title: sncRNA organ atlas, Homo sapiens, heart-pericardium_3

value: heart-pericardium


title: sncRNA organ atlas, Homo sapiens, muscle_5

status: Public on Dec 19 2021

type: SRA

city: Saarbrücken

first: Tobias

last: Fehlmann

address: Campus E2 1

country: Germany

institute: Saarland University

library_source: transcriptomic

data_processing:
We performed the primary data analysis using a stand-alone version of our web-based tool miRMaster, version 1.1. We carried out all analyses using the standard parameter settings as in the online version, allowing one mismatch in the quantification of ncRNAs. The following ncRNA databases are included in our analysis: miRBase version 22.1, Ensembl ncRNA version 100, RNACentral version 15 and GtRNAdb version 18.1.
Adapters at the 3′ end were trimmed, while allowing an error of maximum one base and requiring a minimum overlap with the read of 10 bases. Reads were quality trimmed when the average quality dropped below 20 in a window of four consecutive bases to ensure a high quality of reads used for the downstream processing. All reads shorter than 17 bases after trimming were discarded from all further analyses.
MiRNAs were quantified with up to one mismatch and a variability of two bases allowed at the 5′ end and five bases at the 3′ end.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: sncRNA_counts_human.txt: tab-delimited text file containing the RPMM normalized counts of all quantified sncRNAs in the human samples.
Supplementary_files_format_and_content: sncRNA_counts_mouse.txt: tab-delimited text file containing the RPMM normalized counts of all quantified sncRNAs in the mouse samples.

molecule: total RNA

organism: Homo sapiens

growth_protocol: The bodies were stored at 4°C upon arrival at the anatomical institute and tissue samples were collected between 8 and 48 hours post-mortem. To increase the resolution for selected organs, e.g. brain or intestine, further dissection of these organs was performed to include several subareas. After collection, samples were immediately stored in RNALater (Sigma-Aldrich) or frozen at -80 °C to prevent further degradation. Mice tissues were prepared as described for GSE132042.

extract_protocol:
Total RNA including smallRNAs was isolated using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendations. In brief, tissues were lysed and homogenized in 700 µl QIAzol Lysis Reagent using 5 mm stainless steel beads and the TissueLyser LT (Qiagen) for 5 min at 50 Hz. After 5 min incubation, samples were mixed with 140 µl chloroform and phase separation was performed at 12000 x g and 4 °C for 15 min. The RNA in the aqueous phase was precipitated by adding 1.5 Volume of 100 % ethanol and purified using the RNeasy columns provided with the kit, either manually or semi-automated using the Qiacube instrument with the respective protocols provided for the miRNeasy Mini kit.
We performed library preparation for sequencing on the BGISEQ-500RS following the instructions of the MGIEasy Small RNA Library Prep Kit (MGI Technologies). To limit the bias the manual library preparation performed previously was replaced by a semi-automated workflow on the MGI-SP100. In general, 100 ng total RNA was used as input material for the library preparation. The library construction includes of 3’ adapter ligation, 3’ adapter digestion, 5’ adapter ligation followed by reverse transcription (RT) of RNA into cDNA using RT primers which contained specific barcodes. Next, cDNA was amplified by PCR in 22 cycles. The PCR products were separated using 6 % TBE gels and bands of the size around 110 bp were cut from the gel.  After purification, the DNA yield was measured with the Qubit® 1xdsDNA HS Assay Kit (Invitrogen). A total of 16 different barcoded samples were pooled together in equal amounts and circularized to generate a single-stranded DNA library. The BGISEQ-500RS uses DNA nanoballs (DNBs) for sequencing, which were generated by rolling circle amplification (RCA). DNBs were then loaded into the patterned nanoarray using the BGIDL-50 DNB loader. Finally, single-end sequencing was performed on the BGISEQ-500RS using the High-throughput Sequencing Set (SE50) (Small RNA) according to the manufacturer’s instructions. The mouse samples have been processed with an advanced pipeline using the higher-throughput SP-960 sample prep system and MGISEQ-400 sequencing system. In the latter case we made further use of the CoolMPS sequencing chemistry.

tag: strain

value: Not applicable

tag: age (years)

tag: developmental stage

value: adult

tag: Sex

value: female

tag: tissue

value: muscle


title: sncRNA organ atlas, Homo sapiens, brain-occipital lobe_1

source_name: brain-occipital lobe_1

value: male

value: brain-occipital lobe


title: sncRNA organ atlas, Homo sapiens, kidney_1 (3)

source_name: kidney_1 (3)

value: kidney


title: sncRNA organ atlas, Homo sapiens, lung_2

value: lung


title: sncRNA organ atlas, Homo sapiens, stomach_5

value: stomach


title: sncRNA organ atlas, Homo sapiens, brain-parietal lobe_3

source_name: brain-parietal lobe_3

value: brain-parietal lobe


title: sncRNA organ atlas, Homo sapiens, brain-temporal lobe_2

source_name: brain-temporal lobe_2

value: brain-temporal lobe


title: sncRNA organ atlas, Homo sapiens, heart-atrium_4 (2)

source_name: heart-atrium_4 (2)

value: heart-atrium


title: sncRNA organ atlas, Homo sapiens, artery_6

value: artery


title: sncRNA organ atlas, Homo sapiens, pleurae_5

value: pleurae


title: sncRNA organ atlas, Homo sapiens, brain-pituitary gland_1

source_name: brain-pituitary gland_1

value: brain-pituitary gland


title: sncRNA organ atlas, Homo sapiens, thyroid_2

value: thyroid


title: sncRNA organ atlas, Homo sapiens, skin_4

value: skin


title: sncRNA organ atlas, Homo sapiens, kidney_1 (2)

source_name: kidney_1 (2)

value: Not applicable


title: sncRNA organ atlas, Homo sapiens, testis_4

value: adult

value: testis


title: sncRNA organ atlas, Homo sapiens, brain-substantia nigra_2 (2)

source_name: brain-substantia nigra_2 (2)

value: brain-substantia nigra


title: sncRNA organ atlas, Homo sapiens, kidney_4

value: male


title: sncRNA organ atlas, Homo sapiens, bowel-jejunum_1

value: bowel-jejunum


title: sncRNA organ atlas, Homo sapiens, nerve_2 (2)

source_name: nerve_2 (2)

value: nerve


title: sncRNA organ atlas, Homo sapiens, adrenal gland_3

source_name: adrenal gland_3

value: female

value: adrenal gland


title: sncRNA organ atlas, Homo sapiens, brain-hippocampus_2

value: brain-hippocampus


title: sncRNA organ atlas, Homo sapiens, bone_1

value: bone


title: sncRNA organ atlas, Homo sapiens, trachea_4 (2)

source_name: trachea_4 (2)

value: trachea


title: sncRNA organ atlas, Homo sapiens, heart-muscle_1

value: heart-muscle


title: sncRNA organ atlas, Homo sapiens, bladder_4

value: bladder


title: sncRNA organ atlas, Homo sapiens, brain-cerebellum_1

value: brain-cerebellum


title: sncRNA organ atlas, Homo sapiens, heart-muscle_6


title: sncRNA organ atlas, Homo sapiens, skin_3


title: sncRNA organ atlas, Homo sapiens, brain-pituitary gland_3

source_name: brain-pituitary gland_3

value: brain-pituitary gland


title: sncRNA organ atlas, Homo sapiens, spleen_3

value: spleen


title: sncRNA organ atlas, Homo sapiens, testis_6

value: Not applicable


title: sncRNA organ atlas, Homo sapiens, adrenal gland_1

source_name: adrenal gland_1

value: adult


title: sncRNA organ atlas, Homo sapiens, brain-white matter_2 (1)

source_name: brain-white matter_2 (1)

value: brain-white matter


title: sncRNA organ atlas, Homo sapiens, pleurae_3

value: pleurae


title: sncRNA organ atlas, Homo sapiens, brain-white matter_1

source_name: brain-white matter_1

value: male


title: sncRNA organ atlas, Homo sapiens, bowel-duodenum_1

value: bowel-duodenum


title: sncRNA organ atlas, Homo sapiens, brain-nucleus caudatus_1

source_name: brain-nucleus caudatus_1

value: brain-nucleus caudatus


title: P9m9

city: Boston

first: Vadim

middle: N.

last: Gladyshev

state: MA

address: 77 Avenue Louis Pasteur

department: Department of Medicine

country: USA

institute: Brigham and Women's Hospital and Harvard Medical School

library_source: genomic

data_processing:
Reads were trimmed and quality filtered by TrimGalore! using the --rrbs option for RRBS.
Methylation levels were extracted using Bismark with Bowtie 2 mapping to the NMR genome (HetGla_female_1.0).
As the number of contigs exceeded the maximum allowed to be used in mapping, we concatenated short contigs (less than 1,000,000 bp) into a pseudocontig separated by 1,000 ‘N’.
For further analysis, we used only the CpG sites that are covered by at least 5 reads in at least 90% of the samples.
Genome_build: HetGla_female_1.0
Supplementary_files_format_and_content: Bismark coverage (cov) files containing read coverage and methylation level of each CpG site

molecule: genomic DNA

organism: Heterocephalus glaber

source_name: Blood

extract_protocol:
To collect blood, animals were placed headfirst into a plastic restraining cone (decapicone, Braintree Scientific) such that the tail remained accessible outside of the cone. The tail was then positioned on a benchtop, ventral side up. A sterile razor blade was used to make a superficial incision across the ventral surface of the tail about halfway between the body and end of the tail. The incision induced bleeding from the tail vein. The animal was then positioned above a blood collection tube (BD Microtainer, tubes with K2EDTA, Becton, Dickinson and Company) so that blood drops from the incision were collected into the collection tube. The collected blood was immediately snap-frozen. After the blood collection, gentle pressure was applied to the tail incision site for one to two minutes to stop further bleeding. The blood DNA was extracted by DNeasy Blood & Tissue Kit (Qiagen 69506) and cleaned up using RNase treatment followed by concentration. The DNA was eluted from Qiagen columns in 100 µl of 10 mM Tris-HCl buffer, pH 8.0. RNA removal was performed with 2 µl of RNase A (Life Technologies) at room temperature for 2 minutes and isolated genomic DNA was purified using Genomic DNA Clean & Concentrator™-10 (Zymo D4011), eluted in 25 µl of 10 mM Tris-HCl buffer, pH 8.0, and quantified using a Qubit 2.0 (Life Technologies AM2271).
RRBS libraries were prepared from 100 ng of purified DNA per sample following a protocol described in Petkovich et al. 2017. The libraries were sequenced with Illumina HiSeq2500, PE150. 20% of PhiX genomic DNA was spiked to compensate for the low complexity of the libraries.

tag: breeding status

value: Non-breeder

tag: colony

value: Park

tag: lab

value: Thomas Park

tag: date of collection

value: Blood


title: P9m6


title: P9m5


title: sncRNA organ atlas, Homo sapiens, liver_1

value: liver


title: sncRNA organ atlas, Homo sapiens, muscle_1

value: muscle


title: sncRNA organ atlas, Homo sapiens, nerve_1

value: nerve


title: P9m4


title: sncRNA organ atlas, Homo sapiens, pancreas_3

value: female

value: pancreas


title: P9m3


title: P9m12


title: P9m2


title: sncRNA organ atlas, Homo sapiens, lung_1

value: lung


title: sncRNA organ atlas, Homo sapiens, stomach_3

value: Not applicable

value: stomach


title: P5y2


title: sncRNA organ atlas, Homo sapiens, kidney_1 (1)

source_name: kidney_1 (1)

value: adult

value: kidney


title: P9m11


title: sncRNA organ atlas, Homo sapiens, brain-grey matter_1

source_name: brain-grey matter_1

value: male

value: brain-grey matter


title: sncRNA organ atlas, Homo sapiens, brain-nucleus caudatus_2

source_name: brain-nucleus caudatus_2

value: brain-nucleus caudatus


title: sncRNA organ atlas, Homo sapiens, spleen_1

value: spleen


title: P5y1

value: Non-breeder

value: Park


title: sncRNA organ atlas, Homo sapiens, liver_4 (2)

source_name: liver_4 (2)


title: sncRNA organ atlas, Homo sapiens, lymph node_4 (2)

source_name: lymph node_4 (2)

