title: ZW2PLASMAB183A18

tag: anatomical location

tag: rna source

tag: ethnicity


title: ZW2PLASMAB182A20

status: Public on Aug 10 2024

type: SRA

city: New York

first: Klaas

middle: E. A.

last: Max

state: NY

address: 1230 York Avenue

department: RNA Molecular Biology

country: USA

institute: Rockefeller University

library_source: transcriptomic

data_processing:
Sequencing data were processed using an in-house RNA-sequencing data analysis platform (RSDAP), see Brown et al. (2013) Front. Genet. for details.
Read extractions and demultiplexing was done using extraction lenth of 16 – 45 nt, a minimum 3’ overlap of adapter with 0/1 mismatches of 4/5 nt, respectively, removal of low complexity sequences.
For the read mapping and the generation of the read count matrix table, read annotations used profile annoDB_jul2014c, which included reference sequences for human and virus RNAs based on miRBASE 18 with modifications and HG19.
Supplementary_files_format_and_content: Matrixtable_exRNAdata20210810_cluster_miRNA_read_counts.csv

molecule: total RNA

organism: Homo sapiens

source_name: 10,000 x g pellet

extract_protocol:
Low speed centrifugation (2500 g x 15 minutes, room temperature) was performed, then transfer of supernatant, 2nd round of centrifugation (same parameters), then transfer of supernatant. A self-developed method and self-developed solutions were used for nucleic-acid extraction, nucleic-acid partitioning, and column purification (RNA isolation), see Max et al. (2018) PNAS for details. For exRNA carrier subfractionation, selected samples were fractionated by differential ultracentrifugation into 10,000 xg pellet, 100,000 xg pellet and corresponding supernatant fractions: 11 ml of platelet-depleted plasma was centrifuged at 10,000 × g in 12 ml tubes (Sorvall, #03699) for 30 min. The supernatant was transferred by aspiration into a fresh 15 ml tube and mixed by inversion. Two aliquots of 500 µl of this supernatant were transferred into 1.5 ml microcentrifuge tubes for later RNA isolation. The 10,000 × g fragile pellet was suspended in 2.0 ml of phosphate-buffered saline (PBS), transferred into a 2.0 ml microcentrifuge tube, and centrifuged at 10,000 × g in a microcentrifuge for 30 min. The PBS supernatant was removed by aspiration, and the residual ≤10 µl volume pellet was resuspended in 450 µl PBS. The residual 10 ml of 10,000 × g supernatant was transferred into a 12 ml tube (Sorvall, #03699) and centrifuged at 100,000 × g for 90 min. The supernatant was transferred as described above, and two 500 µl aliquots of the 100,000 × g supernatant were transferred into 1.5 ml microcentrifuge tubes. The 100,000 × g pellet was washed with 10 ml PBS and centrifuged again at 100,000 × g for 90 min. The PBS supernatant was carefully removed as described above. The pellet was resuspended in 450 µl PBS. All pellet and supernatant fractions were flash-frozen in liquid nitrogen. Automated RNA isolation was conducted as previously described {Max:2018km} with the following modifications: Samples were organized in batches of 24 samples of 450 µl full plasma or plasma subfractions. Vesicle fractions were adjusted with PBS to 450 µl. Calibrator Set1, composed of ten 21-nt 5’-phosphorylated RNA oligos was added at an absolute amount of 2 attomoles per oligonucleotide along with the denaturant to each sample.
Large cohort sample library preparations used 3’ adapters, and PCR amplification methodologie, however, P12 family and plasma subfraction samples used novel 3’ adapters and PCR primers to accommodate changes in Illumina flow cell design after HiSeq was discontinued. RNA equivalent to an input 225 µl plasma was spiked with calibrator Set2 composed of another ten 21-nt 5’-phosphorylated RNA oligos at an absolute amount of 1 attomol per oligonucleotide and entered the first step of the cDNA library preparation. In sample libraries of plasma subfraction RNA from 225 µl supernatant or 5 ml pellet was used to which 0.2 attomoles per oligonucleotide of calibrator Set2 was added. After the 3’ ligation, up to 24 samples were multiplexed, size-selected by denaturing 15%, ligated to 5’ adapter, reverse-transcribed and PCR-amplified. To enable comparisons with earlier results (28), the PAGE size-selection limits were maintained at 19 to 45 for the large (n = 496) and P12 family cohorts (n = 12 samples). After discovering that miRNAs were noticeably underrepresented in the 10K and 100K pellet fractions, the size range for all plasma subfraction libraries (4 plasma subfractions, n = 17 samples, each) was adjusted to 19 to 24 nt in favor of miRNAs. cDNA libraries were sequenced as single-lane high-output single-read 75-bp HiSeq 2000 (Large cohort, n = 496 samples) or as Nextseq-500 100-bp single-read runs (P12 family, n = 12 samples; 4 Plasma subfractions, n = 17 samples each). Sequencing data were processed using an in-house RNA-sequencing data analysis platform (RSDAP) using extraction lenth of 16 – 45 nt, a minimum 3’ overlap of adapter with 0/1 mismatches of 4/5 nt, respectively, removal of low complexity sequences. For read annotations, profile annoDB_jul2014c was used, which included reference sequences for definitions for human and virus RNA sequences based on miRBASE 18 with modifications. Calibrator sequences (labeled by set) are: >Set1_cali_01_rc TCCACGACGTCTCATGTATTTC, >Set1_cali_04_rc GGGTACCATACCGGTTGTCTTA, >Set1_cali_17_rc TCATGAGTCCGTACCTTGATTG, >Set1_cali_18_rc ATCATTTACGATTCGGAGCTGT, >Set1_cali_20_rc GATAGTTCGGGATCGCTGTAAC, >Set1_cali_24_rc TGCTACTCCGATCTTTAGCCTC, >Set1_cali_25_rc AGGGCCCTTTAGGCACTAATAG, >Set1_cali_27_rc GTAGCTGTCAGTACGTTCGTGC, >Set1_cali_43_rc TCTAGTTGCGTGATGGAGAGAA, >Set1_cali_44_rc AGCCGCATTTCGTAGTGATATT, >Set2_cali_07_rc GTCCCACTCCGTAGATCTGTTC, >Set2_cali_11_rc GATGTAACGAGTTGGAATGCAA, >Set2_cali_12_rc TAGCATATCGAGCCTGAGAACA, >Set2_cali_14_rc CATCGGTCGAACTTATGTGAAA, >Set2_cali_15_rc GAAGCACATTCGCACATCATAT, >Set2_cali_16_rc TCTTAACCCGGACCAGAAACTA, >Set2_cali_26_rc AGGTTCCGGATAAGTAAGAGCC, >Set2_cali_28_rc TAACTCCTTAAGCGAATCTCGC, >Set2_cali_31_rc AAAGTAGCATCCGAAATACGGA, >Set2_cali_35_rc TGATACGGATGTTATACGCAGC

tag: cohort

value: Plasma Subfractions

value: Entire cardiovascular system

value: fractionated cell-free biofluid RNA

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

value: P12 family member

tag: individual

tag: visit

tag: pregnant

value: no

tag: trimester

tag: date of collection

tag: gender

value: M

tag: age

tag: age group

tag: race

value: White

tag: sequencing technology

value: NextSeq 500


title: ZW2PLASMAB183A16

source_name: 100,000 x g pellet

tag: anatomical location

tag: rna source

value: Pregnant individual

value: yes

value: F

tag: ethnicity


title: ZW2PLASMAB183A11

tag: cohort

tag: rna isolation kit

tag: shortid

value: Hispanic


title: ZW2PLASMAB183A13

tag: batch

tag: adapter

tag: sample subgroup (condition)


title: ZW2PLASMAB182A19

tag: individual

tag: visit

tag: pregnant


title: ZW2PLASMAB183A15

tag: trimester

tag: date of collection

tag: gender


title: ZW2PLASMAB182A18

tag: age

tag: age group

tag: race


title: ZW2PLASMAB182A17

tag: anatomical location

tag: rna source

tag: sequencing technology


title: ZW2PLASMAB183A10

tag: cohort

tag: rna isolation kit

tag: ethnicity


title: ZW2PLASMAB184A11

source_name: 10,000 x g supernatant

tag: shortid

tag: batch

tag: adapter


title: ZW2PLASMAB184A05

tag: sample subgroup (condition)

value: Normal female reference, not pregnant

tag: individual

tag: visit


title: ZW2PLASMAB183A09

value: Normal male reference

tag: pregnant

tag: trimester

tag: date of collection


title: ZW2PLASMAB182A10

tag: gender

tag: age

tag: age group


title: ZW2PLASMAB183A07

tag: anatomical location

tag: rna source

tag: race


title: ZW2PLASMAB182A07

tag: cohort

tag: rna isolation kit

tag: sequencing technology


title: ZW2PLASMAB182A03

tag: shortid

tag: batch

tag: ethnicity


title: ZW2PLASMAB182A24

tag: adapter

tag: sample subgroup (condition)

