Chuo-ku

department: Grad. Sch. Med

country: Japan

institute: Chiba Univ.

data_processing:
Reads were mapped on hg19 human reference genome and quantified using CLC Genomics Workbench version 10.1.1 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0. (Qiagen).
Filtering characteristics of fold-change -2 to 2 (false discovery rate (FDR) at P < 0.05) were used to identify the DEGs.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

source_name: Human myofibroblasts

growth_protocol: Lung tissue from a 46-y old male patient who underwent lung transplantation by reason of severe IPF (usual interstitial pneumonia pattern) was obtained after surgery. The patient provided informed consent, and the study was approved by the Ethics Committee of Chiba University, Graduate School of Medicine and Hospital, Japan. Lung tissue was minced into small pieces, and then were incubated in DMEM supplemented with 1 mg/ml collagenase type I, 0.5 mg/ml dispase, 2 U/ml DNase, 0.1 mg/ml streptomycin, and 100 U/ml penicillin at 37°C for 15 min with gentle shaking. After washing twice with DMEM, the resulting pieces were transferred to a 90 mm-culture dish and were dipped with culture medium (10% FBS in DMEM supplemented with streptomycin and penicillin) and cultured at 37°C and 5% CO2. Outgrowth of cells was monitored daily with changing the culture medium every 4 d. When the dish reached confluence (about 14 days in vitro), outgrown cells were harvested as cells at passage 0. Expanded cells at passage 3 were subjected to the immunofluorescent study to verify population of α-SMAhighED-A-FN+S100A4- cells as myofibroblasts. More than 90% of the cells were myofibroblasts.

extract_protocol:
Total RNA of the cells was extracted using ISOGEN plus (Nippon Gene, Toyama, Japan) according to manufacturer instructions. 500 ng of total RNA were ribosomal RNA-depleted using NEBNext rRNA Depletion Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Expanded myofibroblasts at passage 5 were used for the following experiments. After 24 h of serum deprivation in DMEM containing 0.2% fat-free bovine serum albumin, myofibroblasts were treated with or without JQ1 (1 µM) for a further 48 h.

value: Lung of Idiopathic pulmonary fibrosis patient

value: Lung

tag: cell type

value: myofibroblasts


title: CN3CN4_SMA_wt_p2_M28_LCM105

description:
LCM105
rpkms_SMA_LCMseq.txt

tag: genotype


title: JQ-1_Rep2

tag: strain


title: D0_WT_R1-3_RNA-seq


title: CN3CN4_SMA_wt_p2_M26_LCM101

description:
LCM101
rpkms_SMA_LCMseq.txt


title: siControl_S44

description: si Control

value: si Control


title: JQ-1_Rep1


title: D0_WT_R1-2_RNA-seq


title: Fibro_CTL_1_rep2

description: Sequencing Strategy: Single End, 100bp

tag: disease state


title: D0_WT_R2-1_RNA-seq


title: CN3CN4_SMA_ko_p2_M209_LCM183

description:
LCM183
rpkms_SMA_LCMseq.txt


title: D0_KrasG12D_R2-3_RNA-seq


title: siHDAC8_S45

description: si HDAC8


title: 10x scATAC-seq of para-tumor from P2

data_processing:
Raw data was processed by cellranger-atac  (1.1.0) from 10X genomics website.
Genome_build: GRCh38
Supplementary_files_format_and_content: peak

source_name: para-tumor tissue

extract_protocol:
Fresh specimens of control pancreases and PDAC were collected at the time of surgical resection under the supervision of a qualified pathologist. Tissues were transported in RPMI 1640 with 1 mM protease inhibitor on ice to preserve viability, washed 2–3 times with phosphate buffered saline , then minced on ice. We used dissociation enzyme cocktail 1 mg/ml Type VIII Collagenase 2 mg/ml Dispase II, 1 mg/ml Trypsin Inhibitor and 1 unit/ml DNase I dissolved in PBS with 5% Fetal Bovine Serum to digest the tissues. Neoplastic tissues were dissociated at 37 °C with a shaking speed of 50 r.p.m for about 40 min. We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield and viability. As for control pancreases, minced tissues were incubated with the same digestion buffer at 37 °C without shaking for about 40 min. We repeatedly collected the dissociated cells at interval of 10 min. Cell suspensions were fifiltered using a 40 μm nylon cell strainer and red blood cells (RBC) were removed by RBC. Dissociated cells were washed with PBS containing 0.04% Bovine Serum Albumin with step by step descending centrifuging speed and increasing time. Cells were stained with 0.4% Trypan blue to check the viability, and then diluted with PBS containing 0.04% BSA to about 5 × 106 cells/ml for single cell ATAC sequencing.Nuclei Isolation is totally followed by demonstrated protocol Nuclei Isolation for Single Cell ATAC Sequencing from 10xgenomics official website.Targeted Nuclei Recovery number is 1 × 104 performed by CG000168_Chromium Single Cell ATAC_Reagent Kits User Guide from 10xgenomics official website.
CG000168_Chromium Single Cell ATAC_Reagent Kits