value: lymph node


title: P5d2

value: Thomas Park

value: Blood


title: P4y3


title: P4y2


title: sncRNA organ atlas, Homo sapiens, skin_5

value: skin


title: sncRNA organ atlas, Homo sapiens, stomach_2


title: P5d1


title: sncRNA organ atlas, Homo sapiens, esophagus_3

value: female

value: esophagus


title: P30d1


title: P30d2


title: P2w1


title: sncRNA organ atlas, Homo sapiens, artery_3

value: artery


title: sncRNA organ atlas, Homo sapiens, adipocyte_1

value: Not applicable

value: adipocyte


title: P27d1


title: sncRNA organ atlas, Homo sapiens, lymph node_1

source_name: lymph node_1

value: adult


title: G88

tag: gender

value: Female

value: Vera Gorbunova


title: G90

value: Male


title: sncRNA organ atlas, Homo sapiens, testis_1

value: male

value: testis


title: P18d1

value: Non-breeder


title: sncRNA organ atlas, Homo sapiens, pleurae_1

value: pleurae


title: sncRNA organ atlas, Homo sapiens, bladder_6

value: bladder


title: sncRNA organ atlas, Homo sapiens, brain-temporal lobe_3

source_name: brain-temporal lobe_3

value: brain-temporal lobe


title: G86

value: Blood


title: G85


title: sncRNA organ atlas, Homo sapiens, lung_4 (2)

value: lung


title: P3y1nbm

description: P3y1nbm_CKDL190140058-1B-15_H3W52CCX2_L1

value: Park

value: Thomas Park


title: sncRNA organ atlas, Homo sapiens, lymph node_4 (1)

source_name: lymph node_4 (1)

value: lymph node


title: sncRNA organ atlas, Homo sapiens, prostate_1

value: Not applicable

value: prostate


title: G83

value: Queen


title: G84

value: Female


title: sncRNA organ atlas, Homo sapiens, kidney-cortex_3

value: adult

value: female

value: kidney-cortex


title: sncRNA organ atlas, Homo sapiens, brain-thalamus_1

value: male

value: brain-thalamus


title: sncRNA organ atlas, Homo sapiens, liver_3

value: liver


title: sncRNA organ atlas, Homo sapiens, bowel-small intestine_5

source_name: bowel-small intestine_5

value: bowel-small intestine


title: sncRNA organ atlas, Homo sapiens, pancreas_1

value: pancreas


title: G87

value: Male

value: Breeding male

value: Vera Gorbunova

value: Blood


title: sncRNA organ atlas, Homo sapiens, brain-substantia nigra_2 (1)

source_name: brain-substantia nigra_2 (1)

value: brain-substantia nigra


title: G81


title: G79

value: Non-breeder


title: sncRNA organ atlas, Homo sapiens, bowel-ileum_3

value: Not applicable

value: bowel-ileum


title: G75


title: G76


title: G77


title: G74


title: sncRNA organ atlas, Homo sapiens, heart-muscle_3 (2)

source_name: heart-muscle_3 (2)

value: heart-muscle


title: G73


title: G72

value: Female


title: sncRNA organ atlas, Homo sapiens, tongue_4

value: adult

value: tongue


title: G70


title: G82


title: sncRNA organ atlas, Homo sapiens, artery_1

value: male

value: artery


title: sncRNA organ atlas, Homo sapiens, bowel-colon_1

value: bowel-colon


title: G68


title: G69


title: G67


title: sncRNA organ atlas, Homo sapiens, esophagus_1

value: esophagus


title: sncRNA organ atlas, Homo sapiens, liver_4 (1)

source_name: liver_4 (1)

value: liver


title: sncRNA organ atlas, Homo sapiens, heart-atrium_4 (1)

source_name: heart-atrium_4 (1)

value: heart-atrium


title: G66


title: sncRNA organ atlas, Homo sapiens, brain-dura mater_3

source_name: brain-dura mater_3

value: female

value: brain-dura mater


title: G65

value: Male

value: Vera Gorbunova

value: Blood


title: sncRNA organ atlas, Homo sapiens, brain-frontal lobe_3

source_name: brain-frontal lobe_3

value: Not applicable

value: brain-frontal lobe


title: G78

value: Non-breeder


title: sncRNA organ atlas, Homo sapiens, artery_4


title: G62

value: Female


title: sncRNA organ atlas, Homo sapiens, brain-thalamus_3

value: adult

value: brain-thalamus


title: sncRNA organ atlas, Homo sapiens, vein_1

value: male

value: vein


title: G64


title: sncRNA organ atlas, Homo sapiens, brain-dura mater_1

source_name: brain-dura mater_1


title: sncRNA organ atlas, Homo sapiens, uterus_3

value: uterus


title: G63

source_name: Blood


title: G61


title: G71


title: G59


title: sncRNA organ atlas, Homo sapiens, pancreas_4

value: pancreas


title: sncRNA organ atlas, Homo sapiens, lung_5

value: lung


title: G58


title: G60


title: G57


title: sncRNA organ atlas, Homo sapiens, artery_5

value: artery


title: sncRNA organ atlas, Homo sapiens, brain-occipital lobe_3

source_name: brain-occipital lobe_3

value: female

value: brain-occipital lobe


title: sncRNA organ atlas, Homo sapiens, bowel-jejunum_3

value: bowel-jejunum


title: sncRNA organ atlas, Homo sapiens, vein_5


title: G54

value: Vera Gorbunova


title: sncRNA organ atlas, Homo sapiens, heart-muscle_3 (1)

source_name: heart-muscle_3 (1)

value: heart-muscle


title: G53

value: Male

value: Blood


title: sncRNA organ atlas, Homo sapiens, brain-white matter_3

source_name: brain-white matter_3

value: Not applicable

value: brain-white matter


title: sncRNA organ atlas, Homo sapiens, brain-hypothalamus_3

value: adult

value: brain-hypothalamus


title: G51

value: Non-breeder


title: sncRNA organ atlas, Homo sapiens, brain-arachnoid mater_3

source_name: brain-arachnoid mater_3

value: brain-arachnoid mater


title: sncRNA organ atlas, Homo sapiens, bowel-small intestine_4 (1)

source_name: bowel-small intestine_4 (1)

value: male

value: bowel-small intestine


title: G47


title: sncRNA organ atlas, Homo sapiens, spinal cord_1

source_name: spinal cord_1

value: spinal cord


title: sncRNA organ atlas, Homo sapiens, lung_4 (1)

value: lung


title: sncRNA organ atlas, Homo sapiens, nerve_5

value: female

value: nerve


title: G49


title: G48

value: Female


title: sncRNA organ atlas, Homo sapiens, brain-temporal lobe_1

source_name: brain-temporal lobe_1

value: brain-temporal lobe


title: G56

value: Vera Gorbunova


title: G55

value: Male


title: G46

value: Blood


title: G44


title: sncRNA organ atlas, Homo sapiens, lung_3

value: Not applicable


title: G45

value: Breeding male


title: sncRNA organ atlas, Homo sapiens, pancreas_2 (1)

source_name: pancreas_2 (1)

value: adult

value: pancreas


title: G42

value: Non-breeder


title: G43

value: Queen


title: G40


title: G52


title: G41


title: sncRNA organ atlas, Homo sapiens, brain-grey matter_3

source_name: brain-grey matter_3

value: brain-grey matter


title: sncRNA organ atlas, Homo sapiens, brain-cerebellum_3

value: brain-cerebellum


title: sncRNA organ atlas, Homo sapiens, bone_4

value: male

value: bone


title: sncRNA organ atlas, Homo sapiens, bowel-duodenum_3

value: female

value: bowel-duodenum


title: sncRNA organ atlas, Homo sapiens, adipocyte_4

value: adipocyte


title: sncRNA organ atlas, Homo sapiens, nerve_6

value: nerve


title: G50

value: Female

value: Vera Gorbunova


title: sncRNA organ atlas, Homo sapiens, lung-bronchus_4

value: lung-bronchus


title: G38

value: Blood


title: G34


title: G39

value: Male


title: G36


title: G35


title: G37


title: sncRNA organ atlas, Homo sapiens, brain-frontal lobe_1

source_name: brain-frontal lobe_1

value: Not applicable

value: adult

value: brain-frontal lobe


title: sncRNA organ atlas, Homo sapiens, brain-nucleus caudatus_3

source_name: brain-nucleus caudatus_3

value: brain-nucleus caudatus


title: sncRNA organ atlas, Homo sapiens, bone_2


title: sncRNA organ atlas, Homo sapiens, bowel-small intestine_6

source_name: bowel-small intestine_6

value: bowel-small intestine


title: sncRNA organ atlas, Homo sapiens, submandibular gland_2

source_name: submandibular gland_2

value: submandibular gland


title: sncRNA organ atlas, Homo sapiens, nerve_3 (2)

source_name: nerve_3 (2)


title: G31

value: Breeding male


title: G33

value: Non-breeder


title: sncRNA organ atlas, Homo sapiens, heart-ventricle_4 (2)

source_name: heart-ventricle_4 (2)

value: male

value: heart-ventricle


title: G32


title: G30


title: sncRNA organ atlas, Homo sapiens, bowel-colon_2

value: bowel-colon


title: sncRNA organ atlas, Homo sapiens, brain-medulla oblongata_3

source_name: brain-medulla oblongata_3

value: female

value: brain-medulla oblongata


title: sncRNA organ atlas, Homo sapiens, brain-thalamus_2

value: brain-thalamus


title: G29

source_name: Blood

value: Vera Gorbunova


title: G25

value: Blood


title: G26

value: Female


title: sncRNA organ atlas, Homo sapiens, spinal cord_3

source_name: spinal cord_3

value: Not applicable

value: spinal cord


title: G24

value: Male


title: G27


title: sncRNA organ atlas, Homo sapiens, heart-pericardium_5

value: adult

value: heart-pericardium


title: G23

value: Queen


title: G22


title: G21

value: Breeding male


title: sncRNA organ atlas, Homo sapiens, skin_6

value: skin


title: sncRNA organ atlas, Homo sapiens, bowel-colon_4

value: male


title: sncRNA organ atlas, Homo sapiens, muscle_4

value: muscle


title: G20

value: Non-breeder


title: G19


title: sncRNA organ atlas, Homo sapiens, thyroid_3

value: female

value: thyroid


title: G18


title: sncRNA organ atlas, Homo sapiens, lung-bronchus_2

value: lung-bronchus


title: sncRNA organ atlas, Homo sapiens, nerve_3 (1)

source_name: nerve_3 (1)

value: nerve


title: sncRNA organ atlas, Homo sapiens, bladder_2

value: bladder


title: G16

value: Vera Gorbunova

value: Blood


title: sncRNA organ atlas, Homo sapiens, trachea_4 (1)

source_name: trachea_4 (1)

value: Not applicable

value: trachea


title: G15

value: Male


title: G17


title: sncRNA organ atlas, Homo sapiens, stomach_4

value: adult

value: stomach


title: sncRNA organ atlas, Homo sapiens, urethra_4

value: urethra


title: G12

description: G12_NMR3_CKDL190140059-1a-27_H3TYLCCX2_L1

value: Female

value: Queen


title: sncRNA organ atlas, Homo sapiens, liver_6

value: male

value: liver


title: sncRNA organ atlas, Homo sapiens, bowel-colon_3

value: female

value: bowel-colon


title: G11

value: Non-breeder


title: pig_HMA2

city: New York

first: Bi-Sen

last: Ding

state: NY

address: York Avenue

institute: Weill Cornell

data_processing:
Liver tissues minipig were washed twice with cold PBS, minced, and incubated in a digestive mixture (1 mg/ml collagenase I and 1mg/ml dispase II in PBS) on an orbital shaker at 37 °C, for 15 min. After 15 min, liver tissues were suspended to ensure complete dissociation. Digested liver sample was homogenous with minimal chunks. Digested tissues were filtered through cell strainer multiple times, and cells were collected at 400 g for 5 min. After red blood cells were removed with RBC lysis buffer ( Solarbio) and washed once, hepatocytes and NPCs were separated by an additional centrifugation step at 50 g for 5 min at 4 °C. Single cells were processed in the following steps: GEM generation & Barcoding, GEM-RT cleanup & cDNA amplification, and library construction, and finally were sequenced on an Illumina Nova-seq 6000 (Illumina).
The sequences from scRNA-Seq of pig and minipig liver NPCs were aligned to pig (Sus scrofa) transcriptome (Sscrofa11.1) and human (Homo sapiens) transcriptome (GRCh37)using Hisat2 v2.0.5 Low-quality cells expressing less than 200 genes as well as genes expressed in less than 3 cells were filtered. Mitochondrial gene content percentage thresholds were set to filter pig liver NPCs. Genome_build: Sscrofa11.1 Supplementary_files_format_and_content: matrix files
Genome_build: Sscrofa11.1/GRCh37
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Sus scrofa

source_name: liver NPC

extract_protocol:
liver were removed, NPC were isolated  on  ice, and
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: MGCD&AZA treatment after fibrosis

tag: cell type

value: Non-Parenchymal Cells (NPC)


title: pig_HC2

value: Oil with Ccl4


title: sncRNA organ atlas, Homo sapiens, adipocyte_3

value: adipocyte


title: sncRNA organ atlas, Homo sapiens, heart-muscle_2

value: Not applicable

value: heart-muscle


title: S2

city: Changchun City, Jilin Province

first: Yuanyuan

last: Tian

address: The Xinmin Street No. 26

country: China

institute: The Key Laboratory of Pathobiology, Ministry of Education, The College of Basic Medical Sciences, Jilin University

description:
axillary lymph node/vascular epithelium
endothelial, SV40 transformed
adult
Iso-Seq

data_processing:
Raw reads were first filtered with minimum average read quality score=6 and minimum read length=500bp. Ribosomal RNA were discarded after mapping to rRNA database.
Full-length, non-chimeric (FLNC) transcripts were determined by searching for primer at both ends of reads. Clusters of FLNC transcripts were obtained after mapping to reference genome with mimimap 2 and consensus isoforms were obtained after polishing within each cluster by pinfish.
Gene structure optimization: Full-length sequencing can accurately identify the structure of transcripts. Gffcompare is used to align transcripts obtained by full-length sequencing to known transcripts of the genome, so novel genes and transcripts can be obtained to supplement genome annotation.  If regions beyond the original gene boundaries are supported by Mapped Reads, the Untranslated Region (UTR) of genes can be extended to its upstream and downstream to amend gene boundaries.
Astalavista is used to obtain the alternative splicing types of each sample. For fusion transcript analysis, we need to use the consensus sequence before remove-redundant analysis treatment. TAPIS pipeline was used to further analyze full-length non-chimeric sequence (FLNC) to identify APA. The transcripts above 500bp were screened from the novel transcripts, and MISA software was used for SSR analysis. Predict lncRNA in novel transcripts, including CPC analysis, CNCI analysis, CPAT analysis and pfam protein domain analysis. A total of 954 lncRNA transcripts were predicted by all four methods.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: processed_data_files_ref_ont_gene_full_table.txt: Tab-delimited text file includes counts and CPM values for each Sample.