tag: individual


title: ZW2PLASMAB182A02

tag: visit

tag: pregnant

tag: trimester


title: ZW2PLASMAB183A14

tag: date of collection

tag: gender

tag: age


title: ZW2PLASMAB182A22

tag: anatomical location

tag: rna source

tag: age group


title: ZW2PLASMAB183A12

tag: cohort

tag: rna isolation kit

tag: race


title: ZW2PLASMAB165A19

source_name: Platelet depleted plasma

value: P12 family

value: total cell-free biofluid RNA

tag: shortid

tag: batch

tag: sequencing technology


title: ZW2PLASMAB182A12

value: Plasma Subfractions

tag: adapter

tag: sample subgroup (condition)

tag: ethnicity


title: ZW2PLASMAB182A15

value: Entire cardiovascular system

tag: individual

tag: visit

tag: pregnant


title: ZW2PLASMAB165A12

tag: trimester

tag: date of collection

tag: gender


title: ZW2PLASMAB182A11

tag: anatomical location

tag: rna source

value: fractionated cell-free biofluid RNA

tag: age


title: ZW2PLASMAB165A10

tag: cohort

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: age group


title: ZW2PLASMAB182A09

tag: shortid

tag: batch

tag: race


title: ZW2PLASMAB182A08

tag: adapter

tag: sample subgroup (condition)

tag: sequencing technology


title: ZW2PLASMAB122A23

value: Large cohort

value: Healthy volunteer

tag: individual

tag: visit

tag: ethnicity

value: HiSeq


title: ZW2PLASMAB165A6

tag: pregnant

value: no

tag: trimester

tag: date of collection

value: M


title: ZW2PLASMAB182A06

tag: anatomical location

tag: rna source

value: Pregnant individual

tag: gender

value: Asian

value: NextSeq 500


title: ZW2PLASMAB165A22

tag: cohort

tag: rna isolation kit

tag: age

value: White

value: Hispanic


title: ZW2PLASMAB165A11

tag: shortid

tag: batch

value: P12 family member

tag: age group


title: ZW2PLASMAB122A21

tag: adapter

tag: sample subgroup (condition)

tag: race


title: ZW2PLASMAB182A14

value: Normal male reference

tag: individual

tag: visit

tag: sequencing technology


title: ZW2PLASMAB122A19

value: total cell-free biofluid RNA

tag: pregnant

tag: trimester

tag: ethnicity


title: ZW2PLASMAB122A18

tag: anatomical location

tag: rna source

tag: date of collection


title: ZW2PLASMAB165A8

tag: cohort

value: P12 family

tag: rna isolation kit

tag: gender


title: ZW2PLASMAB122A16

value: Entire cardiovascular system

tag: shortid

tag: batch

value: F

tag: age

value: Latin


title: ZW2PLASMAB122A13

value: Large cohort

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: adapter

tag: sample subgroup (condition)

tag: age group


title: ZW2PLASMAB165A5

tag: individual

tag: visit

tag: race


title: ZW2PLASMAB122A11

value: Healthy volunteer

tag: pregnant

tag: trimester

tag: sequencing technology

value: HiSeq


title: ZW2PLASMAB165A1

tag: anatomical location

tag: rna source

value: no

tag: ethnicity


title: ZW2PLASMAB165A4

tag: cohort

tag: rna isolation kit

tag: date of collection

value: M


title: ZW2PLASMAB122A9

tag: shortid

tag: batch

tag: gender


title: ZW2PLASMAB122A22

tag: adapter

tag: sample subgroup (condition)

tag: age


title: ZW2PLASMAB122A20

tag: individual

tag: visit

tag: age group


title: ZW2PLASMAB122fA12

value: Pregnant individual

tag: pregnant

value: yes

tag: trimester

tag: race


title: ZW2PLASMAB165A18

tag: anatomical location

tag: rna source

tag: sequencing technology

value: NextSeq 500


title: ZW2PLASMAB165A14

tag: cohort

tag: rna isolation kit

value: White

tag: ethnicity


title: ZW2PLASMAB122A14

tag: shortid

tag: batch

tag: date of collection


title: ZW2PLASMAB122A1

tag: adapter

tag: sample subgroup (condition)

tag: gender

value: Asian


title: ZW2PLASMAB122A15

tag: individual

tag: visit

tag: age


title: ZW2PLASMAB122A12

tag: pregnant

tag: trimester

tag: age group


title: ZW2PLASMAB122A10

tag: anatomical location

tag: rna source

tag: race


title: ZW2PLASMAB114fA18

tag: cohort

tag: rna isolation kit

tag: sequencing technology


title: ZW2PLASMAB114A22

tag: shortid

tag: batch

tag: ethnicity


title: ZW2PLASMAB122A7

tag: adapter

tag: sample subgroup (condition)

tag: date of collection


title: ZW2PLASMAB114A15

tag: individual

tag: visit

tag: gender

value: Not specified


title: ZW2PLASMAB122A5

value: total cell-free biofluid RNA

tag: pregnant

tag: trimester

tag: age


title: ZW2PLASMAB114A14

tag: anatomical location

tag: rna source

tag: age group


title: ZW2PLASMAB122A6

tag: cohort

tag: rna isolation kit

tag: race


title: ZW2PLASMAB122A4

tag: shortid

tag: batch

tag: sequencing technology


title: ZW2PLASMAB122A3

tag: adapter

tag: sample subgroup (condition)

tag: ethnicity


title: ZW2PLASMAB114A12

tag: individual

tag: visit

tag: date of collection


title: ZW2PLASMAB122A2

tag: pregnant

tag: trimester

tag: gender


title: ZW2PLASMAB122A17

tag: anatomical location

tag: rna source

tag: age


title: ZW2PLASMAB114A23

tag: cohort

tag: rna isolation kit

tag: age group


title: ZW2PLASMAB114A1

tag: shortid

tag: batch

tag: race


title: ZW2PLASMAB114A3

tag: adapter

tag: sample subgroup (condition)

tag: sequencing technology


title: ZW2PLASMAB114A21

tag: individual

tag: visit

tag: ethnicity


title: ZW2PLASMAB114A20

tag: pregnant

tag: trimester

tag: date of collection


title: ZW2PLASMAB114A19

tag: anatomical location

tag: rna source

tag: gender


title: ZW2PLASMAB114A18

tag: cohort

tag: rna isolation kit

tag: age


title: ZW2PLASMAB114A17

tag: shortid

tag: batch

tag: age group


title: ZW2PLASMAB114A13

tag: adapter

tag: sample subgroup (condition)

tag: race


title: ZW2PLASMAB114A10

tag: individual

tag: visit

tag: sequencing technology


title: ZW2PLASMAB114A9

tag: pregnant

tag: trimester

tag: ethnicity


title: ZW2PLASMAB128A17

tag: anatomical location

tag: rna source

tag: date of collection


title: ZW2PLASMAB114A7

tag: cohort

tag: rna isolation kit

tag: gender


title: ZW2PLASMAB114A11

tag: shortid

tag: batch

tag: age


title: ZW2PLASMAB114A8

tag: adapter

tag: sample subgroup (condition)

tag: age group


title: ZW2PLASMAB114A6

tag: individual

tag: visit

tag: race


title: ZW2PLASMAB114A4

tag: pregnant

tag: trimester

tag: sequencing technology


title: ZW2PLASMAB114A5

tag: anatomical location

tag: rna source

tag: ethnicity


title: ZW2PLASMAB114A2

tag: cohort

tag: rna isolation kit

tag: date of collection


title: ZW2PLASMAB128A19

tag: shortid

tag: batch

tag: gender


title: ZW2PLASMAB128A20

tag: adapter

tag: sample subgroup (condition)

tag: age


title: ZW2PLASMAB128A18

tag: individual

tag: visit

tag: age group


title: ZW2PLASMAB128A16

tag: pregnant

tag: trimester

tag: race


title: ZW2PLASMAB128A15

tag: anatomical location

tag: rna source

tag: sequencing technology


title: ZW2PLASMAB128A12

tag: cohort

tag: rna isolation kit

tag: ethnicity


title: ZW2PLASMAB128A14

tag: shortid

tag: batch

tag: date of collection


title: ZW2PLASMAB128A11

tag: adapter

tag: sample subgroup (condition)