tag: tissue/cell type

value: pancreatic para-tumor tissue


title: CN3CN4_SMA_wt_p2_M244_LCM210

description:
LCM210
rpkms_SMA_LCMseq.txt

tag: tissue


title: CN3CN4_SMA_wt_p2_M14_LCM109

description:
LCM109
rpkms_SMA_LCMseq.txt

tag: age (days)


title: RN_SMA_ko_p10_M258_LCM254

description:
LCM254
rpkms_SMA_LCMseq.txt

source_name: Red nucleus neurons

value: Red nucleus neurons

tag: group


title: siControl_Poly_IC_S47

description: si Control Poly:IC


title: NC_Rep3


title: D0_KrasG12D_R2-2_RNA-seq


title: 10x scATAC-seq of normal from P1

source_name: pancreatic normal tissue

value: pancreatic normal tissue


title: RN_SMA_ko_p10_M249_LCM219

description:
LCM219
rpkms_SMA_LCMseq.txt

tag: mouse id


title: D0_KrasG12D_R2-1_RNA-seq


title: D0_WT_R2-2_RNA-seq


title: D0_KrasG12D_R1-3_RNA-seq


title: D0_WT_R1-1_RNA-seq


title: RN_SMA_ko_p10_M196_LCM193

description:
LCM193
rpkms_SMA_LCMseq.txt


title: D0_KrasG12D_R1-2_RNA-seq


title: Donor1

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: scRNA-seq

data_processing:
Read alignment and gene-expression quantification of human single-cell RNA-seq (scRNA-seq) and single-nuclear RNA-seq (snRNA-seq) data were performed using Cell Ranger version 2.0.0/3.0.2 pipeline (10x Genomics).
For scRNA-seq alignment and quantification, Cell Ranger pre-built human (hg19) reference package was used. For snRNA-seq alignment and quantification, a Cell Ranger compatible human (hg19) "pre-mRNA" reference package was generated according to Cell Ranger’s instructions
Genome_build: hg19
Supplementary_files_format_and_content: tar file containing  barcodes.tsv, genes.tsv,  matrix.mtx

source_name: Normal control

extract_protocol:
Single-cell and single-nuclei suspensions were processed through the 10X Chromium to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA was prepared for sequencing using a modified Nextera XT protocol
single-cell RNA-seq, single-nuclear RNA-seq

tag: subject status

value: Normal control

value: lung


title: RN_SMA_wt_p10_M254_LCM248

description:
LCM248
rpkms_SMA_LCMseq.txt


title: Normal uterus

description: snRNA-seq

value: Uterus


title: NC_Rep2


title: D0_KrasG12D_R1-1_RNA-seq


title: RN_SMA_wt_p10_M253_LCM242

description:
LCM242
rpkms_SMA_LCMseq.txt


title: AML

description: scRNA-seq

source_name: AML patient_kidney

value: AML patient

value: kidney


title: Klf5+KrasG12D_ChIP

data_processing:
The adapters of paired-end reads were trimmed and quality control checks were carried out using trim-galore (version 0.6.0). Trimmed reads were aligned to mouse genome reference (GRCm38.p6) from GENCODE using bowtie2 (version 2.3.4.3) of which the parameter is “–very-sensitive –X 2000”. Aligned reads stored in SAM format were manipulated to generate bam files using samtools (version 1.9) with parameter is “samtools view –b –h –F 1028 –f 3”. Peaks of ChIP-seq were called using MACS2 (version 2.1.2) using the parameter “macs2 callpeak --verbose 3 -g mm -B -q 1e-3 -f BEDPE”. Analysis of differential peaks intensity was processed using MAnorm (version 1.1.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deeptools

source_name: pancreatic adenocarcinoma

growth_protocol: To KrasG12D cell line: DMEM+10%FBS+1%P/S+1ug/ml Doxycycline; PDA cell line:DMEM+10%FBS+1%P/S