organism: Mus musculus

source_name: axillary lymph node

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA was subjected to library synthesis using Direct RNA Sequencing Kit (SQK-RNA002).
Experiment workflow will be performed according to standard protocol provided by Oxford Nanopore Technologies (ONT).

tag: cell line

value: normal endothelial cells


title: S3


title: S1


title: H3

value: tumor endothelial cells


title: G14

value: Male

value: Vera Gorbunova

value: Blood


title: H2


title: H1


title: G9


title: D73

city: chongqing

first: Xiaoliang

last: Liu

address: xinqiao street

institute: Xinqiao Hospital, Army Medical University (Third Military Medical University)

data_processing:
Sequencing data quality control, data comparison analysis and transcriptome in-depth analysis
The Seurat package was used to normalize data, dimensionality reduction, clustering, differential expression.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package
Genome_build: GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene

molecule: polyA RNA

organism: Danio rerio

source_name: Zebrafish kidney regeneration transcriptome

growth_protocol: Zebrafish were maintained in standard conditions under a 14-hours-light and 10-hours-dark cycle and fed three times daily

extract_protocol:
After the zebrafish kidney was obtained by dissection, it was lysed in trizo, then extracted with PCI / CI, precipitated with isopropanol and eluted with 75% alcohol to obtain total RNA
After the total RNA sample is tested to be qualified, magnetic beads with oligo (DT) are selected for enrichment and purification. Fragment buffer is added to the purified mRNA to make its fragment into a short fragment. Then the second strand of cDNA is synthesized with the fragment mRNA as a template and purified by qiaquick PCR kit. The purified double stranded cDNA was then treated by terminal repair, base A and sequencing. Then the target fragment was recovered by agarose gel electrophoresis and PCR was amplified to complete the whole library preparation.

value: AB

value: kidney

value: 6 months

value: 7 dpi sample 3


title: G10


title: sncRNA organ atlas, Homo sapiens, stomach_1

value: adult

value: male

value: stomach


title: D53

value: 5 dpi sample 3


title: D71

value: 7 dpi sample 1


title: G8

value: Female

value: Non-breeder


title: D52

value: 5 dpi sample 2


title: sncRNA organ atlas, Homo sapiens, heart-pericardium_2

value: Not applicable

value: heart-pericardium


title: G6

value: Male

value: Breeding male


title: D51

value: 5 dpi sample 1


title: G13

value: Vera Gorbunova

value: Blood


title: sncRNA organ atlas, Homo sapiens, skin_2

value: skin


title: sncRNA organ atlas, Homo sapiens, brain-arachnoid mater_6

source_name: brain-arachnoid mater_6

value: brain-arachnoid mater


title: D72

value: AB

value: kidney

value: 6 months

value: 7 dpi sample 2


title: D33

value: 3 dpi sample 3


title: G5

value: Female

value: Queen


title: D32

value: 3 dpi sample 2


title: sncRNA organ atlas, Homo sapiens, brain_6

value: Not applicable

value: adult

value: male

value: brain


title: D31

value: 3 dpi sample 1


title: sncRNA organ atlas, Homo sapiens, stomach_6

value: stomach


title: G4

value: Male

value: Non-breeder

value: Vera Gorbunova

value: Blood


title: sncRNA organ atlas, Homo sapiens, thyroid_1

value: thyroid


title: G3


title: D12

value: AB

value: kidney

value: 6 months

value: 1 dpi sample 2


title: D11

value: 1 day after-injury (1 dpi ) sample 1


title: Con3

value: control sample 3


title: Con2

value: control sample 2


title: D13

value: 1 dpi sample 3


title: G2

value: Female


title: sncRNA organ atlas, Homo sapiens, vein_3

value: Not applicable

value: adult

value: female

value: vein


title: sncRNA organ atlas, Homo sapiens, heart-ventricle_4 (1)

source_name: heart-ventricle_4 (1)

value: male

value: heart-ventricle


title: Con1

value: control sample 1


title: G7

value: Male

value: Non-breeder

value: Vera Gorbunova

value: Blood


title: sncRNA organ atlas, Homo sapiens, bone_3

value: bone


title: zebrafish kidney cells

data_processing:
Sequencing was performed with Illumina (NovaSeq) according to the manufacturer’s instructions (Illumina)
The Seurat package was used to normalize data, dimensionality reduction, clustering, differential expression.
Genome_build: danRer11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene

source_name: adult zebrafish kedney cells

extract_protocol:
Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry.
sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit (10X Genomics) according to the manufacturer’s instructions
10× Chromium Controller (10X Genomics)

value: AB

value: kidney

value: 6 months


title: G1


title: human_cir1

value: Non-Parenchymal Cells (NPC)

tag: disease state

value: Cirrhotic


title: sncRNA organ atlas, Homo sapiens, gallbladder_2

value: Not applicable

value: gallbladder


title: human_ctrl2

value: ctrl


title: sncRNA organ atlas, Homo sapiens, heart-atrial appendage_3

source_name: heart-atrial appendage_3

value: adult

value: female

value: heart-atrial appendage


title: human_cir2


title: human_ctrl1


title: sncRNA organ atlas, Homo sapiens, vein_2

value: male

value: vein


title: sncRNA organ atlas, Homo sapiens, nerve_2 (1)

source_name: nerve_2 (1)

value: nerve


title: In vitro T-cells - replicate 2

city: Vancouver

first: John

middle: M

last: Edgar

state: BC

address: 2222 Health Sciences Mall, Room 404

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

data_processing:
Data processing by Adaptive Biotechnologies. The preferred method of accessing this data is through immuneACCESS (https://doi.org/10.21417/JME2021NPJRM). This deposition is to provide INSDC-compliant access as mandated by journal policy.
immunoSEQ hsTCRB_v4b Service (Survey).
Supplementary_files_format_and_content: *.tsv: Processed data contains TRBV, TRBD, and TRBJ usage, complementarity-determining regions sequences, and associated statistics.

source_name: In vitro generated T-cells from umbilical cord blood-derived CD34+ cells

growth_protocol: UCB-derived CD34+ cells were seeded at 2000 cells/well in a 96 well plate coated with DL4+VCAM-1 and cultured for 42 days in optimized cytokines for T-cell development.

extract_protocol:
Genomic DNA was extracted from cells using QuickExtract DNA Extraction Solution (Lucigen) and diluted using Tris-EDTA buffer.
Library prep by Adaptive Biotechnologies. Targeted TRB gene sequencing by Adaptive Biotechnologies.

value: In vitro generated T-cells from UCB-derived CD34+ cells


title: In vitro T-cells - replicate 3


title: Postnatal thymocytes - control

source_name: Postnatal thymus obtained during cardiovascular surgery

growth_protocol: Human thymus was collected from patients 3 years or younger while undergoing cardiovascular surgery after parental consent at BC Children’s Hospital, Vancouver, British Columbia, in accordance with institutional research ethics board policies. Thymus tissues were washed with RPMI 1640 (ThermoFisher) with 100 µg/ml DNase I (Roche), thinly sliced with a scalpel, and then dissociated using gentleMACs Dissociator (Miltenyi Biotec). Isolated thymocytes were washed once with Hanks Balanced Salt Solution (HBSS) with 2% FBS (Gibco; collectively referred to as HF buffer) and then incubated with ACK lysing buffer (Lonza) for 5 minutes at room temperature. Thymocytes were rinsed again with HF buffer and passed through a 40µM filter to create as a single cell suspension. Isolated thymocytes were subsequently cryopreserved in FBS with 10% DMSO and stored in vapor phase nitrogen until use.

value: Thymocytes


title: In vitro T-cells - replicate 4


title: In vitro T-cells - replicate 5


title: sncRNA organ atlas, Homo sapiens, brain-dura mater_2

source_name: brain-dura mater_2

value: brain-dura mater


title: In vitro T-cells - replicate 1


title: ESR1-D538G

city: Houston

first: Jonathan

middle: Thomas

last: Lei

state: TX

address: 1 Baylor Plaza

department: Medicine - Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

data_processing:
Reads were aligned to hg19 (GRCh37) reference genome using RSEM v1.2.31 and Bowtie 2
Differential gene expression was performed using edgeR (FDR < 0.05)
Unsupervised hierarchical clustering was performed using a metric of Euclidean distance and the average linkage method
Heatmap was generated using Morpheus
Genome_build: hg19
Supplementary_files_format_and_content: Processed RSEM tab-delimited files are provided for each sample containing read count quantification, FPKM, and TPM.

source_name: T47D cells

growth_protocol: Stable T47D cells expressing ESR1 constructs were cultured in RPMI1640 media supplemented with 10% FBS, 4.5 g/L glucose, 10 mM HEPES,  1 mM sodium pyruvate, and 50 µg/mL gentamycin.

extract_protocol:
Cells were grown in hormone-deprived media for 5 days followed by treatment with or without 10 nM E2 for 2 days. RNA was isolated using Qiagen RNeasy kit and treated with Dnase.
Illumina TruSeq Stranded mRNA prep kit was used for library preparation.

treatment_protocol: Cells were hormone-deprived in phenol red-free, RPMI media containing charcoal stripped serum as supplemented as above for 7 days before RNA-seq processing

tag: cell subtype

value: Stable ESR1-D538G expressing cell

tag: condition

value: Hormone-deprived media


title: sncRNA organ atlas, Homo sapiens, glandular breast tissue_5

source_name: glandular breast tissue_5

value: glandular breast tissue


title: ESR1-D538G, +E2

value: Hormone-deprived media, +E2


title: ESR1-Y537S, +E2

value: Stable ESR1-Y537S expressing cell


title: ESR1-Y537S


title: sncRNA organ atlas, Homo sapiens, bowel-colon_6

value: Not applicable

value: bowel-colon


title: sncRNA organ atlas, Mus musculus, Small_Intestine_53

tag: age (months postnatal)

value: postnatal

value: Small Intestine


title: sncRNA organ atlas, Mus musculus, Small_Intestine_51

tag: strain


title: ESR1-e6>TNRC6B, +E2

value: Stable ESR1-e6>TNRC6B fusion expressing cell


title: sncRNA organ atlas, Homo sapiens, muscle_2

tag: age (years)

value: adult

value: muscle


title: sncRNA organ atlas, Mus musculus, MAT_9

tag: developmental stage

value: female

value: Mesenteric Adipose Tissue (MAT)


title: ESR1-e6>TNRC6B


title: sncRNA organ atlas, Mus musculus, MAT_8

tag: Sex

value: male


title: WT_lowDNTP_rep3

city: Tel Aviv

first: Aldema

last: Sas-Chen

state: Israel

address: Tel Aviv University

department: Shmunis School of Biomedicine and Cancer Research

country: Israel

institute: Tel Aviv University

description:
Total RNA extracted from mitochondria enriched fractions.
Libraries created with 2uM dNTPs.
Paired-end

data_processing:
Library strategy: 2OMe-Seq
Alignment using STAR (V. 2.5.3a).
Base-calling
Calculation of number of read starts, ends and coverage per base.
Calculation of cleavage protection scores and stop rates.
Genome_build: chrM from the GENCODE release 32 (GRCh38.p13).
Supplementary_files_format_and_content: mitochondria_2OMe_profiling.xlsx: Excel file detailing 2-O-methylation scores of mitochondrial RNA at base resolution.