tag: gender


title: ZW2PLASMAB128A7

tag: individual

tag: visit

tag: age


title: ZW2PLASMAB128A5

tag: pregnant

tag: trimester

tag: age group


title: ZW2PLASMAB128A4

tag: anatomical location

tag: rna source

tag: race


title: ZW2PLASMAB127A24

tag: cohort

tag: rna isolation kit

tag: sequencing technology


title: ZW2PLASMAB128A9

tag: shortid

tag: batch

tag: ethnicity


title: ZW2PLASMAB128A10

tag: adapter

tag: sample subgroup (condition)

tag: date of collection


title: ZW2PLASMAB127A21

tag: individual

tag: visit

tag: gender


title: ZW2PLASMAB128A6

tag: pregnant

tag: trimester

tag: age


title: ZW2PLASMAB128A3

tag: anatomical location

tag: rna source

tag: age group


title: ZW2PLASMAB127A22

tag: cohort

tag: rna isolation kit

tag: race


title: ZW2PLASMAB127A19

tag: shortid

tag: batch

tag: sequencing technology


title: ZW2PLASMAB128A2

tag: adapter

tag: sample subgroup (condition)

tag: ethnicity


title: ZW2PLASMAB127A23

tag: individual

tag: visit

tag: date of collection


title: ZW2PLASMAB127A20

tag: pregnant

tag: trimester

tag: gender


title: ZW2PLASMAB128A13

tag: anatomical location

tag: rna source

tag: age


title: ZW2PLASMAB127A18

tag: cohort

tag: rna isolation kit

tag: age group


title: ZW2PLASMAB128A1

tag: shortid

tag: batch

tag: race


title: ZW2PLASMAB127A16

tag: adapter

tag: sample subgroup (condition)

tag: sequencing technology


title: ZW2PLASMAB127A15

tag: individual

tag: visit

tag: ethnicity


title: ZW2PLASMAB127A13

tag: pregnant

tag: trimester

tag: date of collection


title: ZW2PLASMAB127A14

tag: anatomical location

tag: rna source

tag: gender


title: ZW2PLASMAB127A12

tag: cohort

tag: rna isolation kit

tag: age


title: ZW2PLASMAB127A9

tag: shortid

tag: batch

tag: age group


title: ZW2PLASMAB128A8

tag: adapter

tag: sample subgroup (condition)

tag: race


title: ZW2PLASMAB127A8

tag: individual

tag: visit

tag: sequencing technology


title: ZW2PLASMAB127A7

tag: pregnant

tag: trimester

tag: ethnicity


title: ZW2PLASMAB127A6

tag: anatomical location

tag: rna source

tag: date of collection


title: ZW2PLASMAB127A10

tag: cohort

tag: rna isolation kit

tag: gender


title: ZW2PLASMAB127A3

tag: shortid

tag: batch

tag: age


title: ZW2PLASMAB127A5

tag: adapter

tag: sample subgroup (condition)

tag: age group


title: ZW2PLASMAB127A4

tag: individual

tag: visit

tag: race


title: ZW2PLASMAB127A1

tag: pregnant

tag: trimester

tag: sequencing technology


title: ZW2PLASMAB126A23

tag: anatomical location

tag: rna source

tag: ethnicity


title: ZW2PLASMAB126A22

tag: cohort

tag: rna isolation kit

tag: date of collection


title: ZW2PLASMAB126A20

tag: shortid

tag: batch

tag: gender


title: ZW2PLASMAB126A19

tag: adapter

tag: sample subgroup (condition)

tag: age


title: ZW2PLASMAB126A21

tag: individual

tag: visit

tag: age group


title: ZW2PLASMAB126A17

tag: pregnant

tag: trimester

tag: race


title: ZW2PLASMAB126A16

tag: anatomical location

tag: rna source

tag: sequencing technology


title: ZW2PLASMAB126A15

tag: cohort

tag: rna isolation kit

tag: ethnicity


title: ZW2PLASMAB126A12

tag: shortid

tag: batch

tag: date of collection


title: ZW2PLASMAB126A14

tag: adapter

tag: sample subgroup (condition)

tag: gender


title: ZW2PLASMAB126A5

tag: individual

tag: visit

tag: age


title: ZW2PLASMAB126A11

tag: pregnant

tag: trimester

tag: age group


title: ZW2PLASMAB127A11

tag: anatomical location

tag: rna source

tag: race


title: ZW2PLASMAB126A9

tag: cohort

tag: rna isolation kit

tag: sequencing technology


title: ZW2PLASMAB126A10

tag: shortid

tag: batch

tag: ethnicity


title: ZW2PLASMAB126A1

tag: adapter

tag: sample subgroup (condition)

tag: date of collection


title: ZW2PLASMAB125A21

tag: individual

tag: visit

tag: gender


title: ZW2PLASMAB125A23

tag: pregnant

tag: trimester

tag: age


title: ZW2PLASMAB127A2

tag: anatomical location

tag: rna source

tag: age group


title: ZW2PLASMAB126A2

tag: cohort

tag: rna isolation kit

tag: race


title: ZW2PLASMAB126A13

tag: shortid

tag: batch

tag: sequencing technology


title: ZW2PLASMAB125A19

tag: adapter

tag: sample subgroup (condition)

tag: ethnicity


title: ZW2PLASMAB126A7

tag: individual

tag: visit

tag: date of collection


title: ZW2PLASMAB126A6

tag: pregnant

tag: trimester

tag: gender


title: ZW2PLASMAB126A8

tag: anatomical location

tag: rna source

tag: age


title: ZW2PLASMAB125A22

tag: cohort

tag: rna isolation kit

tag: age group


title: ZW2PLASMAB125A16

tag: shortid

tag: batch

tag: race


title: ZW2PLASMAB125A20

tag: adapter

tag: sample subgroup (condition)

tag: sequencing technology


title: ZW2PLASMAB125A17

tag: individual

tag: visit

tag: ethnicity


title: ZW2PLASMAB125A14

tag: pregnant

tag: trimester

tag: date of collection


title: ZW2PLASMAB125A18

tag: anatomical location

tag: rna source

tag: gender


title: ZW2PLASMAB125A10

tag: cohort

tag: rna isolation kit

tag: age


title: ZW2PLASMAB126A18

tag: shortid

tag: batch

tag: age group


title: ZW2PLASMAB125A9

tag: adapter

tag: sample subgroup (condition)

tag: race


title: ZW2PLASMAB125A8

tag: individual

tag: visit

tag: sequencing technology


title: ZW2PLASMAB125A15

tag: pregnant

tag: trimester

tag: ethnicity


title: ZW2PLASMAB125A12

tag: anatomical location

tag: rna source

tag: date of collection


title: ZW2PLASMAB125A13

tag: cohort

tag: rna isolation kit

tag: gender


title: ZW2PLASMAB125A11

tag: shortid

tag: batch

tag: age


title: ZW2PLASMAB125A6

tag: adapter

tag: sample subgroup (condition)

tag: age group


title: ZW2PLASMAB125A7

tag: individual

tag: visit

tag: race


title: ZW2PLASMAB125A4

tag: pregnant

tag: trimester

tag: sequencing technology


title: ZW2PLASMAB125A1

tag: anatomical location

tag: rna source

tag: ethnicity


title: ZW2PLASMAB125A2

tag: cohort

tag: rna isolation kit

tag: date of collection


title: ZW2PLASMAB125A3

tag: shortid

tag: batch

tag: gender


title: ZW2PLASMAB124A19

tag: adapter

tag: sample subgroup (condition)

tag: age


title: ZW2PLASMAB124A14

tag: individual

tag: visit

tag: age group


title: ZW2PLASMAB124A12

tag: pregnant

tag: trimester

tag: race


title: ZW2PLASMAB124A13

tag: anatomical location

tag: rna source

tag: sequencing technology


title: ZW2PLASMAB124A20

tag: cohort

tag: rna isolation kit

tag: ethnicity


title: ZW2PLASMAB124A18

tag: shortid

tag: batch

tag: date of collection


title: ZW2PLASMAB124A17

tag: adapter

tag: sample subgroup (condition)

tag: gender


title: ZW2PLASMAB124A24

tag: individual

tag: visit

tag: age


title: ZW2PLASMAB124A8

tag: pregnant

tag: trimester

tag: age group


title: ZW2PLASMAB124A4

tag: anatomical location

tag: rna source

tag: race


title: ZW2PLASMAB124A15

tag: cohort

tag: rna isolation kit

tag: sequencing technology


title: ZW2PLASMAB124A16

tag: shortid

tag: batch

tag: ethnicity


title: ZW2PLASMAB124A11

tag: adapter

tag: sample subgroup (condition)