extract_protocol:
Briefly, cells were crosslinked at room temperature for 10 min with 1% formaldehyde,  washed twice with PBS and sonicated in lysis buffer (50 mM HEPES/KOH pH 7.5, 140  mM NaCl, 0.1% Na-Deoxycholate, 1% Triton X-100, 1 mM EDTA, complete protease  inhibitor cocktail). Samples were immunoprecipitated at 4 ºC overnight and washed six  times with ChIP wash buffer (20 mM Tris, pH 7.9, 500 mM NaCl, 2 mM EDTA, 1% Triton  X-100, 0.1% SDS) and once with TE buffer. Bound DNA was eluted in 1% SDS buffer  and reverse-crosslinked for 6 h at 65 ºC
DNA samples were treated sequentially with  RNase A and Protease K and then purified with ChIP DNA Clean & Concentrator-5  (Zymo Research, D4014)

treatment_protocol: To KrasG12D cell line: +KrasG12D means treatment with Dox;-KrasG12D  means No Dox add.PDA cell line:+KrasG12D means endogenous KrasG12D expression.

value: pancreatic adenocarcinoma cancer Tet-on KrasG12D cell line

tag: chip antibody

value: anti-Klf5 (Abcam, ab137676)


title: LAM4

description: snRNA-seq

source_name: LAM patient_lung

value: Lymphangioleiomyomatosis (LAM) patient


title: NC_Rep1


title: RN_SMA_wt_p10_M252_LCM231

description:
LCM231
rpkms_SMA_LCMseq.txt

value: control


title: Klf5-KrasG12D_ChIP


title: LAM3

description: scRNA-seq


title: RN_SMA_ko_p10_M199_LCM198

description:
LCM198
rpkms_SMA_LCMseq.txt

value: SMA


title: Junb+KrasG12D_ChIP

value: pancreatic adenocarcinoma cancer cell line

value: anti-Junb (Cell Signaling, #3753)


title: CDHFD_primary hepatocytes_S phase synchronized, rep1

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® ClariomS Mouse (LifeTechnologies) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.  RMA normalization is performed using R with Version 22 of Entrezgene CDF brain array.

label: biotin

source_name: CDHFD 1

label_protocol: 100 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Affymetrix) .  Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix). After purification according to Affymetrix protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled.

growth_protocol: Hepatocyte primary culture were growth in Williams medium supplemented with 10% FBS, 100U/mL of penicillin/Streptomycin, 100ug/mL of fungizone antimycotic B, 4ug/mL of Insulin, 25nM of Dexamethasone; and synchronized in the cell cycle with 50ng/mL of Epidermal growth factor and 20mM of pyruvate dodium.

extract_protocol: RNA extracted according to standard trizol procedures

tag: gender

value: male

value: primary hepatocytes culture

tag: diet

value: CDHFD


title: CDHFD_primary hepatocytes_S phase synchronized, rep2

source_name: CDHFD 2


title: CDHFD_primary hepatocytes_S phase synchronized, rep3

source_name: CDHFD 3


title: LAM2

description: scRNA-seq


title: 10x scATAC-seq of tumor 1 from P1

source_name: PDAC

value: PDAC tumor tissue


title: RN_SMA_wt_p10_M247_LCM233

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

institute: Stockholm University

description:
LCM233
rpkms_SMA_LCMseq.txt

value: Red nucleus neurons


title: HFHS_primary hepatocytes_S phase synchronized, rep3

source_name: HFHS 3

value: HFHS


title: HFHS_primary hepatocytes_S phase synchronized, rep2

source_name: HFHS 2


title: RN_SMA_ko_p5_M77_LCM84

description:
LCM84
rpkms_SMA_LCMseq.txt


title: Junb_input_ChIP


title: LAM1

description: scRNA-seq

value: lung


title: RN_SMA_ko_p5_M76_LCM77

description:
LCM77
rpkms_SMA_LCMseq.txt


title: hTert rep4

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

institute: Francis Crick Institute

description:
Processed data file: deseq2_counts.txt
Processed data file: rnaseq_C15vsHTERT_R2R3R4.deseq2.refseq.results_INVITRO.xlsx

data_processing:
Reads were aligned using Tophat2 and counted using featureCounts.
Only reversely-stranded fragments (instead of individual paired end reads) that have both ends successfully aligned were counted, grouped by gene id and ignoring chimeric fragments (on separate chromosomes).
Count data was filtered to remove lowly expressed transcripts (quantile of rowsums at 0.3), and normalised and analysed for differential expression using DESeq2. Data was annotated to hg19 using biomaRt.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: deseq2_counts.txt: Tab-delimited text file includes raw counts for each Sample.
Supplementary_files_format_and_content: rnaseq_C15vsHTERT_R2R3R4.deseq2.refseq.results_INVITRO.xlsx: Excel file includes DESeq2 differential gene expression.