source_name: human cell line

growth_protocol: The generated knock-out cells were cultured in medium supplemented with 20% FBS and 50 mg mL-1 uridine.

extract_protocol:
RNA was purified using TRI reagent (Sigma).
Fragmentation, 3' adapter ligation, cDNA synthesis using dNTPs at 2uM or 500uM, second adapter ligation and enrichment.

treatment_protocol: Mitochondria isolation was conducted as previously described (Sas-Chen, Nir and Schwartz, 2021; doi: 10.1007/978-1-0716-0834-0_9).

tag: genotype

value: WT

tag: cell fraction

value: mitochondria

tag: dntp concentration

value: Low


title: WT_lowDNTP_rep2


title: sncRNA organ atlas, Mus musculus, MAT_7

tag: tissue


title: sncRNA organ atlas, Homo sapiens, skin_1

value: skin


title: WT_lowDNTP_rep1


title: sncRNA organ atlas, Homo sapiens, sclera_5

value: sclera


title: WT_highDNTP_rep3

description:
Total RNA extracted from mitochondria enriched fractions.
Libraries created with 500uM dNTPs.
Paired-end

value: MRM3 KO

value: High


title: ESR1-e6>GRIP1

value: Stable ESR1-e6>GRIP1 fusion expressing cell

value: Hormone-deprived media


title: WT_highDNTP_rep2


title: ESR1-e6>CLINT1, +E2

value: Stable ESR1-e6>CLINT1 fusion expressing cell

value: Hormone-deprived media, +E2


title: sncRNA organ atlas, Mus musculus, MAT_6

value: postnatal


title: sncRNA organ atlas, Mus musculus, MAT_5


title: sncRNA organ atlas, Homo sapiens, adipocyte_5

value: Not applicable

value: adult

value: adipocyte


title: sncRNA organ atlas, Mus musculus, Small_Intestine_50

value: female

value: Small Intestine


title: sncRNA organ atlas, Homo sapiens, esophagus_2

value: male

value: esophagus


title: sncRNA organ atlas, Mus musculus, Small_Intestine_12


title: sncRNA organ atlas, Homo sapiens, pleurae_2

value: pleurae


title: sncRNA organ atlas, Homo sapiens, artery_2

value: artery


title: sncRNA organ atlas, Mus musculus, MAT_47

value: Mesenteric Adipose Tissue (MAT)


title: sncRNA organ atlas, Mus musculus, MAT_48


title: sncRNA organ atlas, Homo sapiens, thyroid_5

value: thyroid


title: ESR1-e6>TCF12, +E2

value: Stable ESR1-e6>TCF12 fusion expressing cell


title: MRM3_KO_lowDNTP_rep3

value: MRM2 KO

value: mitochondria

value: Low


title: ESR1-e6>GRIP1, +E2

value: Stable ESR1-e6>GRIP1 fusion expressing cell

value: Hormone-deprived media, +E2


title: WT_highDNTP_rep1

value: MRM3 KO

value: High


title: sncRNA organ atlas, Homo sapiens, adipocyte_2

value: Not applicable

value: adult

value: adipocyte


title: ESR1-e6>NCOA1, +E2

value: Stable ESR1-e6>NCOA1 fusion expressing cell

value: Hormone-deprived media


title: plusIR_48h_pos_2

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
Illumina adapters were removed, along with the first 12 base pairs using BBDuk and reads <50bp after trimming were discarded
Reads were aligned and quantified using STAR (2.6.0a) to the Ensembl Drosophila melanogaster genome (BDGP6.22, release 97)
Lowly abundant genes were removed as those <1 mean raw count or <1 mean count per million (CPM) across the dataset
Differential gene expression was calculated using the voom function in limma
Differential trajectory analysis was performed using the TimeSeriesExperiment R package.
Genome_build: BDGP6
Supplementary_files_format_and_content: Text file containing STAR gene count values.

organism: Drosophila melanogaster

source_name: fruit fly

growth_protocol: 30A>G-trace/SM5 virgin females were crossed to w1118 males and RFP+GFP+ larvae were sorted manually

extract_protocol:
Poly-A RNA was isolated using a RNeasy kit (Qiagen) and a KAPA mRNA capture hyper prep kit (Roche) according to manufacturer’s instructions
RNA was sequenced with ERCC spike-ins (ThermoFisher) using a NexSeq 500 sequencer

treatment_protocol: The larvae in food were placed in petri dishes and irradiated in a Faxitron Cabinet X-ray System Model RX-650 (Lincolnshire, IL) at115kv and 5.33rad/second

value: Wing disc

value: POS


title: sncRNA organ atlas, Mus musculus, MAT_45

value: postnatal

value: female

value: Mesenteric Adipose Tissue (MAT)


title: MRM3_KO_lowDNTP_rep2

value: MRM2 KO


title: ESR1-e6>NCOA1


title: plusIR_48h_pos_1


title: sncRNA organ atlas, Mus musculus, MAT_44


title: sncRNA organ atlas, Mus musculus, MAT_41

value: male


title: plusIR_48h_neg_2

value: NEG


title: ESR1-e6>CLINT1

value: Stable ESR1-e6>CLINT1 fusion expressing cell


title: ESR1-e6>LPP, +E2

value: Stable ESR1-e6>LPP fusion expressing cell

value: Hormone-deprived media, +E2


title: MRM3_KO_highDNTP_rep3

value: MRM1 KO

value: mitochondria

value: High


title: ESR1-e6>LPP


title: MRM3_KO_highDNTP_rep1


title: MRM3_KO_highDNTP_rep2


title: sncRNA organ atlas, Mus musculus, MAT_40


title: plusIR_48h_neg_1


title: sncRNA organ atlas, Mus musculus, MAT_46


title: sncRNA organ atlas, Mus musculus, MAT_4


title: MRM2_KO_lowDNTP_rep3

value: WT

value: Low


title: plusIR_24h_pos_1


title: plusIR_24h_pos_2


title: MRM2_KO_lowDNTP_rep2


title: MRM3_KO_lowDNTP_rep1


title: MRM2_KO_lowDNTP_rep1


title: plusIR_24h_neg_2


title: sncRNA organ atlas, Mus musculus, MAT_38


title: sncRNA organ atlas, Mus musculus, MAT_12


title: ESR1-e6>ARNT2-e2

value: Stable ESR1-e6>ARNT2-e2 fusion expressing cell

value: Hormone-deprived media


title: YFP_rep2, +E2

value: Stable YFP-HA expressing cell


title: sncRNA organ atlas, Mus musculus, MAT_37

value: postnatal


title: YFP_rep2


title: MRM2_KO_highDNTP_rep3

value: MRM3 KO


title: sncRNA organ atlas, Mus musculus, MAT_11

value: Mesenteric Adipose Tissue (MAT)


title: MRM2_KO_highDNTP_rep2


title: MRM2_KO_highDNTP_rep1


title: minusIR_pos_2

value: Wing disc

value: POS


title: ESR1-WT, +E2

value: Stable ESR1 wild-type expressing cell


title: minusIR_pos_1


title: sncRNA organ atlas, Mus musculus, MAT_10

value: male


title: plusIR_24h_neg_1

value: NEG


title: ESR1-e6>ARNT2-e2, +E2

value: Hormone-deprived media, +E2


title: ESR1-e6, +E2

value: Stable ESR1-e6 truncation expressing cell


title: ESR1-WT


title: minusIR_neg_2


title: sncRNA organ atlas, Mus musculus, Limb_Muscle_9

value: Limb Muscle


title: MRM1_KO_lowDNTP_rep3

value: MRM2 KO

value: mitochondria


title: ESR1-e6


title: sncRNA organ atlas, Mus musculus, Limb_Muscle_8


title: sncRNA organ atlas, Mus musculus, Limb_Muscle_7


title: MRM1_KO_lowDNTP_rep2

value: Low


title: minusIR_neg_1


title: ESR1-e6>ARID1B, +E2

value: Stable ESR1-e6>ARID1B fusion expressing cell


title: ESR1-e6>TCF12

value: Stable ESR1-e6>TCF12 fusion expressing cell

value: Hormone-deprived media


title: sncRNA organ atlas, Mus musculus, Limb_Muscle_6

value: postnatal


title: MRM1_KO_highDNTP_rep3

value: MRM1 KO

value: High


title: sncRNA organ atlas, Mus musculus, Limb_Muscle_5

value: female


title: ESR1-e6>ARID1B


title: ESR1-e6>PCMT1, +E2

value: Stable ESR1-e6>PCMT1 fusion expressing cell


title: MRM1_KO_lowDNTP_rep1


title: MRM1_KO_highDNTP_rep2


title: 38A

city: Temple

first: Carl

middle: A

last: Gregory

state: Texas

address: 5701 Airport Road

department: Molecular and Cellular Medicine

institute: Texas A&M Health Sciences Center

data_processing:
De novo assembly was done stringtie between samples in vitro and in vivo respectively based on GRCm38.98 reference genome
The reads were aligned using HISAT2 v 2.1.0
Gene counts were obtained by using SAMtools v.1.9 and featureCounts (Subread v.2.0.0)
Downstream analysis was done in R
Genome_build: De novo assembly genome based on GRCm38.98
Supplementary_files_format_and_content: Normalized count using vst in DEseq2

source_name: MOSJ-Dkk1 xenograft

growth_protocol: Red fluorescent protein (RFP)-labeled MOSJ-Dkk1 and vector backbone control MOSJ-pLenti cells were generated as previously described (1). MOSJ-Dkk1 cells are a murine osteochondral sarcoma cell line (2) modified by the pLenti vector (Life Technologies, Carlsbad, CA) to constitutively express and secrete human Dkk-1 via the cytomegalovirus (CMV) promoter.  The control line, MOSJ-pLenti, harbors the vector backbone with no cDNA cassette. Both cell lines were cultured in medium containing alpha-minimal-essential-medium (αMEM, Life Technologies) supplemented with 10% (v/v) fetal bovine serum (FBS, Atlanta Biologicals, Norcross, GA), 100 U.mL-1 penicillin & 100 µg.mL-1 streptomycin (Life Technologies) and 2 mM L-glutamine (Life Technologies). For expansion, cells were seeded at 500 cells per cm2 with media changes every two days. Adherent cells were recovered using 0.25% (w/v) trypsin/ethylene diamine tetra-acetic acid when a density of approximately 80-90% confluency was reached.

extract_protocol:
FFPE-extraction protrocol for in vivo sample
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. The suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeq TM 4000, DNBseq or other sequencer when necessary.

treatment_protocol: For proliferative cultures, MOSJ-Dkk1 cells were seeded at 500 cells per cm2 in 175 cm2 flasks and allowed to enter the logarithmic stage of growth after 6 days of culture with changes of media every 2 days. Groups (n=3) were no morpholino, 5 M DkkMo, 5 M scrambled morpholino control (scrMo) which was added 24 h after seeding. For the nutritional stress cohort, cells were seeded and cultured in the same manner, but exposed to 48 hr of confluence without media change for 4 days. Cells were collected after one week of treatment. In all cases, cells were recovered by trypsinization, washed in PBS, and stored as flash frozen pellet (1x106 cells) in liquid nitrogen until mRNA extraction.    For tumor sequencing, mice were initially fixed by trans-cardiac perfusion and stored in phosphate-buffered 3% formaldehyde with 10 mM CaCl2 at 4oC. Four specimens from each group were randomly selected for RNA sequencing. Tumor/stroma was carefully dissected from bone and muscle tissue

value: NU/J

value: MOSJ-Dkk1 xenograft

value: Combination

value: DRB+DkkMo


title: ESR1-e6>PCMT1


title: sncRNA organ atlas, Mus musculus, Limb_Muscle_3

value: male


title: 36A


title: ESR1-e6>ARNT2, +E2

value: Stable ESR1-e6>ARNT2 fusion expressing cell

value: Hormone-deprived media, +E2


title: MRM1_KO_highDNTP_rep1

value: mitochondria


title: 34A


title: sncRNA organ atlas, Mus musculus, Limb_Muscle_11

value: Limb Muscle


title: ESR1-e6>ARNT2


title: sncRNA organ atlas, Mus musculus, Limb_Muscle_4


title: 29A

value: DkkMo


title: 31A


title: sncRNA organ atlas, Mus musculus, Limb_Muscle_10


title: CD11b cells_SYN3 Mdb

city: Pamplona

first: Maria S.