tag: date of collection


title: ZW2PLASMAB124A10

tag: individual

tag: visit

tag: gender


title: ZW2PLASMAB123A21

tag: pregnant

tag: trimester

tag: age


title: ZW2PLASMAB124A9

tag: anatomical location

tag: rna source

tag: age group


title: ZW2PLASMAB123A18

tag: cohort

tag: rna isolation kit

tag: race


title: ZW2PLASMAB124A7

tag: shortid

tag: batch

tag: sequencing technology


title: ZW2PLASMAB124A6

tag: adapter

tag: sample subgroup (condition)

tag: ethnicity


title: ZW2PLASMAB124A5

tag: individual

tag: visit

tag: date of collection


title: ZW2PLASMAB124A3

tag: pregnant

tag: trimester

tag: gender


title: ZW2PLASMAB123A10

tag: anatomical location

tag: rna source

tag: age


title: ZW2PLASMAB123A9

tag: cohort

tag: rna isolation kit

tag: age group


title: ZW2PLASMAB124A1

tag: shortid

tag: batch

tag: race


title: ZW2PLASMAB123A24

tag: adapter

tag: sample subgroup (condition)

tag: sequencing technology


title: ZW2PLASMAB124A2

tag: individual

tag: visit

tag: ethnicity


title: ZW2PLASMAB123A5

tag: pregnant

tag: trimester

tag: date of collection


title: ZW2PLASMAB123A6

tag: anatomical location

tag: rna source

tag: gender


title: ZW2PLASMAB124A23

tag: cohort

tag: rna isolation kit

tag: age


title: ZW2PLASMAB123A19

tag: shortid

tag: batch

tag: age group


title: ZW2PLASMAB123A20

tag: adapter

tag: sample subgroup (condition)

tag: race


title: ZW2PLASMAB123A22

tag: individual

tag: visit

tag: sequencing technology


title: ZW2PLASMAB124A22

tag: pregnant

tag: trimester

tag: ethnicity


title: ZW2PLASMAB123A2

tag: anatomical location

tag: rna source

tag: date of collection


title: ZW2PLASMAB123A3

tag: cohort

tag: rna isolation kit

tag: gender


title: ZW2PLASMAB123A17

tag: shortid

tag: batch

tag: age


title: ZW2PLASMAB123A16

tag: adapter

tag: sample subgroup (condition)

tag: age group


title: ZW2PLASMAB123A1

tag: individual

tag: visit

tag: race


title: ZW2PLASMAB121A23

tag: pregnant

tag: trimester

tag: sequencing technology


title: ZW2PLASMAB123A15

tag: anatomical location

tag: rna source

tag: ethnicity


title: ZW2PLASMAB123A12

tag: cohort

tag: rna isolation kit

tag: date of collection


title: ZW2PLASMAB123A13

tag: shortid

tag: batch

tag: gender


title: ZW2PLASMAB123A14

tag: adapter

tag: sample subgroup (condition)

tag: age


title: ZW2PLASMAB121A20

tag: individual

tag: visit

tag: age group


title: ZW2PLASMAB123A11

tag: pregnant

tag: trimester

tag: race


title: ZW2PLASMAB123A8

tag: anatomical location

tag: rna source

tag: sequencing technology


title: ZW2PLASMAB123A23

tag: cohort

tag: rna isolation kit

tag: ethnicity


title: ZW2PLASMAB121A18

tag: shortid

tag: batch

tag: date of collection


title: ZW2PLASMAB123A4

tag: adapter

tag: sample subgroup (condition)

tag: gender


title: ZW2PLASMAB121A14

tag: individual

tag: visit

tag: age


title: ZW2PLASMAB121A16

tag: pregnant

tag: trimester

tag: age group


title: ZW2PLASMAB121A12

tag: anatomical location

tag: rna source

tag: race


title: ZW2PLASMAB121A24

tag: cohort

tag: rna isolation kit

tag: sequencing technology


title: ZW2PLASMAB121A10

tag: shortid

tag: batch

tag: ethnicity


title: ZW2PLASMAB121A7

tag: adapter

tag: sample subgroup (condition)

tag: date of collection


title: ZW2PLASMAB121A21

tag: individual

tag: visit

tag: gender


title: ZW2PLASMAB121A3

tag: pregnant

tag: trimester

tag: age


title: ZW2PLASMAB120A24

tag: anatomical location

tag: rna source

tag: age group


title: ZW2PLASMAB121A1

tag: cohort

tag: rna isolation kit

tag: race


title: ZW2PLASMAB121A4

tag: shortid

tag: batch

tag: sequencing technology


title: ZW2PLASMAB121A22

tag: adapter

tag: sample subgroup (condition)

tag: ethnicity


title: ZW2PLASMAB121A17

tag: individual

tag: visit

tag: date of collection


title: ZW2PLASMAB121A19

tag: pregnant

tag: trimester

tag: gender


title: ZW2PLASMAB120A19

tag: anatomical location

tag: rna source

tag: age


title: ZW2PLASMAB120A20

tag: cohort

tag: rna isolation kit

tag: age group


title: ZW2PLASMAB120A17

tag: shortid

tag: batch

tag: race


title: ZW2PLASMAB121A11

tag: adapter

tag: sample subgroup (condition)

tag: sequencing technology


title: ZW2PLASMAB121A15

tag: individual

tag: visit

tag: ethnicity


title: ZW2PLASMAB121A8

tag: pregnant

tag: trimester

tag: date of collection


title: ZW2PLASMAB121A9

tag: anatomical location

tag: rna source

tag: gender


title: ZW2PLASMAB121A6

tag: cohort

tag: rna isolation kit

tag: age


title: ZW2PLASMAB121A2

tag: shortid

tag: batch

tag: age group


title: ZW2PLASMAB120A14

tag: adapter

tag: sample subgroup (condition)

tag: race


title: ZW2PLASMAB121A5

tag: individual

tag: visit

tag: sequencing technology


title: ZW2PLASMAB120A23

tag: pregnant

tag: trimester

tag: ethnicity


title: ZW2PLASMAB120A22

tag: anatomical location

tag: rna source

tag: date of collection


title: ZW2PLASMAB120A21

tag: cohort

tag: rna isolation kit

tag: gender


title: ZW2PLASMAB120A16

tag: shortid

tag: batch

tag: age


title: ZW2PLASMAB120A3

tag: adapter

tag: sample subgroup (condition)

tag: age group


title: ZW2PLASMAB120A6

tag: individual

tag: visit

tag: race


title: ZW2PLASMAB120A7

tag: pregnant

tag: trimester

tag: sequencing technology


title: ZW2PLASMAB120A11

tag: anatomical location

tag: rna source

tag: ethnicity


title: ZW2PLASMAB120A13

tag: cohort

tag: rna isolation kit

tag: date of collection


title: ZW2PLASMAB120A9

tag: shortid

tag: batch

tag: gender


title: ZW2PLASMAB120A18

tag: adapter

tag: sample subgroup (condition)

tag: age


title: ZW2PLASMAB120A8

tag: individual

tag: visit

tag: age group


title: ZW2PLASMAB120A12

tag: pregnant

tag: trimester

tag: race


title: ZW2PLASMAB119A21

tag: anatomical location

tag: rna source

tag: sequencing technology


title: ZW2PLASMAB119A20

tag: cohort

tag: rna isolation kit

tag: ethnicity


title: ZW2PLASMAB120A10

tag: shortid

tag: batch

tag: date of collection


title: ZW2PLASMAB119A17

tag: adapter

tag: sample subgroup (condition)

tag: gender


title: ZW2PLASMAB120A5

tag: individual

tag: visit

tag: age


title: ZW2PLASMAB119A14

tag: pregnant

tag: trimester

tag: age group


title: ZW2PLASMAB120A4

tag: anatomical location

tag: rna source

tag: race


title: ZW2PLASMAB119A23

tag: cohort

tag: rna isolation kit

tag: sequencing technology


title: ZW2PLASMAB119A9

tag: shortid

tag: batch

tag: ethnicity


title: ZW2PLASMAB119A22

tag: adapter

tag: sample subgroup (condition)

tag: date of collection


title: ZW2PLASMAB120A15

tag: individual

tag: visit

tag: gender


title: ZW2PLASMAB120A1

tag: pregnant

tag: trimester

tag: age


title: ZW2PLASMAB119A18

tag: anatomical location

tag: rna source

tag: age group


title: ZW2PLASMAB119A12

tag: cohort

tag: rna isolation kit

tag: race


title: ZW2PLASMAB119A15

tag: shortid

tag: batch

tag: sequencing technology


title: ZW2PLASMAB119A6

tag: adapter

tag: sample subgroup (condition)