source_name: hTERT immortalised human skin fibroblasts

growth_protocol: Cells were grown in minimum essential medium (MEM) containing 15% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2.

extract_protocol:
RNA extraction was performed using the RNeasy Plus Micro Kit (Qiagen).
Stranded total RNA sequencing was performed on rRNA-depleted samples (Ribozero Gold, Epigentre Madison). RNA library quality was assessed on a Picochip BioAnalyser 2100 chip (Agilent), and sequenced on an Illumina HiSeq2500 sequencer with 101bp paired-end reads.

treatment_protocol: SSEA1+ cells were isolated by cell sorting from a population of in vitro-transformed fibroblasts derived from hTERT-immortalized skin fibroblasts.

tag: phenotype

value: Non-tumourigenic

tag: treatment

value: No treatment


title: RN_SMA_ko_p5_M61_LCM98

city: Stockholm

description:
LCM98
rpkms_SMA_LCMseq.txt


title: HFHS_primary hepatocytes_S phase synchronized, rep1

source_name: HFHS 1


title: H3K4me+KrasG12D_ChIP

value: anti-H3K4me1 (ab8895)


title: RN_SMA_ko_p5_M31_LCM39

description:
LCM39
rpkms_SMA_LCMseq.txt


title: Control_primary hepatocytes_S phase synchronized, rep2

source_name: SD 2

value: Control


title: hTert rep3

value: hTERT immortalised human skin fibroblasts


title: H3K4me_Klf5_H3K27ac_input+KrasG12D_ChIP

value: pancreatic adenocarcinoma cancer Tet-on KrasG12D cell line


title: 130b Legionella pneumophila infected Acanthamoeba castellanii_24h_2

city: Melbourne

first: Shivani

last: Pasricha

address: 792 Elizabeth Street

department: Microbiology and Immunology

country: Australia

institute: Peter Doherty Institute

data_processing:
raw fastq files were aligned to the Acanthamoeba castellanii (Neff) genome using Hisat2
reads mapping to genes were counted using featureCounts
differential gene expression analysis was performed using DESeq2
Genome_build: Acanthamoeba castellanii (Neff)
Supplementary_files_format_and_content: raw counts table from featureCounts

organism: Acanthamoeba castellanii

source_name: A. castellanii cells

growth_protocol: 2 × 105 A. castellanii were seeded in technical and biological triplicate in PYG medium in 24-well plates (4 × 105 cells per ml) and incubated for 24 h at RT. A. castellanii was then washed with minimal medium to remove non-adherent cells followed by L. pneumophila infection with MOI of 50 (Coil et al., 2008). After 1 h incubation at 37 ℃ with 5% CO2, cells were washed with minimal medium and incubated in fresh PYG medium at 37 ℃ with 5% CO2.

extract_protocol:
For RNA-sequencing analysis RNA was isolated from A. castellanii using TRIsure™ (Bioline) according to manufacturer’s instructions at 3 h, 8 h, 16 h and 24 h post infection.
cDNA library preparation and sequencing was carried out as described previously (Tanaka et al., 2013). Briefly, 1µg RNA was used for poly(A) selection and cDNA libraries were prepared using the Illumina sample preparation kit. 100 base pair paired-end sequencing was performed on the HiSeq 2500 (Illumina) platform, with the use of TruSeq Stranded mRNA LT sample Prep Kit (IIIumina) according to manufacturer’s instructions

treatment_protocol: A. castellanii trophozoites were left uninfected or infected with wild type L. pneumophila or the isogenic DdotA mutant for 3 h, 8 h (early infection), 16 h (mid infection) or 24 h (late infection).

value: Acanthamoeba castellanii (Neff)

tag: l.pn infection

value: WT 130b L.pnuemophila

tag: hours of infection


title: H3K4me_Klf5_H3K27ac_input-KrasG12D_ChIP

city: Beijing

first: Yi

last: He

address: 30 Shuangqing Rd, Haidian Qu, Beijing Shi, China

institute: Tsinghua university

tag: cell type


title: Control_primary hepatocytes_S phase synchronized, rep3

source_name: SD 3


title: Control_primary hepatocytes_S phase synchronized, rep1

source_name: SD 1


title: hTert rep2


title: 130b Legionella pneumophila infected Acanthamoeba castellanii_16h_3


title: 130b Legionella pneumophila infected Acanthamoeba castellanii_24h_1