last: Aymerich

state: Navarra

address: Calle Irunlarrea, 1

department: Biochemistry and Genetics

country: Spain

institute: Universidad de Navarra

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 genome using Kallisto
Calculate raw counts with Kallisto
Genome_build: mm10
Supplementary_files_format_and_content: abundance files from Kallisto

source_name: midbrain

extract_protocol:
Samples were prepared with the Illumina TruSeq Stranded mRNA kit following manufacturer’s indications and sequenced as reverse paired-end (50 bp) runs on the Nextseq sequencer
Truseq mRNA (Illumina)

value: myeloid cells (CD11b)

value: midbrain

tag: model

value: parkinsonian


title: CD11b cells_SYN2 Mdb


title: CD11b cells_SYN1 Mdb


title: CD11b cells_CT3 Mdb

value: control


title: ESR1-e6SOX9, +E2

value: Stable ESR1-e6>SOX9 fusion expressing cell


title: ESR1-e6>SOX9

value: Hormone-deprived media


title: 40A


title: 24A


title: sncRNA organ atlas, Mus musculus, Limb_Muscle_1

value: postnatal

value: female


title: ESR1-e6>GYG1, +E2

value: Stable ESR1-e6>GYG1 fusion expressing cell


title: CD11b cells_CT2 Mdb


title: ESR1-e6>GYG1


title: sncRNA organ atlas, Mus musculus, Heart_9

value: Heart


title: CD11b cells_CT1 Mdb


title: 19A

value: NU/J

value: MOSJ-Dkk1 xenograft

value: DRB


title: sncRNA organ atlas, Mus musculus, Heart_8

value: male


title: sncRNA organ atlas, Mus musculus, Limb_Muscle_2


title: CD11b cells_SYN1 Str

source_name: striatum

value: striatum


title: ESR1-e6>DAB2

value: Stable ESR1-e6>DAB2 fusion expressing cell


title: sncRNA organ atlas, Mus musculus, Heart_7


title: 28A

value: DkkMo


title: CD11b cells_SYN3 Str

value: myeloid cells (CD11b)


title: ESR1-e6>DAB2, +E2

value: Hormone-deprived media, +E2


title: ESR1-e6>PCDH11X, +E2

value: Stable ESR1-e6>PCDH11X fusion expressing cell


title: CD11b cells_SYN2 Str

value: parkinsonian


title: 7A

value: NT

value: vehicle


title: CD11b cells_CT3 Str

value: control


title: ESR1-e6>PCDH11X

value: Hormone-deprived media


title: 6A


title: 14A


title: sncRNA organ atlas, Mus musculus, Heart_5

value: postnatal


title: 5A


title: sncRNA organ atlas, Mus musculus, Heart_4

value: Heart


title: 20A

value: NU/J


title: sncRNA organ atlas, Mus musculus, Heart_3


title: ESR1-e6>YAP1, +E2

value: Stable ESR1-e6>YAP1 fusion expressing cell


title: ESR1-e6>YAP1


title: CD11b cells_CT1 Str


title: 1A

value: MOSJ-Dkk1 xenograft


title: CD11b cells_CT2 Str


title: sncRNA organ atlas, Mus musculus, Heart_12

value: male


title: YFP_rep1, +E2

value: Stable YFP-HA expressing cell


title: 18A

value: DRB


title: YFP_rep1


title: sncRNA organ atlas, Mus musculus, Heart_11


title: sncRNA organ atlas, Mus musculus, Heart_6


title: 17_SCM2A

source_name: MOSJ-Dkk1 cell

value: MOSJ-Dkk1 cultures

value: Stress scrMo

value: scrMo


title: sncRNA organ atlas, Mus musculus, Heart_10


title: ACSA2 cells_SYN2 Mdb

value: astrocytes (ACSA2)

value: midbrain


title: 18_SCM3A


title: ACSA2 cells_SYN1 Mdb

value: parkinsonian


title: 16_SCM1A


title: sncRNA organ atlas, Mus musculus, Brain_9

value: Brain


title: WT-NHS-Rep2

city: Beijing

first: Hongchen

last: Zhang

state: Please Select

address: No.5 Yiheyuan Road Haidian District, Bei, jing,china

institute: Peking University

data_processing:
For RNA-seq data analysis, the paired-end reads were aligned to human genome build GRCh38/hg18 using Subread-align. Only uniquely mapped reads were retained for further analysis.
The number of read counts for each gene was calculated using Subread -featureCounts.
For each library, the read counts were adjusted using iDEP web tool
Differential expression analysis of two groups was performed using the DESeq2 package. The P values were adjusted using the Benjamini–Hochberg method.
Genes with an adjusted P < 0.005 and absolute log2[fold change] > 1 were considered as significantly differentially expressed genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw read count

source_name: HeLa cells

growth_protocol: Human cancer cell line HeLa S6 was cultured in DMEM (Gibco) containing 10% FBS (Lifetech), 50 μg mL penicillin and streptomycin (Lifetech). Cells were maintained at 37 °C in a humidified incubator with an atmosphere containing 5% CO2.

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA from HeLa cells and KAPA HyperPrep Kits (Roche, cat. no. KR0961) was used to prepare the cDNA libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One day before transfection, the cells were passaged into a 35-mm petri-dish at approximately 50% density. Transfection of cells was performed using Lipofectamine 3000 (Lifetech) in accordance with the manufacturer’s protocol. For Hex group, cells were treated with 1.5% 1,6-hexanediol for 60 mins during HS at 42 °C before lysed.

value: HeLa cells

value: Cancer Cell Line HeLa S6

value: untreated

value: WT cells


title: WT-NHS-Rep1


title: sncRNA organ atlas, Mus musculus, Brain_8

value: postnatal

value: female


title: ACSA2 cells_CT3 Mdb

value: control


title: 15_SVM3A

value: Stress DkkMo

value: DkkMo


title: ACSA2 cells_CT2 Mdb


title: 14_SVM2A


title: sncRNA organ atlas, Mus musculus, Brain_7

value: male


title: WT-HS-Rep1

value: Heat shock at 42 °C for 60 min


title: sncRNA organ atlas, Mus musculus, Brain_6


title: ACSA2 cells_SYN3 Mdb


title: WT-HS-Hex-Rep2

value: Heat shock at 42 °C and treated with 1.5% 1,6-hexanediol for 60 min


title: H3K36me3 CUT&Tag mCTXN, rep2

city: Yokohama

first: Sefan

last: Asamitsu

state: Kanagawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
Library strategy: CUT&Tag
Fastq files were processed for quality check and adapter trimming with the Trimgalore! (v0.5.0)
Trimmed reads were used for mapping to the mouse genome (mm10) using the Bowtie2 (v2.3.4).
Significant peaks relative to IgG control were obtained using the MACS2 (v2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Cultured mouse cortex neurons

extract_protocol:
Cells were permeabilized with 0.05% digitonin and processed according to a Direct-to-PCR CUT&Tag method.
Libraries were prepared according to a protocols provided by EpiCypher, Inc (EpiCypher® CUTANA® Direct-to-PCR CUT&Tag Protocol).

value: fetus

value: primary cultured neurons from the fetus mouse cortex

tag: antibody

value: H3K36me3 (Active motif, 61902)

value: 2 µM Ara-C at DIV3


title: 12_SN2A

value: MOSJ-Dkk1 cultures

value: Stress NT

tag: treatment

value: vehicle


title: WT-HS-Hex-Rep1

value: HeLa cells

tag: cell type

value: Cancer Cell Line HeLa S6


title: sncRNA organ atlas, Mus musculus, Brain_4

value: postnatal

value: Brain


title: H3K36me3 CUT&Tag mCTXN, rep1


title: 10_SN1A


title: M3-HS-Rep2

tag: cell line

value: HSF1 KO and transfected with HSF1 M3


title: M3-HS-Rep1


title: sncRNA organ atlas, Mus musculus, Brain_3


title: H3K27me3 CUT&Tag mCTXN, rep2

value: H3K27me3 (Active motif, 39055)


title: 09_S3

value: Log-phase scrMo

value: scrMo


title: WT-HS-Rep2

value: Heat shock at 42 °C for 60 min

value: WT cells


title: sncRNA organ atlas, Mus musculus, Brain_11

value: male


title: H3K9me3 CUT&Tag mCTXN, rep2

value: fetus

value: primary cultured neurons from the fetus mouse cortex

value: H3K9me3 (Active motif, 39062)


title: ACSA2 cells_CT1 Mdb

value: astrocytes (ACSA2)

value: midbrain

value: control


title: M1-NHS-Rep2

value: HeLa cells

value: untreated

value: HSF1 KO and transfected with HSF1 M1


title: 07_S1

value: MOSJ-Dkk1 cultures


title: H3K9me3 CUT&Tag mCTXN, rep1

value: 2 µM Ara-C at DIV3


title: 08_S2


title: sncRNA organ atlas, Mus musculus, Bone_9

value: postnatal

value: female

value: Bone


title: 13_SVM1A

value: Stress DkkMo

value: DkkMo


title: H3K4me3 CUT&Tag mCTXN, rep2

value: H3K4me3 (Active motif, 39159)


title: M1-NHS-Rep1

value: Cancer Cell Line HeLa S6


title: 06_V3

value: Log-phase DkkMo


title: H3K4me3 CUT&Tag mCTXN, rep1

value: fetus

value: primary cultured neurons from the fetus mouse cortex


title: 11_SN2A

value: Stress NT

value: vehicle


title: sncRNA organ atlas, Mus musculus, Brain_5

value: male

value: Brain


title: 05_V2


title: sncRNA organ atlas, Mus musculus, Bone_6


title: A549_IL17D_1

city: Tianjin

first: Zhenzhen

last: Lin

address: 22 Qixiangtai Road

institute: tianjin medical university

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie2.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: A549 cell line overexpress IL17D

growth_protocol: Control and IL17D-expressing A549 cell line were cultred in RPMI1640 medium containg 10%FBS

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA sequencing libraries were prepared using NovaSeq™ 6000 v1.5.

value: Lung adenocarcinoma

tag: genotype/variation

value: overexpress IL17D


title: A549_IL17D_3


title: A549_IL17D_2


title: H3K27me3 CUT&Tag mCTXN, rep1

value: H3K27me3 (Active motif, 39055)

value: 2 µM Ara-C at DIV3


title: 04_V1

value: MOSJ-Dkk1 cultures


title: sncRNA organ atlas, Mus musculus, Bone_3

value: postnatal

value: Bone


title: sncRNA organ atlas, Mus musculus, Brain_10


title: iG4 CUT&Tag mCTXN, rep1

value: recombinant BG4


title: 03_N3

value: Log-phase NT


title: sncRNA organ atlas, Mus musculus, Bone_12


title: iG4 CUT&Tag mCTXN, rep2


title: A549_empty_2

source_name: A549 cell line overexpress empty vector

value: overexpress empty vector


title: 02_N2


title: sncRNA organ atlas, Mus musculus, Bone_11


title: Input mCTXN, rep2

value: Rabbit IgG


title: A549_empty_1


title: Input mCTXN, rep1

value: fetus


title: 01_N1


title: sncRNA organ atlas, Mus musculus, Bone_7

value: female


title: A549_empty_3


title: expression_Sample_KO_cor_1

status: Public on Dec 18 2021

city: 上海

first: yu

last: yao

address: 上海市宝山区南陈路333号

institute: 上海大学

description: KO_cor-vs-WT_cor-diff-pval-0.05-FC-1.5.gene.xls

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.10.1). DESeq2 provides statistical routines for determining differential expression of digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg's approach to controlling the false discovery rate. Genes with pvalue < 0.05 and |log2FC| > 0.58 found by DESeq were assigned as differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: xls files include the expression of DEGs for each Sample …

source_name: cortex

extract_protocol:
Hippocampus and cortex were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, United States)  was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cortex


title: expression_Sample_KO_cor_3

address: 上海市宝山区南陈路333号


title: expression_Sample_KO_cor_2

address: 上海市宝山区南陈路333号


title: expression_Sample_WT_cor_3

address: 上海市宝山区南陈路333号

value: wild type


title: RNA_dex_5dpi_ha3

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description:
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
adapter sequence: GATCGGAAGAGCACACGT

data_processing:
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al, 2015)
Syrian hamster: Sequencing reads were aligned to the MesAur 1.0 version of the Mesocricetus auratus genome using standard parameter, using the Refseq gtf file described in GEO accession number GSE162208
Roborovski hamster: Sequencing reads were aligned to the draft assembly and gtf file described previously (doi: 10.1101/2021.10.02.462569)
For single-cell RNA-sequencing data, fastq files were processed using a merged Roborvski hamster/SARS-CoV-2 genome by applying CellRanger 6.0.2 with standard parameters
Seurat R and loom objects were processed as described on the github page https://github.com/Berlin-Hamster-Single-Cell-Consortium/Dwarf-Hamster-Dexamethasone-Antibody
Genome_build: MesAur 1.0
Genome_build: Phodopus roborvskii draft assembly
Genome_build: SARS-CoV-2 MN908947
Supplementary_files_format_and_content: tab-separated values
Supplementary_files_format_and_content: h5 matrix
Supplementary_files_format_and_content: Seurat R object
Supplementary_files_format_and_content: loom object

organism: Mesocricetus auratus

source_name: Dexamethasone treated animal 3, 5dpi, lung sample for bulk RNA-seq

growth_protocol:
Hamsters were weighted daily and monitored for signs of disease twice-daily. Severely sick animals were euthanized according to defined humane endpoints including body temperature <33 °C, acute respiratory distress or weight loss >20%. Hamsters were selected randomly for all scheduled take-out time points (day 3 and 5 for Roborovski hamsters, day 5 and 7 for Syrian hamsters).
Euthanasia prior analysis occurred by exsanguination under anesthesia as previously described (PMID 32698441, 33271063). Peripheral blood was collected in EDTA-coated syringes and lung lobes were collected for follow-up analyses, in which the left lobe was used for histopathology, the right caudal lobe for single-cell analysis, the right cranial lobe for virological assessments and the right medial as backup to repeat virological analyses as needed.