tag: ethnicity


title: ZW2PLASMAB119A16

tag: individual

tag: visit

tag: date of collection


title: ZW2PLASMAB119A19

tag: pregnant

tag: trimester

tag: gender


title: ZW2PLASMAB118A22

tag: anatomical location

tag: rna source

tag: age


title: ZW2PLASMAB119A13

tag: cohort

tag: rna isolation kit

tag: age group


title: ZW2PLASMAB119A3

tag: shortid

tag: batch

tag: race


title: ZW2PLASMAB119A4

tag: adapter

tag: sample subgroup (condition)

tag: sequencing technology


title: ZW2PLASMAB119A11

tag: individual

tag: visit

tag: ethnicity


title: ZW2PLASMAB119A7

tag: pregnant

tag: trimester

tag: date of collection


title: ZW2PLASMAB118A23

tag: anatomical location

tag: rna source

tag: gender


title: ZW2PLASMAB119A2

tag: cohort

tag: rna isolation kit

tag: age


title: ZW2PLASMAB118A18

tag: shortid

tag: batch

tag: age group


title: ZW2PLASMAB119A24

tag: adapter

tag: sample subgroup (condition)

tag: race


title: ZW2PLASMAB119A5

tag: individual

tag: visit

tag: sequencing technology


title: ZW2PLASMAB119A1

tag: pregnant

tag: trimester

tag: ethnicity


title: ZW2PLASMAB118A21

tag: anatomical location

tag: rna source

tag: date of collection


title: ZW2PLASMAB118A20

tag: cohort

tag: rna isolation kit

tag: gender


title: ZW2PLASMAB118A17

tag: shortid

tag: batch

tag: age


title: ZW2PLASMAB118A16

tag: adapter

tag: sample subgroup (condition)

tag: age group


title: ZW2PLASMAB118A13

tag: individual

tag: visit

tag: race


title: ZW2PLASMAB118A10

tag: pregnant

tag: trimester

tag: sequencing technology


title: ZW2PLASMAB119A8

tag: anatomical location

tag: rna source

tag: ethnicity


title: ZW2PLASMAB118A15

tag: cohort

tag: rna isolation kit

tag: date of collection


title: ZW2PLASMAB118A7

tag: shortid

tag: batch

tag: gender


title: ZW2PLASMAB118A8

tag: adapter

tag: sample subgroup (condition)

tag: age


title: ZW2PLASMAB118A19

tag: individual

tag: visit

tag: age group


title: ZW2PLASMAB118A6

tag: pregnant

tag: trimester

tag: race


title: ZW2PLASMAB117A23

tag: anatomical location

tag: rna source

tag: sequencing technology


title: ZW2PLASMAB118A4

tag: cohort

tag: rna isolation kit

tag: ethnicity


title: ZW2PLASMAB117A22

tag: shortid

tag: batch

tag: date of collection


title: ZW2PLASMAB118A3

tag: adapter

tag: sample subgroup (condition)

tag: gender


title: WV8

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

description:
WV8
W_V_8_CGATGT_L006_R1_001.fastq

data_processing:
Reads from the HiSeq 2000 were processed and analyzed through a series of steps. Base calling and de-multiplexing of samples within each lane were done with Casava 1.8.2.
STAR (version 2.7.6a) was employed to map RNA-Seq reads to version mm39 of the Mus musculus reference genome, GRCm39, from NCBI Genome Reference Consortium Mouse Build 39.
Gene expression values (raw read counts) from BAM files were calculated using FeatureCounts function from the Subread module (version 2.0.0).
DESeq normalization algorithm with DESeq2 module in R using default values was used.  Differentially expressed genes were then determined by fold-change and p-value for each gene for each treatment relative to the vehicle control.
Genome_build: mm39
Supplementary_files_format_and_content: DE*csv: Differential expression results csv file
Supplementary_files_format_and_content: *rnaseq_featurecounts.txt: Genome mapping feature count file

organism: Mus musculus

source_name: Liver

extract_protocol:
For gene expression analysis, total RNA was extracted from 3 biological replicates for each ligand treatment using Trizol reagent and further cleaned using the RNAeasy kit from QIAGEN.
Once the sample quality and replicate reproducibility was verified 2 samples from each group were subjected to sequencing. RNA at a concentration of 100 ng/µL in nuclease-free water was used for library construction.The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNAseq Sample Prep kit.  The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a HiSeq2000  using a TruSeq SBS sequencing kit version 3. Fastq files were generated with the software Casava 1.8.2 (Illumina).. Briefly, the poly-A containing mRNA was purified from total RNA, RNA was fragmented, double-stranded cDNA was generated from fragmented RNA, and adapters were ligated to the ends.

tag: mouse model

value: diet-induced obesity (DIO)

tag: Sex

value: Female

tag: treatment

value: Vehicle

tag: tissue

value: Liver

tag: strain


title: WV9

description:
WV9
W_V_9_TTAGGC_L006_R1_001.fastq


title: ZW2PLASMAB118A5

value: Large cohort

tag: anatomical location

value: Entire cardiovascular system

tag: individual

tag: visit

tag: pregnant

tag: trimester

value: F

tag: age

tag: age group

tag: race


title: ZW2PLASMAB118A1

tag: cohort

tag: rna source

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: batch

value: Healthy volunteer

tag: date of collection

tag: ethnicity

tag: sequencing technology

value: HiSeq


title: ZW2PLASMAB117A24

tag: adapter

tag: sample subgroup (condition)

value: no

tag: gender

value: Latin


title: ZW2PLASMAB118A2

tag: anatomical location

tag: individual

tag: visit


title: ZW2PLASMAB118A11

tag: pregnant

tag: trimester

tag: age


title: ZW2PLASMAB117A21

tag: cohort

value: M

tag: age group

tag: race


title: WV7

description:
WV7
W_V_7_ATCACG_L006_R1_001.fastq

tag: mouse model

tag: Sex

tag: treatment

tag: tissue

tag: strain


title: ZW2PLASMAB117A20

tag: rna source

tag: rna isolation kit

tag: shortid

tag: batch

tag: adapter

tag: date of collection

tag: ethnicity

tag: sequencing technology


title: WP24

description:
WP24
W_P_24_GATCAG_L006_R1_001.fastq

value: PaPE


title: WP12

description:
WP12
W_P_12_ACTTGA_L006_R1_001.fastq


title: ZW2PLASMAB118A14

tag: anatomical location

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: pregnant

tag: trimester

tag: gender

tag: age

value: White


title: ZW2PLASMAB117A18

tag: cohort

tag: age group

tag: race


title: WE14

description:
WE14
W_E_14_ACAGTG_L006_R1_001.fastq

tag: mouse model

tag: Sex

tag: treatment

tag: tissue

tag: strain


title: ZW2PLASMAB117A16

tag: rna source

tag: rna isolation kit

tag: shortid

tag: batch

tag: adapter

tag: date of collection

tag: ethnicity

tag: sequencing technology


title: ZW2PLASMAB117A13

tag: anatomical location

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: pregnant

tag: trimester

tag: gender

tag: age


title: WE3

description:
WE3
W_E_3_TGACCA_L006_R1_001.fastq

tag: mouse model

tag: Sex

tag: treatment

tag: tissue

tag: strain


title: WP11

description:
WP11
W_P_11_CAGATC_L006_R1_001.fastq


title: L16

description:
L16
L16_ATCACGAT_L00M_R1_001.fastq

value: leptin-deficient (ob/ob)


title: ZW2PLASMAB117A11

tag: cohort

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

tag: shortid

tag: batch

tag: adapter

tag: age group

tag: race


title: L19

description:
L19
L19_ATGTCAGA_L00M_R1_001.fastq


title: ZW2PLASMAB117A12

tag: anatomical location

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: pregnant

tag: date of collection

tag: ethnicity

tag: sequencing technology


title: L12

description:
L12
L12_ACAGTGAT_L00M_R1_001.fastq

tag: mouse model

tag: Sex

tag: treatment

tag: tissue

tag: strain


title: ZW2PLASMAB117A19

tag: cohort

tag: rna source

tag: rna isolation kit

tag: shortid

tag: batch

tag: trimester

tag: gender

tag: age

value: Not specified


title: L13

description:
L13
L13_AGTCAACA_L00M_R1_001.fastq

value: Female


title: L8

description:
L8
L8_CTTGTAAT_L00M_R1_001.fastq

value: Vehicle


title: ZW2PLASMAB117A8

tag: anatomical location

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: pregnant

tag: age group

tag: race


title: ZW2PLASMAB117A9

value: Pregnant individual

value: yes

tag: date of collection

tag: ethnicity

tag: sequencing technology


title: ZW2PLASMAB117A7

tag: cohort

value: Large cohort

value: Entire cardiovascular system

tag: rna source

tag: rna isolation kit


title: ZW2PLASMAB117A5

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: batch

tag: trimester

value: Asian


title: ZW2PLASMAB117A17

tag: anatomical location

value: Healthy volunteer

tag: gender

value: F

tag: age

value: HiSeq


title: L3

description:
L3
L3_GCCAATAT_L00M_R1_001.fastq

tag: mouse model

tag: Sex

tag: treatment

tag: tissue

value: Liver

tag: strain


title: L5

description:
L5
L5_GTGAAACG_L00M_R1_001.fastq

value: PaPE


title: WE18

description:
WE18
W_E_18_GCCAAT_L006_R1_001.fastq

value: diet-induced obesity (DIO)


title: ZW2PLASMAB117A4

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: pregnant

value: no

tag: date of collection

tag: age group

tag: race


title: L1

description:
L1
L1_AGTTCCGT_L00M_R1_001.fastq

value: leptin-deficient (ob/ob)


title: ZW2PLASMAB117A2

tag: cohort

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

tag: shortid

tag: batch

tag: trimester

value: White

tag: ethnicity

tag: sequencing technology


title: ZW2PLASMAB117A3

tag: anatomical location

tag: gender

value: M

tag: age

value: Latin


title: NRVM_Cfz_1

city: Tianjin

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

country: China

institute: Tianjin Medical University

data_processing:
FastQC (version 0.11.8) were used to check raw sequencing reads.
Adapter trimming and low-quality filtering was analyzed by Cutadapt (v2.0) to get the clean reads.
After obtaining clean reads, we used HISAT to align the clean reads to the reference genome sequence, and used Bowtie2 to align the clean reads to the reference gene sequence.
The gene expression was quantified by featureCounts (v1.6.0), and differential expressed genes (DEGs) between treatment groups were created by DESeq2 (R version 3.3.2).
Assembly: GCF_000001895.5_Rnor_6.0(from NCBI)
Supplementary files format and content: tab-delimited text file includes gene expression data for each Sample
Supplementary files format and content: tab-delimited text file includes differentially expressed gene with log2fc_CON-vs-CFZ, q value and p value

organism: Rattus norvegicus

source_name: heart

growth_protocol: NRVMs were isolated from 1–3-day-old Sprague Dawley rats follow the exist protocol.The primary cardiomyocytes were cultured ex vivo in DMEM supplemented with 15% FBS in the presence of 100 U/ml of penicillin, 100mg/ml of streptomycin, 2mM L-glutamine and 0.1 mM 5-bromo-2-deoxyuridine to inhibit the growth of non-myocardial cells.Cells were all cultured at 37°C in a humidified incubator with 5% CO2 and 95% air (v/v).

extract_protocol:
RNA was harvested using Trizol reagent(Invitrogen,#15596018CN) according to the manufacturer’s instructions.Quality of the purified RNA was tested on Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit).
RNA libraries for RNA-seq were prepared using standard BGI protocols

treatment_protocol: NRVMs were treated with 1μM carfilzomib or vehicle for 24h.

tag: tissue

value: heart

tag: cell line

value: Neonatal rat ventricular myocytes(NRVM)

tag: cell type

value: primary myocardial cell

tag: genotype

value: WT

tag: treatment


title: ZW2PLASMAB116A24

value: Large cohort

value: Entire cardiovascular system

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: pregnant

tag: date of collection

tag: age group

tag: race

value: Not specified


title: ZW2PLASMAB117A1

tag: cohort

tag: rna source

tag: rna isolation kit

tag: shortid

tag: batch

value: Healthy volunteer

tag: trimester

tag: ethnicity

tag: sequencing technology

value: HiSeq


title: NRVM_Veh_2

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: vehicle


title: ZW2PLASMAB116A23

tag: anatomical location

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: pregnant

value: no

tag: gender

value: F

tag: age


title: ZW2PLASMAB117A10

tag: cohort

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

tag: shortid

tag: batch

tag: date of collection

tag: age group

tag: race


title: NRVM_Veh_1

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: ZW2PLASMAB116A22

tag: anatomical location

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: trimester

tag: ethnicity

tag: sequencing technology


title: ZW2PLASMAB116A20

tag: cohort

tag: rna source

tag: rna isolation kit

tag: shortid

tag: batch

tag: pregnant

tag: gender

tag: age

value: White


title: ZW2PLASMAB117A6

tag: date of collection

value: M

tag: age group

tag: race


title: ZW2PLASMAB116A21

tag: anatomical location

tag: adapter

tag: sample subgroup (condition)

value: Latin


title: L6

description:
L6
L6_GTTTCGGA_L00M_R1_001.fastq

tag: mouse model

value: leptin-deficient (ob/ob)

tag: Sex

value: Female

tag: treatment

value: PaPE

tag: tissue

value: Liver

tag: strain


title: ZW2PLASMAB116A19

tag: cohort

value: Large cohort

tag: rna source

tag: rna isolation kit

value: Pregnant individual

tag: individual

tag: visit

value: yes

tag: trimester

tag: ethnicity

tag: sequencing technology


title: rde-1, mRNA, rep 3

city: Fort Collins

first: Taiowa

middle: A

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

description:
total rRNA-depleted RNA
wt_rde-1_RNA-seq_DESeq2_normalized_counts.csv

data_processing:
Small RNA data processing was done using the default configuration in the tinyRNA pipeline (https://github.com/MontgomeryLab/tinyRNA). mRNA data prcocessing was done using a custom pipeline including fastp, RSEM, STAR, and DESeq2.
Assembly: WS279
Supplementary files format and content: wt_rde-1_rpm_normalized_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in wild type and rde-1 mutants.
Supplementary files format and content: GFP-RDE-1_co-IP_normalized_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in GFP::RDE-1 co-IPs and cell lysates.

organism: Caenorhabditis elegans

source_name: gravid hermaphroditic adult whole animals

growth_protocol: Worms were grown for 72-75 hours from synchronized L1 larvae at 20C on media containing E. coli (OP50 or HT115).

extract_protocol: Small RNAs (~16-30-nt) were purified from total RNA by size selection using 17% polyacrylamide gels and in some instances treated with NEB RNA 5' Pyrophosphohydrolase (RppH)to facilitate capture of 22G-RNAs. Libraries were then prepared according to the NEBNext Multiplex Small RNA kit protocol. PCR products (~134-148 bp) were size selected using 10% polyacrylamide gels. For mRNA-seq DNase-treated total RNA was depleted of rRNA using Ribo-Zero and libraries were prepared using the Illumina TruSeq Stranded Total RNA kit.

tag: genotype


title: NRVM_Cfz_2

value: heart

tag: cell line

value: Neonatal rat ventricular myocytes(NRVM)

tag: cell type

value: primary myocardial cell

value: WT


title: rde-1, mRNA, rep 2

value: gravid hermaphroditic adult whole animals


title: ZW2PLASMAB116A17

tag: anatomical location

value: Entire cardiovascular system

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

value: Healthy volunteer

tag: pregnant

value: no

tag: date of collection

tag: gender

value: F

tag: age

tag: age group

tag: race

value: HiSeq


title: ZW2PLASMAB116A18

tag: cohort

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

tag: individual

tag: visit

tag: trimester

value: M

value: White

value: Latin


title: rde-1, mRNA, rep 1

tag: tissue

tag: genotype

tag: treatment


title: wild type, mRNA, rep 3

value: wild type (N2)


title: ZW2PLASMAB116A15

value: Large cohort

tag: anatomical location

tag: shortid

tag: batch

tag: adapter

tag: ethnicity

tag: sequencing technology


title: ZW2PLASMAB116A12

tag: sample subgroup (condition)

tag: pregnant

tag: date of collection

tag: gender

tag: age

tag: age group


title: wild type, mRNA, rep 2


title: ZW2PLASMAB116A13

tag: cohort

tag: rna source

tag: rna isolation kit

tag: individual

tag: visit

tag: race


title: wild type, mRNA, rep 1

tag: tissue

tag: genotype

tag: treatment


title: ZW2PLASMAB116A10

tag: anatomical location

tag: shortid

tag: batch

tag: adapter

tag: trimester

tag: ethnicity


title: ZW2PLASMAB116A9

tag: sample subgroup (condition)

tag: pregnant

tag: date of collection

tag: gender

tag: age

tag: sequencing technology


title: GFP::alg-2, rde-1 RNAi, co-IP, rep 2

description:
16-30 nt purified RNAs from GFP::ALG-2 co-IPs
GPF-ALG-2_co-IP_rpm_normalized_counts.csv

value: rde-1 RNAi


title: ZW2PLASMAB116A7

tag: cohort

tag: rna source

tag: rna isolation kit

tag: individual

tag: visit

tag: age group


title: ZW2PLASMAB116A8

tag: anatomical location

tag: shortid

tag: race


title: GFP::alg-2, rde-1 RNAi, co-IP, rep 1

tag: tissue

tag: genotype

tag: treatment


title: ZW2PLASMAB116A16

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: pregnant

tag: trimester

tag: ethnicity


title: ZW2PLASMAB116A6

tag: cohort

tag: rna source

tag: date of collection

tag: gender

tag: age

tag: sequencing technology


title: ZW2PLASMAB116A14

tag: anatomical location

tag: rna isolation kit

tag: shortid

tag: individual

tag: visit

tag: age group


title: PCAF_RU486_DEX_PAT4

type: RNA

city: Innsbruck

first: Martin

last: Puhr

state: Tyrol

address: Anich street 35

department: Department of Urology

country: Austria

institute: Medical University of Innsbruck

description: gene expression profiling of treated primary CAFs

hyb_protocol: The generated target RNA was loaded onto the Affymetrix Clariom D human array cartridge and hybridized for 16 hours at 45°C using GeneTitan Hybridization modul (by commercial service provider Eurofins/Aros, Aarhus, Denmark)

scan_protocol: Array were scanned in the GeneChip Scanner 7G. The image files were imported into the Affymetrix Expression Console software.