extract_protocol:
For isolation of single cells lobus caudalis of the right lung was removed and placed in storage medium (1× PBS, 0.5 % BSA) until further processing. Storage and isolation media contained 2 µg/mL ActinomycinD. Tissues and cells were always spun at 350 x g for 6 minutes at 4 °C. Mechanical dissociation of lung lobes was achieved by clapping motions with tweezers for 2 minutes in enzymatic digestion medium (3,4 mg/mL Collagenase Cls II (Merck), 1 mg/mL DNase I (PanReac AppliChem), in 2 mL Dispase medium per lung lobe (Corning), 50 Caseinolytic Units/mL followed by 30 minutes incubation at 37°C and 5 % CO2.
Further tissue dissociation was achieved by repeated pipetting of digested lung tissue with 5 mL pipettes and passing of cell suspension with plungers through 70 µm cell strainers. Cells were pelleted from suspension by centrifugation and resuspended in red blood cell lysis buffer (BioLegend). Lysis reaction was stopped and cells washed with excessive volumes of PBS/BSA. Cells were centrifuged, resuspended in low-BSA buffer (1× PBS, 0.04 % BSA) and counted via hemocytometer and trypan blue.
Then, 1,000,000 lung cells per sample were subjected to Cell Multiplexing Oligo (CMO) labeling according to the manufacturers’ instructions (3ʹ-CellPlex-Kit-Set-A, 10x Genomics). Labelled cells from 12 samples were pooled, filtered (40 µm) and counted. Pooled cells were adjusted to a final concentration of ~1,600 cells / μL and filtered with 40 µm FloMi filters (Merck) suitable for low volumes prior subjection to scRNA sequencing.
For Lung RNA Bulk sequencing the lobus medialis of the right lung lobe was removed carefully and homogenzied in Trizol reagent using a bead mill procedure (Speedmill, Analytic Jena), RNA was extracted according to the manufacturer’s instructions.
Bulk and single-cell RNA-sequencing libraries were constructed using commercial kits (New England Biolabs, 10xGenomics), see column "library construction protocol" in the SAMPLES section.

treatment_protocol: At 6-10 weeks of age hamsters were infected intranasally as previously described (PMID 32698441, 33271063). Briefly, hamster received 1 x 105 pfu SARS-CoV-2 Variant B1 (BavPat1) intranasally under anesthesia.

value: Lung

value: dexamethasone

tag: sampling timepoint


title: expression_Sample_WT_cor_2

address: 上海市宝山区南陈路333号


title: expression_Sample_WT_cor_1

address: 上海市宝山区南陈路333号


title: expression_Sample_KO_hippo_3

address: 上海市宝山区南陈路333号

description: KO_hippo-vs-WT_hippo-diff-pval-0.05-FC-1.5.gene.xls

source_name: hippocampus

value: hippocampus


title: RNA_dex_5dpi_ha2

source_name: Dexamethasone treated animal 2, 5dpi, lung sample for bulk RNA-seq


title: expression_Sample_KO_hippo_2

address: 上海市宝山区南陈路333号


title: RNA_abdex_7dpi_ha2

source_name: Antibody+Dexamethasone treated animal 2, 7dpi, lung sample for bulk RNA-seq

value: antibody+dexamethasone


title: expression_Sample_KO_hippo_1

address: 上海市宝山区南陈路333号


title: SAMPLE 6_ApoE_H

type: RNA

city: Eggenfelden

first: Christian

middle: Albert

last: Gleissner

address: Simonsöder Allee 20

department: Cardiology

institute: Rottal-Inn Kliniken KU

hyb_protocol: Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed once in High Temp Wash buffer (Illumina Inc.) at 55°C and then twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes (in between washed with ethanol at room temperature). After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.

scan_protocol: Microarray scanning was done using an iScan array scanner. Data extraction was done for all beads individually, and outliers are removed when > 2.5 MAD (median absolute deviation). All remaining data points are used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated.

data_processing:
The analysis is done with R on the bead-level data which you can find in the raw data produced by the scanner. All analyses are done using the following mechanisms: 1) outlier removal (see below). 2) average values over beads are means (not median). 3) statistical tests are t-tests over all beads (e.g for one probeID over all beads of all samples of a group) in original scale (not log2 scale).    Calculation of GeneView data: The calculations are also done on the set of beads which belong to a given Gene Symbol (annotation column Symbol).       Outlier removal on bead level: Outliers are removed by taking only beads with an expression value > 20 before using the 2.5 MADs rule. The ProbeIDs expression value is than the mean of the remaining beads.    The remaining bead level lists of different length for each sample are randomly filled with NAs (NA=not available) and build the bead level matrix on which quantile normalization is performed.    MAD rule: mad = median absolute deviation, x = one bead level expression value of some specific probeID, Than: outliers are those x where abs((x-median)/mad) > 2.5    The analysis is done with R on the bead-level data which you can find in the raw data produced by the scanner. All analyses are done using the following mechanisms: 1) outlier removal (see below). 2) average values over beads are means (not median). 3) statistical tests are t-tests over all beads (e.g for one probeID over all beads of all samples of a group) in original scale (not log2 scale).    Calculation of GeneView data: The calculations are also done on the set of beads which belong to a given Gene Symbol (annotation column Symbol).       Outlier removal on bead level: Outliers are removed by taking only beads with an expression value > 20 before using the 2.5 MADs rule. The ProbeIDs expression value is than the mean of the remaining beads.    The remaining bead level lists of different length for each sample are randomly filled with NAs (NA=not available) and build the bead level matrix on which quantile normalization is performed.    MAD rule: mad = median absolute deviation, x = one bead level expression value of some specific probeID, Than: outliers are those x where abs((x-median)/mad) > 2.5    The analysis is done with R on the bead-level data which you can find in the raw data produced by the scanner. All analyses are done using the following mechanisms: 1) outlier removal (see below). 2) average values over beads are means (not median). 3) statistical tests are t-tests over all beads (e.g for one probeID over all beads of all samples of a group) in original scale (not log2 scale).    Calculation of GeneView data: The calculations are also done on the set of beads which belong to a given Gene Symbol (annotation column Symbol).       Outlier removal on bead level: Outliers are removed by taking only beads with an expression value > 20 before using the 2.5 MADs rule. The ProbeIDs expression value is than the mean of the remaining beads.    The remaining bead level lists of different length for each sample are randomly filled with NAs (NA=not available) and build the bead level matrix on which quantile normalization is performed.    MAD rule: mad = median absolute deviation, x = one bead level expression value of some specific probeID, Than: outliers are those x where abs((x-median)/mad) > 2.5
As test for significance the student’s t-test is used on the bead expression values of the two groups of interest. In the case of significance of expression against background we tested for greater than all negative beads for this sample and in the case of comparing separate groups we tested for inequality of the means of the groups. In both cases Benjamini-Hochberg correction was applied to the complete set of p-values of all ProbeIDs on the chip. The average expression value is calculated as mean of the measured expressions of beads together with the standard deviation of the beads.

label: biotin

label_protocol: The laboratory work was done in the Genomics and Proteomics Core Facility at the German Cancer Research Center, Heidelberg, Germany (DKFZ). Biotin-labeled cRNA samples for hybridization on Illumina MouseWG-6 v2.0 arrays (Illumina, Inc.) were prepared according to Illumina's recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine et al., 1992). In brief, 100 ng total RNA was used for complementary DNA (cDNA) synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA according to the Illumina® Total Prep™ RNA Amplification Kit (Life Technologies).  Biotin-16-UTP was purchased from Roche Applied Science, Penzberg, Germany. The cRNA was column purified according to TotalPrep RNA Amplification Kit, and eluted in 60 µl of water. Quality of cRNA was controlled using the RNA Nano Chip Assay on an Agilent 2100 Bioanalyzer and spectrophotometrically quantified (NanoDrop).

growth_protocol: CD11c+ cells were isolated from mouse spleens explanted from WT mice fed with standard diet (normal chow, NC), WT mice fed with high cholesterol diet (HC), ApoE-/- mice fed with NC and ApoE-/- mice fed with HC using CD11c MicroBeads UltraPure, MS Columns and a MiniMACS™ Separator (Miltenyi Biotec, USA). For each condition, RNA was isolated using columns including a DNAse-step followed by reverse transcription (all reagents from Qiagen, Valencia, CA). RNA was labeled and hybridized to Illumina MouseWG-6 v.2.0 Expression Bead Chips (Illumina, San Diego, USA) according to the manufacturer’s instructions at the Genomics and Proteomics Core Facility of the German Cancer Research Center, Heidelberg. For each sample, RNA was hybridized to a separate gene array.

treatment_protocol: No specific treatment of cells was performed.

tag: strain/genotype

value: ApE-/-

value: high cholesterol diet (HC)

tag: tissue/cell type

value: CD11c+ cells isolated from mouse spleens


title: SAMPLE 5_ApoE_H

extract_protocol: RNA was isolated using columns including a DNAse-step followed by reverse transcription (all reagents from Qiagen, Valencia, CA).


title: SAMPLE 8_B6_NC

value: standard diet (normal chow, NC)


title: RNA_dex_5dpi_ha1

source_name: Dexamethasone treated animal 1, 5dpi, lung sample for bulk RNA-seq


title: RNA_dex_7dpi_ha2

source_name: Dexamethasone treated animal 2, 7dpi, lung sample for bulk RNA-seq


title: RNA_dex_7dpi_ha3

source_name: Dexamethasone treated animal 3, 7dpi, lung sample for bulk RNA-seq


title: RNA_abdex_7dpi_ha3

source_name: Antibody+Dexamethasone treated animal 3, 7dpi, lung sample for bulk RNA-seq


title: SAMPLE 7_B6_NC


title: SAMPLE 11_B6_H


title: expression_Sample_WT_hippo_3

address: 上海市宝山区南陈路333号

tag: strain


title: SAMPLE 9_B6_NC


title: SAMPLE 4_ApoE_H


title: SAMPLE 12_B6_H


title: SAMPLE 3_ApoE_NC


title: SAMPLE 2_ApoE_NC


title: SAMPLE 1_ApoE_NC


title: RNA_abdex_5dpi_ha3

source_name: Antibody+Dexamethasone treated animal 3, 5dpi, lung sample for bulk RNA-seq


title: SAMPLE 10_B6_H


title: RNA_abdex_7dpi_ha1

source_name: Antibody+Dexamethasone treated animal 1, 7dpi, lung sample for bulk RNA-seq


title: expression_Sample_WT_hippo_1

address: 上海市宝山区南陈路333号


title: RNA_abdex_5dpi_ha2

source_name: Antibody+Dexamethasone treated animal 2, 5dpi, lung sample for bulk RNA-seq


title: RNA_dex_7dpi_ha1

source_name: Dexamethasone treated animal 1, 7dpi, lung sample for bulk RNA-seq


title: RNA_ab_7dpi_ha3

source_name: Antibody treated animal 3, 7dpi, lung sample for bulk RNA-seq

value: antibody


title: RNA_ab_7dpi_ha2

source_name: Antibody treated animal 2, 7dpi, lung sample for bulk RNA-seq


title: LI24hrep1

city: San Francisco

first: jake

last: bieber

address: 1700 4th Street

institute: University of California, San Francisco

data_processing:
Paired-end sequencing reads were aligned to the reference genome GRCm38 and annotated to vM25.primary_assembly obtained from gencode (htttps://www.gencodegenes.org/mouse) using STAR v.2.7.9a and featureCounts v.2.0.2
The obtained gene count data was normalized by using DESeq2 v.3.13
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: large intestine