data_processing: Preprocessing were performed with Affymetrix Expression Console software and RMA was used for background modeling, quantile normalization, and probe summarization. Analysis were performed on the gene level (with Refseq annotation) and differentially expressed genes were identified using moderated t-test with limma R package.

label: biotin

source_name: Primary human prostate cancer associated fibroblasts (PAT4; 1869)  treated with RU486+Dex

label_protocol: A target preparation of 150 ng RNA was used for cDNA synthesis, in vitro transcription and terminal labeling utilizing the WT PLUS reagent kit (Affymetrix).

growth_protocol: Primary human prostate cancer associated fibroblasts were grown in minimum essential medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 1 mM sodium pyruvate and antibiotics. Cells were maintained in a humidified incubator at 37°C and 5% CO2.

extract_protocol: Total RNA from cell lines was isolated with the EXTRACTOME TOTAL RNA KIT (DNA-Gdansk) according to manufacturer’s instructions. Quality and amount of isolated RNA were determined on a Nanodrop2000 system (ThermoFisher Scientific).

treatment_protocol: 5 million of primary CAFs from 4 different PCa patients were seeded into T175 tissue flasks. On the next day specific treatments were performed as followed. Group 1: vehicle Ctrl was treated with DMSO for 24 h. Group 2: 100 nM Dex for 24h. Group 3: 100 nM Dex and 12 µM RU486 treatment for 24 h.

tag: treatment

tag: concentration


title: ZW2PLASMAB116A5

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: pregnant

tag: race


title: GFP::alg-2, L4440 RNAi, co-IP, rep 2

tag: tissue

tag: genotype

value: L4440 RNAi


title: PCAF_RU486_DEX_PAT1

source_name: Primary human prostate cancer associated fibroblasts (PAT1; 3148)  treated with RU486+Dex


title: ZW2PLASMAB116A4

tag: cohort

tag: rna source

tag: trimester

tag: date of collection

tag: gender

tag: age

value: Not specified

tag: ethnicity


title: PCAF_DEX_PAT4

source_name: Primary human prostate cancer associated fibroblasts (PAT4; 1869)  treated with Dex

value: Dexamethasone

value: 100nM (Dex)


title: GFP::alg-2, L4440 RNAi, co-IP, rep 1

value: gravid hermaphroditic adult whole animals


title: ZW2PLASMAB116A11

tag: anatomical location

value: Entire cardiovascular system

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: individual

tag: visit

tag: age group

tag: sequencing technology


title: ZW2PLASMAB116A3

tag: batch

tag: adapter

tag: sample subgroup (condition)

value: Healthy volunteer

tag: pregnant

value: no

tag: race


title: PCAF_DEX_PAT3

source_name: Primary human prostate cancer associated fibroblasts (PAT3; 5201)  treated with Dex

tag: treatment

tag: concentration


title: PCAF_RU486_DEX_PAT3

source_name: Primary human prostate cancer associated fibroblasts (PAT3; 5201)  treated with RU486+Dex


title: PCAF_DEX_PAT1

source_name: Primary human prostate cancer associated fibroblasts (PAT1; 3148)  treated with Dex


title: PCAF_RU486_DEX_PAT2

source_name: Primary human prostate cancer associated fibroblasts (PAT2; 1341)  treated with RU486+Dex


title: ZW2PLASMAB116A2

tag: cohort

tag: rna source

tag: trimester

tag: date of collection

tag: gender

value: HiSeq


title: PCAF_DEX_PAT2

source_name: Primary human prostate cancer associated fibroblasts (PAT2; 1341)  treated with Dex


title: ZW2PLASMAB116A1

tag: anatomical location

value: total cell-free biofluid RNA

tag: rna isolation kit

tag: shortid

value: F

tag: age

tag: ethnicity


title: GFP::alg-1, rde-1 RNAi, co-IP, rep 2

description:
16-30 nt purified RNAs from GFP::ALG-1 co-IPs
GFP-ALG-1_co-IP_rpm_normalized_counts.csv

tag: tissue

tag: genotype


title: ZW2PLASMAB115A22

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit

value: M

tag: age group

value: White

tag: sequencing technology


title: PCAF_DMSO_PAT3

source_name: Primary human prostate cancer associated fibroblasts (PAT3; 5201)  treated with DMSO

tag: treatment

value: DMSO

tag: concentration

value: Control


title: ZW2PLASMAB115A21

tag: cohort

value: Large cohort

tag: rna source

tag: pregnant

tag: trimester

tag: date of collection

tag: gender

tag: race

value: Latin


title: ZW2PLASMAB115A20

tag: anatomical location

tag: rna isolation kit

tag: shortid

tag: age

tag: ethnicity


title: MPCC cells， Med12 sg3，repeat2

city: Shanghai

first: JIng

last: Xue

address: No.1630 dongfang road, pudong new district, Shanghai

institute: Renji Hospital, School of Medicine,Shanghai Jiaotong University

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to hg38 with orientation mode using HISAT2  software
The mapped reads of each sample were assembled by StringTie  in a reference-based approach
differential expression analysis was performed using the DESeq2
Assembly: GRCm39
Supplementary files format and content: excel sheet includs tpm of each sample

source_name: MPCC

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA)

tag: cell line

value: MPCC

tag: cell type

value: Pancreatic tumor cell

tag: genotype

value: Med12 Knockout


title: GFP::alg-1, rde-1 RNAi, co-IP, rep 1

tag: tissue

value: gravid hermaphroditic adult whole animals

tag: treatment

value: rde-1 RNAi


title: ZW2PLASMAB115A19

tag: cohort

value: Entire cardiovascular system

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit

tag: age group

value: Asian

tag: sequencing technology


title: ZW2PLASMAB115A24

tag: anatomical location

tag: rna source

tag: rna isolation kit

value: Healthy volunteer

tag: pregnant

value: no

tag: trimester

tag: date of collection

tag: gender

tag: race

value: HiSeq


title: GFP::alg-1, L4440 RNAi, co-IP, rep 2

tag: tissue

tag: genotype

tag: treatment

value: L4440 RNAi


title: MPCC cells， Med12 sg3，repeat1

tag: cell line

tag: cell type


title: ZW2PLASMAB115A18

tag: cohort

value: total cell-free biofluid RNA

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: individual

value: M

tag: age

value: Not specified

tag: ethnicity


title: MPCC cells， Med12 sg3，repeat3


title: ZW2PLASMAB115A17

value: Large cohort

tag: anatomical location

tag: rna source

tag: rna isolation kit

tag: visit

tag: pregnant

tag: trimester

tag: age group

value: White

tag: sequencing technology


title: MPCC cells， Med12 sg2，repeat3

tag: cell line

value: MPCC

tag: cell type

tag: genotype


title: ZW2PLASMAB115A16

tag: cohort

tag: shortid

tag: batch

tag: date of collection

tag: gender

tag: race


title: ZW2PLASMAB115A15

tag: anatomical location

tag: adapter

tag: sample subgroup (condition)

value: Pregnant individual

tag: individual

value: yes

value: F

tag: age

tag: ethnicity

value: Latin


title: GFP::alg-2, rde-1 RNAi, input, rep 2

description:
16-30 nt purified RNAs from cell lysate
GPF-ALG-2_co-IP_rpm_normalized_counts.csv

tag: tissue

value: gravid hermaphroditic adult whole animals

tag: treatment

value: rde-1 RNAi


title: PCAF_DMSO_PAT2

source_name: Primary human prostate cancer associated fibroblasts (PAT2; 1341)  treated with DMSO