growth_protocol: intestinal monolayers were grown for 24 hours before RNA collection

extract_protocol:
all RNA was collected using the RNAEasy Plus Mini Kit from Qiagen
RNA libraries were prepared for sequencing using standard Genewiz protocols

treatment_protocol: intestinal monolayers were cultured in control media

value: large intestine

value: intestinal monolayers


title: SI24hrep3

source_name: small intestine

value: small intestine


title: LI24hrep2


title: SI24hrep2


title: LI24hrep3


title: RNA_ab_7dpi_ha1

source_name: Antibody treated animal 1, 7dpi, lung sample for bulk RNA-seq


title: RNA_ab_5dpi_ha3

source_name: Antibody treated animal 3, 5dpi, lung sample for bulk RNA-seq


title: LIcryptrep3

value: in vivo tissue


title: LIcryptrep2


title: SI24hrep1


title: RNA_ab_5dpi_ha2

source_name: Antibody treated animal 2, 5dpi, lung sample for bulk RNA-seq


title: LIcryptrep1


title: RNA_ab_5dpi_ha1

source_name: Antibody treated animal 1, 5dpi, lung sample for bulk RNA-seq


title: expression_Sample_WT_hippo_2

address: 上海市宝山区南陈路333号

source_name: hippocampus


title: SIcryptrep2


title: RNA_aaUntr_7dpi_ha3

source_name: Untreated animal 3, 7dpi, lung sample for bulk RNA-seq


title: RNA_aaUntr_7dpi_ha2

source_name: Untreated animal 2, 7dpi, lung sample for bulk RNA-seq


title: RNA_aaUntr_7dpi_ha1

source_name: Untreated animal 1, 7dpi, lung sample for bulk RNA-seq


title: RNA_aaUntr_5dpi_ha2

source_name: Untreated animal 2, 5dpi, lung sample for bulk RNA-seq


title: SIcryptrep1


title: RNA_aaUntr_5dpi_ha1

source_name: Untreated animal 1, 5dpi, lung sample for bulk RNA-seq


title: LT_DT_scRNA

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

description: scRNA_raw_count_matrix_for_4_tumor_stages.csv

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Raw sequencing data was demultiplexed, debarcoded, mapped to mm10 genome with an exogenous eGFP sequence, and counted following the Cell Ranger v.3.1.0 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R.
Genome_build: mm10 genome
Supplementary_files_format_and_content: two csv files containing raw count values for cells from 4 stages (Primary, dormant, long-term dormant, and recurrent), and 2 treatment arms (control/IgG and anti-Jagged-1), respectively

source_name: Mammary Gland Tumors

growth_protocol: Mice were raised and maintained under standard laboratory conditions.

extract_protocol:
Tissues were harvested in PBS on ice and single cells were prepared by using the mouse GentleMacs kit. Single cells were frozen in 10%DMSO+90% FBS. When cells were thawed, 99% live cells were sorted by BD sorter using DAPI staining. 10,000 cell were targeted for 10X Genomics sequencing.
Libraries were prepared using Chromium single cell 3’ reagent kit version 2 for Dormant, Primary, Recurrent and LT-DT samples, and version 3 for IgG and Jag1 samples.

treatment_protocol: One day after tumor transplantation, mice were injected intraperitoneally (i.p) with the B/B homodimerizer every 3 days until tumors reached about 4-5mm in diameter. At that point tumors grew independently of the dimerizer. Once tumors reached about 7-9mm in diameter, mice were treated with the FGFR inhibitor NVP-BGJ398 for 14 days by oral gavage) and then drug treatment was stopped for another 14 days. At this timepoint, depending on the experiment, mice were: 1) sacrificed for residual tissue collection, or 2) left untreated for recurrence, or 3) treated with antibodies (anti-IgG or Jagged-1). For treatment studies, dormant tumors were generated and mice were randomized into 2 groups: control IgG and anti-Jagged-1 treatment. Mice were treated with 15mg/kg of drug once a week for 5 weeks and treatment was stopped. One week after the cessacion of drug, samples were collected for 10X Genomics sequencing.

value: FVB (FVB.rGH-Luc-GFP)

value: Mammary Gland

tag: age

value: 32-34 weeks


title: RNA_aaUntr_5dpi_ha3

source_name: Untreated animal 3, 5dpi, lung sample for bulk RNA-seq


title: Programmed_MN_TF_SAG_Replicate_2

city: St Louis

first: Samantha

last: Morris

state: Missouri

address: Department of Developmental Biology, Washington University School of

institute: Washington University in St Louis

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to mm10 genome build via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Induced motor neurons converted from mouse embryonic stem cells, with transcription factors and smoothened agonist

extract_protocol: 10x Genomcis Chromium single cell preparation


title: IgG_scRNA

description: scRNA_raw_count_matrix_for_2_treatment_arms.csv

value: 16 weeks


title: Recurrent_scRNA

value: 20-22 weeks


title: Expanded_iEPs_Replicate_2

source_name: Induced endoderm progenitors converted from mouse embryonic fibroblasts


title: Primary_scRNA

value: 8-10 weeks


title: Dormant_scRNA

value: 10-12 weeks


title: Programmed_MN_TF_RA_SAG_Replicate_2

source_name: Induced motor neurons converted from mouse embryonic stem cells, with transcription factors and retionic acid and smoothened agonist


title: Programmed_MN_TF_RA_SAG_Replicate_1


title: Programmed_MN_TF_SAG_Replicate_1


title: Programmed_MN_TF_RA_Replicate_1

source_name: Induced motor neurons converted from mouse embryonic stem cells, with transcription factors and retionic acid


title: Programmed_MN_TF_RA_Replicate_2


title: SIcryptrep3

source_name: small intestine


title: Programmed_MN_TF_Only_Replicate_1

source_name: Induced motor neurons converted from mouse embryonic stem cells, with transcription factors


title: Programmed_MN_TF_Only_Replicate_2


title: Day14_iCM_Replicate_2

source_name: Induced cardiomyoctes converted from mouse cardiac fibroblast


title: Jag1_scRNA


title: Expanded_iEPs_Matrigel Replicate_2

source_name: Induced endoderm progenitors converted from mouse embryonic fibroblasts, cultured in matrigel sandwich


title: Sorted CAFs_Plate_IV_APTKA_Orthotopic_Tumor_IV

city: Frankfurt

first: Florian

last: Buettner

state: Germany

address: Theodor-Stern-Kai 7

department: DKTK Frankfurt

institute: DKFZ

description: Single-Cell-RNA-Sequencing

data_processing:
Read 1 was assigned 26 bp and was used to identify the Illumina library barcode, cell barcode and UMI
Read 2 was assigned 60 bp and used to map with BWA-MEM against mouse mm10 RefSeq
Mapping and counts tables generation were automated using MapAndGo script
Mapping with BWA-MEM against Mouse mm10 RefSeq
Genome_build: mm10
Supplementary_files_format_and_content: Transcript counts

source_name: In Vivo Orthotopic Tumor IV

extract_protocol:
barcoded SORT-seq-protocol: cells heat lysed at 65°C followed by cDNA synthesis
Library preparation following CEL-Seq2 protocol

treatment_protocol: Single Cell sorted CAFs from untreated APTKA orthotopic tumors transplanted in C57BL6 mice colons

value: Female

value: Sorted Cancer Associated Fibroblasts


title: Sorted CAFs_Plate_III_APTKA_Orthotopic_Tumor_III

description: Single-Cell-RNA-Sequencing

source_name: In Vivo Orthotopic Tumor III


title: Day14_iCM_Replicate_1


title: Sorted CAFs_Plate_II_APTKA_Orthotopic_Tumor_II

description: Single-Cell-RNA-Sequencing

source_name: In Vivo Orthotopic Tumor II


title: Sorted CAFs_Plate_I_APTKA_Orthotopic_Tumor_I

description: Single-Cell-RNA-Sequencing

source_name: In Vivo Orthotopic Tumor I


title: WT.p2

city: Iwaki

first: Yoshiaki

last: Kanemoto

state: Fukushima

address: kaminodai 57, jyobankamiyunagaya-town

institute: Jyoban Hospital

description: chromatin

data_processing:
Peak calling was performed using MACS2 (ver. 2.1.2) and PePr(ver. 1.1.24) with default parameters respectively.
Reads were mapped to the mm10 reference sequence using Burrows-Wheeler Aligner (BWA-MEM: ver. 0.7.17-r1188), and duplicate reads were removed with Picard (ver. 2.18.16).
Peak annotation were conducted by HOMER (ver.4.9.1) with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Known motifs and de novo consensus motifs in central 200 bp of obtained peaks were searched by HOMER with default settings.

source_name: Keratinocyte

growth_protocol: HaCaT WT and VDR KO cells were routinely culutured in DMEM supplemented with 10% fetal bovine serume at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Cell storage reagent, CELLBANKER plus 1.
Fragmentation and amplification of ATAC-seq libraries were conducted according to Buenrostro et al.(2015). Briefly, approximately 50,000 cells were lysed and transposition reaction was performed with the Tn5 Transposase (Illumina Catalog #FC121-1030) at 37°C for 30 minutes. The reaction liquid was purified with Qiagen MinElute PCR Purification Kit. Then 5 cycles of PCR with custom Nextera PCR primers (from Wu and Buenrostro 2013) were conducted using NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolabs). Additional number of PCR cycles was determined by qPCR of the partly amplified products, following Wu and Buenrostro 2013. The PCR products were purified with Agencourt AMPure XP beads (Beckman Coulter:A63881), using double size selection (left ratio: 1.4x, right ratio: 0.5x) according to the manufacturer’s protocol.

treatment_protocol: Two replicates cultured on 100 mm dishes were treated with 1,25(OH)2D3 for 8hrs.

value: treated with 1,25(OH)2D3

value: HaCat

value: WT


title: WT.p1

description: chromatin


title: WT.m2

description: chromatin

value: untreated


title: WT.m1

description: chromatin


title: KO.p2

description: chromatin

value: VDR KO


title: Expanded_iEPs_Matrigel Replicate_1


title: THP1_NC2_E4_R1

city: Rotterdam

first: Rute

last: Marques

address: Dr Molewaterplein 50

country: Netherlands

institute: Erasmus MC

hyb_protocol: 750 ng of labelled cRNA were hybridized overnight onto Illumina HT-12 v3 BeadChip arrays, according to Illumina's protocols

scan_protocol: Following hybridization, the arrays were washed, blocked, stained and scanned on an Illumina BeadStation 500GX, following the manufacturer's protocols. Illumina GenomeStudio v1.5 software was used to generate signal intensity values from the scanned pictures.

data_processing: The Limma and Lumi packages for R were used for the normalization and statistical analysis of the microarray data. Data analysis started with background subtraction, followed by VST transformation and quartile normalization, using the LumiExpresso command. After normalization, VST transformation was inversed to extract the normalized signal intensity values.

source_name: THP1, Negative Control2, Experiment4, Replicate1

label_protocol: 250ng of total RNA was reverse transcribed, amplified and biotinylated using Illumina TotalPrep RNA Amplification Kit (Ambion), according to manufacturer's instructions

growth_protocol: Huh7 and THP1 cells were grown in RPMI medium containing L-glutamine and HEPES, supplemented with 10% FCS and penicillin/streptomycin antibiotics, at 37C and 5% CO2

extract_protocol: Total RNA was extracted using the RNeasy Mini kit from Qiagen, including an on-column DNAse digestion step, according to the manufacturer's manual

treatment_protocol: For the siRNA knockdown we used the Silencer Select Negative Controls #1 and #2 from Ambion, and the intergenic transcript specific siRNA against target sequence AACTACGTGAAGAGGCCTCTG. Cells (300000 per well) were transfected in 6-well plates, in 2.5 ml Optimem medium (Invitrogen) supplemented with 2.5% FCS.  Per well, 250 ul transfection mix was added containing 5ul Lipofectamine 2000 (Invitrogen) and 50 pmol siRNA(Ambion/Applied Biosystems), according to the manufacturer’s protocol. Cells were incubated for 2 days at 37C under 5% CO2 before sample collection.

value: monocytes

value: Negative Control siRNA #2


title: THP1_NC1_E4_R2

source_name: THP1, Negative Control1, Experiment4, Replicate2

value: Negative Control siRNA #1


title: THP1_NC2_E4_R2

source_name: THP1, Negative Control2, Experiment4, Replicate2


title: THP1_NC1_E3_R2

source_name: THP1, Negative Control1, Experiment3, Replicate2


title: KO.p1

description: chromatin


title: THP1_NC2_E3_R1

source_name: THP1, Negative Control2, Experiment3, Replicate1


title: KO.m2

description: chromatin


title: THP1_INTG_E4_R2

source_name: THP1, C5_TRAF1_Intergenic siRNA, Experiment4, Replicate2


title: KO.m1

description: chromatin


title: THP1_NC1_E3_R1

source_name: THP1, Negative Control1, Experiment3, Replicate1


title: THP1_NC2_E2_R2

source_name: THP1, Negative Control2, Experiment2, Replicate2


title: THP1_NC2_E3_R2

source_name: THP1, Negative Control2, Experiment3, Replicate2


title: THP1_INTG_E3_R2

source_name: THP1, C5_TRAF1_Intergenic siRNA, Experiment3, Replicate2


title: THP1_INTG_E4_R1

source_name: THP1, C5_TRAF1_Intergenic siRNA, Experiment4, Replicate1


title: THP1_NC1_E4_R1

source_name: THP1, Negative Control1, Experiment4, Replicate1


title: 3161_S

city: Amsterdam

first: Esther

last: Lips

address: Plesmanlaan 121

department: Molecular Pathology

institute: NKI-AVL

description:
3161_S
3597_40_3161_S_CGAACTTA

data_processing:
Reads were aligned to the human transcriptome (Homo_sapiens.GRCh37.75.gtf) using Tophat v2.1[54]. Readcounts per gene were calculated using lcount[55], and normalized using DESeq2[56]. The SVA R package[57] was used to combine and batch correct gene expression datasets. Gene expression levels were associated with chemotherapy response using samr[58]; differential gene expression between pre- and post-treatment samples was analyzed using DESeq2[56]. Subsequent pathway / GO-term enrichment was performed using the Reactome Cytoscape plugin[59, 60] and geneset enrichment was performed using GSEA[61]. The most significant genes from the samr analysis (FDR < 5%) were selected for a ‘core enrichment’ set, based on unsupervised clustering and pathway and GO-term enrichment (Supplementary Table S1). Metagene scores for all three processes were created by calculating the median expression of genes assigned to each cluster. Expression above or below the metagene median was used to stratify patients into a HHL (Proliferation High, Immune High, ECM Low) or LLH (Proliferation Low, Immune Low, ECM High) profile. RNA-seq reads of the pre-post dataset were also aligned to the human reference genome version 37.75 (hg19) using bwa[45] to be able to confirm somatic mutations and indels in the expression data.
Genome_build: 37.75 (hg19)
Supplementary_files_format_and_content: The processed data file is in txt format, and contains readcounts.

source_name: human breast

extract_protocol:
RNA was isolated from samples with a tumor percentage > 50%, from thirty 30-μm cryosections. A 5-μm section halfway through the biopsy was stained for hematoxylin and eosin and analyzed by a pathologist for tumor percentage. Total RNA was isolated with RNA-Bee (Bio-Connect, Huissen, The Netherlands, Cat No. CS-100B), DNase-treated by using the Qiagen RNase-free DNase Set (Qiagen, Venlo, The Netherlands, Cat No. 79254) and RNeasy spin columns (Qiagen, Cat No. 74104) and dissolved in RNase-free H2O. Quality and quantity of the total RNA was assessed by the 2100 Bioanalyzer using a Nano chip (Agilent, Santa Clara, CA); samples having RIN>6.4 were subjected to library generation.
mRNA libraries were generated using the TruSeq RNA Library Preparation Kit v2 (Illumina Inc., San Diego, Cat.No RS-122-2001/2) according to the manufacturer's instruction (Part # 15026495 Rev. B). The libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent, Santa Clara, CA), diluted and pooled equimolar into a 10nM sequencing pool containing 9 libraries each, and sequenced with 50 basepair single reads (pre-treatment samples only) or 65 basepair single reads (pre-post treatment set) on a HiSeq2000 using V3 chemistry (Illumina Inc., San Diego).

tag: tissue type

tag: chemotherapy

value: 3x ddAC, 9x paclitaxel

tag: neoadjuvant response index (nri)

tag: grade

tag: t-stage

tag: n-stage

tag: subtype

value: LUM

tag: recurrence


title: THP1_INTG_E3_R1

source_name: THP1, C5_TRAF1_Intergenic siRNA, Experiment3, Replicate1

tag: tissue

tag: treatment


title: 3130_S

description:
3130_S
3597_38_3130_S_CCGTGAGA

value: 6x ddAC


title: 3161_B

description:
3161_B
3597_39_3161_B_CCTCCTGA

value: biopsy


title: 3130_B

description:
3130_B
3597_37_3130_B_CCGAAGTA


title: THP1_NC2_E2_R1

source_name: THP1, Negative Control2, Experiment2, Replicate1

tag: cell line


title: 3067_S

description:
3067_S
3597_36_3067_S_CCAGTTCA


title: THP1_NC1_E2_R1

source_name: THP1, Negative Control1, Experiment2, Replicate1


title: 3067_B

description:
3067_B
3597_35_3067_B_CATACCAA


title: THP1_NC1_E2_R2

source_name: THP1, Negative Control1, Experiment2, Replicate2


title: 3036_S

description:
3036_S
3597_32_3036_S_CAATGGAA


title: 3036_B

description:
3036_B
3597_31_3036_B_CAAGACTA


title: 3065_S

description:
3065_S
3597_34_3065_S_CAGCGTTA


title: THP1_INTG_E2_R2

source_name: THP1, C5_TRAF1_Intergenic siRNA, Experiment2, Replicate2


title: THP1_INTG_E1_R1

source_name: THP1, C5_TRAF1_Intergenic siRNA, Experiment1, Replicate1


title: 3001_S

description:
3001_S
3597_30_3001_S_CAACCACA


title: THP1_NC2_E1_R1

source_name: THP1, Negative Control2, Experiment1, Replicate1


title: THP1_INTG_E1_R2

source_name: THP1, C5_TRAF1_Intergenic siRNA, Experiment1, Replicate2


title: 2976_S

description:
2976_S
3597_28_2976_S_ATCCTGTA

value: 3x ddAC, 4x paclitaxel


title: 3001_B

description:
3001_B
3597_29_3001_B_ATTGAGGA


title: 2852_S

description:
2852_S
3597_26_2852_S_AGCAGGAA

value: 3x ddAC


title: THP1_NC2_E1_R2

source_name: THP1, Negative Control2, Experiment1, Replicate2


title: THP1_INTG_E2_R1

source_name: THP1, C5_TRAF1_Intergenic siRNA, Experiment2, Replicate1


title: THP1_NC1_E1_R2

source_name: THP1, Negative Control1, Experiment1, Replicate2


title: THP1_NC1_E1_R1

source_name: THP1, Negative Control1, Experiment1, Replicate1


title: 2976_B

description:
2976_B
3597_27_2976_B_AGTCACTA


title: 3065_B

description:
3065_B
3597_33_3065_B_CACTTCGA


title: MCF7 cells, HSF1-/-_estrogen_4h_repeat 3

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

description:
MCF7 CRISPR/Cas9 HSF1-/- mix knockout cells - estrogen treated for 4 hour - repeat 3
C6

data_processing:
Fastq files were aligned to GRCh38 genome using hisat 2.0.5
Reads were counted using FeatureCounts with transcriptome reference Gencode v26
Counts were normalized using DESeq2 version 1.32.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed files are in tab separated text files. They include raw counts and normalized expression from all samples.

source_name: MCF7 cells

growth_protocol: The wild-type MCF7 cells were purchased from ATCC (HTB-22) and used as a primary model. Cells were grown in DMEM/F12 medium supplemented with 10% fetal bovine serum and antibiotic-antimycotic cocktail (penicillin, streptomycin, amphotericin) at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated from all MCF7 cell variants (untreated and treated with 10 nM E2 for 4 h or heat shocked for 1h at 43°C and recovered for 2 h) using the Direct-ZolTM RNA MiniPrep Kit (Zymo Research) and digested with DNase I (Worthington Biochemical Corporation). For each experimental point, RNAs from three biological replicates were first tested by RT-qPCR for the efficiency of treatments, then pooled and sequenced. For second CRISPR/Cas9 HSF1 knockout model (CRISPR/Cas9 HSF1+/+ mix and HSF1-/- mix samples) three independent biological repeats were done including RNA isolation and sequencing.
RNA libraries were prepared for sequencing according to the standard Illumina protocols

treatment_protocol: Cells were seeded on culture plates. Next day the medium was replaced into phenol-free DMEM/F12 medium supplemented with 10% dextran-activated charcoal-stripped FBS and 48 hours later 17β-estradiol was added to final concentration of 10nM for 4 hour or cells were subjected to hyperthermia (43°C) for 1 hour with 2 hours of recovery.

tag: tumor

value: adenocarcinoma

tag: Sex

value: female

value: 69 years

value: breast

tag: genotype

value: estrogen


title: Huh7_NC1_E4_R2

source_name: Huh7, Negative Control1, Experiment4, Replicate2

value: Liver


title: MCF7 cells, HSF1-/-_estrogen_4h_repeat 1

description:
MCF7 CRISPR/Cas9 HSF1-/- mix knockout cells - estrogen treated for 4 hour - repeat 1
C4


title: 2852_B

description:
2852_B
3597_25_2852_B_AGATCGCA


title: MCF7 cells, HSF1-/-_control repeat 2

description:
MCF7 CRISPR/Cas9 HSF1-/- mix knockout cells - untreated - repeat 2
C2

value: control


title: 2817_B

description:
2817_B
3597_23_2817_B_ACTATGCA

value: 3x AC, 3x CD


title: Huh7_INTG_E4_R1

source_name: Huh7, C5_TRAF1_Intergenic siRNA, Experiment4, Replicate1


title: MCF7 cells, HSF1-/-_estrogen_4h_repeat 2

description:
MCF7 CRISPR/Cas9 HSF1-/- mix knockout cells - estrogen treated for 4 hour - repeat 2
C5


title: Huh7_INTG_E4_R2

source_name: Huh7, C5_TRAF1_Intergenic siRNA, Experiment4, Replicate2


title: MCF7 cells, HSF1-/-_control repeat 1

description:
MCF7 CRISPR/Cas9 HSF1-/- mix knockout cells - untreated - repeat 1
C1


title: Huh7_NC2_E3_R2

source_name: Huh7, Negative Control2, Experiment3, Replicate2


title: Huh7_INTG_E3_R2

source_name: Huh7, C5_TRAF1_Intergenic siRNA, Experiment3, Replicate2


title: MCF7 cells, HSF1+/+_estrogen_4h_repeat 2

description:
MCF7 CRISPR/Cas9 HSF1+/+ mix control cells - estrogen treated for 4 hour - repeat 2
B5


title: 2789_B

description:
2789_B
3597_21_2789_B_ACGCTCGA

source_name: human breast


title: Huh7_NC1_E4_R1

source_name: Huh7, Negative Control1, Experiment4, Replicate1


title: 2789_S

description:
2789_S
3597_22_2789_S_ACGTATCA


title: MCF7 cells, HSF1-/-_control repeat 3

description:
MCF7 CRISPR/Cas9 HSF1-/- mix knockout cells - untreated - repeat 3
C3


title: MCF7 cells, HSF1+/+_estrogen_4h_repeat 3

description:
MCF7 CRISPR/Cas9 HSF1+/+ mix control cells - estrogen treated for 4 hour - repeat 3
B6


title: MCF7 cells, HSF1+/+_estrogen_4h_repeat 1

description:
MCF7 CRISPR/Cas9 HSF1+/+ mix control cells - estrogen treated for 4 hour - repeat 1
B4


title: RNA_abdex_5dpi_ha1

source_name: Antibody+Dexamethasone treated animal 1, 5dpi, lung sample for bulk RNA-seq

value: Lung

value: antibody+dexamethasone

tag: sampling timepoint


title: MCF7 cells, HSF1+/+_control repeat 2

description:
MCF7 CRISPR/Cas9 HSF1+/+ mix control cells - untreated - repeat 2
B2


title: Huh7_NC2_E4_R2

source_name: Huh7, Negative Control2, Experiment4, Replicate2

value: Negative Control siRNA #2


title: Huh7_NC2_E4_R1

source_name: Huh7, Negative Control2, Experiment4, Replicate1


title: 2817_S

description:
2817_S
3597_24_2817_S_AGAGTCAA


title: 2739_S

description:
2739_S
3597_20_2739_S_ACCTCCAA


title: MCF7 cells, HSF1+/+_control repeat 1

description:
MCF7 CRISPR/Cas9 HSF1+/+ mix control cells - untreated - repeat 1
B1


title: 2739_B

description:
2739_B
3597_19_2739_B_ACAGCAGA


title: 2691_S

description:
2691_S
3597_18_2691_S_ACACAGAA


title: MCF7 cells, HSF1+/+_control repeat 3

description:
MCF7 CRISPR/Cas9 HSF1+/+ mix control cells - untreated - repeat 3
B3