value: DMSO

tag: concentration

value: Control


title: PCAF_DMSO_PAT4

source_name: Primary human prostate cancer associated fibroblasts (PAT4; 1869)  treated with DMSO


title: MPCC cells， Med12 sg2，repeat2

tag: cell line

tag: cell type

value: Pancreatic tumor cell

value: Med12 Knockout


title: ZW2PLASMAB115A14

tag: cohort

value: Entire cardiovascular system

tag: rna source

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

value: Healthy volunteer

tag: visit

tag: pregnant

value: no

tag: trimester

tag: age group

tag: sequencing technology

value: HiSeq


title: GFP::alg-2, rde-1 RNAi, input, rep 1

tag: genotype


title: MPCC cells， Med12 sg2，repeat1


title: ZW2PLASMAB115A13

value: Large cohort

tag: anatomical location

value: total cell-free biofluid RNA

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: date of collection

tag: gender

tag: race

value: Not specified


title: GFP::alg-2, L4440 RNAi, input, rep 2

tag: tissue

tag: treatment

value: L4440 RNAi


title: PCAF_DMSO_PAT1

source_name: Primary human prostate cancer associated fibroblasts (PAT1; 3148)  treated with DMSO

tag: concentration


title: MPCC cells， WT，repeat3

tag: cell line

value: MPCC

tag: cell type

value: WT


title: ZW2PLASMAB115A11

source_name: Platelet depleted plasma

tag: cohort

tag: rna source

tag: rna isolation kit

tag: visit

tag: pregnant

tag: trimester

value: F

tag: age

tag: age group

value: White

tag: ethnicity


title: ZW2PLASMAB115A12

tag: anatomical location

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: date of collection

tag: sequencing technology


title: GFP::alg-2, L4440 RNAi, input, rep 1

tag: tissue

value: gravid hermaphroditic adult whole animals

tag: genotype

tag: treatment


title: MPCC cells， WT，repeat2

tag: cell line

tag: cell type


title: ZW2PLASMAB115A9

tag: cohort

tag: rna source

tag: rna isolation kit

tag: visit

tag: pregnant

tag: trimester

tag: gender

tag: race


title: ZW2PLASMAB115A10

tag: anatomical location

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: age

tag: age group

tag: ethnicity

value: Latin


title: ZW2PLASMAB115A7

tag: individual

tag: date of collection

value: M

value: Asian

tag: sequencing technology


title: MPCC cells， WT，repeat1

tag: cell line

tag: cell type

value: Pancreatic tumor cell

tag: genotype


title: ZW2PLASMAB115A6

tag: cohort

value: Entire cardiovascular system

tag: rna source

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: visit

tag: pregnant

tag: trimester


title: GFP::alg-1, L4440 RNAi, co-IP, rep 1

tag: tissue

tag: treatment


title: ZW2PLASMAB115A5

tag: anatomical location

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

value: Healthy volunteer

value: no

tag: gender

tag: age

tag: race


title: FPCP cells， Med12 sg3，repeat3

source_name: FPCP

tag: cell line

value: FPCP

tag: cell type

tag: genotype

value: Med12 Knockout


title: GFP::alg-1, rde-1 RNAi, input, rep 1

description:
16-30 nt purified RNAs from cell lysate
GFP-ALG-1_co-IP_rpm_normalized_counts.csv

value: rde-1 RNAi


title: GFP::alg-1, rde-1 RNAi, input, rep 2


title: ZW2PLASMAB115A4

tag: cohort

value: Large cohort

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

tag: individual

tag: date of collection

tag: age group

tag: ethnicity

tag: sequencing technology

value: HiSeq


title: GFP::alg-1, L4440 RNAi, input, rep 2

tag: tissue

tag: treatment

value: L4440 RNAi


title: ZW2PLASMAB115A3

tag: anatomical location

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: visit

tag: pregnant

tag: trimester

value: Not specified


title: FPCP cells， Med12 sg3，repeat2

tag: cell line

tag: cell type

tag: genotype


title: GFP::alg-1, L4440 RNAi, input, rep 1

value: gravid hermaphroditic adult whole animals


title: ZW2PLASMAB115A2

tag: cohort

tag: rna source

tag: rna isolation kit

tag: individual

tag: date of collection

tag: gender

value: F

tag: age

tag: race


title: ZW2PLASMAB115A1

tag: anatomical location

tag: shortid

tag: batch

tag: age group

value: White

tag: ethnicity

tag: sequencing technology


title: FPCP cells， Med12 sg3，repeat1

tag: cell line


title: ZW2PLASMAB115A8

tag: adapter

tag: sample subgroup (condition)

tag: visit

tag: pregnant

tag: trimester

value: Asian


title: ZW2PLASMAB113A24

tag: cohort

tag: rna source

tag: rna isolation kit

tag: individual


title: dcr-1 RNAi, rep 2

description:
16-30 nt purified RNAs from cell lysate
dcr-1_RNAi_rpm_normalized_counts.csv

tag: tissue

tag: genotype

tag: treatment

value: dcr-1 RNAi


title: ZW2PLASMAB113A22

tag: anatomical location

value: Entire cardiovascular system

tag: shortid

tag: batch

tag: date of collection

tag: gender

value: M

tag: age

tag: race


title: dcr-1 RNAi, rep 1


title: ZW2PLASMAB113A21

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: adapter

tag: sample subgroup (condition)

value: Healthy volunteer

tag: visit

tag: age group

tag: ethnicity

value: Latin

tag: sequencing technology


title: ZW2PLASMAB113A23

tag: cohort

tag: rna source

tag: rna isolation kit

tag: individual

tag: pregnant

value: no

tag: trimester


title: FPCP cells， Med12 sg2，repeat1

tag: cell line

value: FPCP

tag: cell type

value: Pancreatic tumor cell

tag: genotype

value: Med12 Knockout


title: ZW2PLASMAB113A20

value: Large cohort

tag: anatomical location

value: total cell-free biofluid RNA

tag: shortid

tag: batch

tag: date of collection

tag: gender

tag: age

value: HiSeq


title: FPCP cells， Med12 sg2，repeat2


title: ZW2PLASMAB113A18

tag: adapter

tag: sample subgroup (condition)

tag: visit

tag: age group

tag: race

tag: ethnicity


title: L4440 RNAi, rep 1

tag: tissue

value: gravid hermaphroditic adult whole animals

tag: treatment

value: L4440 RNAi


title: ZW2PLASMAB113A16

tag: cohort

tag: rna source

tag: rna isolation kit

tag: individual

tag: pregnant

tag: trimester

value: White

tag: sequencing technology


title: L4440 RNAi, rep 2

tag: genotype


title: ZW2PLASMAB113A19

tag: anatomical location

tag: shortid

tag: batch

tag: date of collection

tag: gender

value: F

tag: age

value: Mixed


title: FPCP cells， WT，repeat3

tag: cell line

tag: cell type

value: WT


title: ZW2PLASMAB113A15

value: Entire cardiovascular system

tag: adapter

tag: sample subgroup (condition)

tag: visit

tag: age group

tag: race

tag: ethnicity


title: ZW2PLASMAB113A14

tag: cohort

tag: rna source

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: individual

tag: pregnant

tag: trimester


title: ZW2PLASMAB113A13

tag: anatomical location

tag: shortid

tag: batch

value: Healthy volunteer

tag: date of collection

tag: sequencing technology


title: PBMCs from CTEPH patient, replicate 5, scRNAseq

city: Fuzhou

first: Chaosheng

last: Deng

state: Fujian

address: No. 20, ChaZhong Road

institute: First Affiliated Hospital of Fujian Medical University

description:
Primary Human PBMCs
GEXSCOPE

library_source: transcriptomic single cell

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the CeleScope (v1.9.0, Singleron).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral blood

extract_protocol:
Venous blood (2 mL) was collected into an EDTA anticoagulant tube and immediately transported to the laboratory on ice for subsequent scRNA-seq analysis. To ensure viability and integrity of the cells, the blood was processed within two hours of collection. Peripheral Blood Mononuclear Cells (PBMCs) were isolated using density gradient centrifugation with Ficoll-Paque Plus medium (GE Healthcare). Following this, red blood cells were lysed using 2 mL of GEXSCOPE® Red Blood Cell Lysis Buffer (RCLB, Singleron) at 25°C for 10 minutes. The lysed sample was then centrifuged at 500 × g for 5 minutes, and the supernatant was discarded. The remaining cells were washed and centrifuged twice at 400 × g for 5 minutes at 4°C to remove any residual lysis buffer. Finally, the PBMCs were resuspended in phosphate-buffered saline to create a single-cell suspension, ready for downstream scRNA-seq library preparation.
Single-cell suspensions (2×105 cells/mL) were prepared using PBS (HyClone), and then the single-cell suspension was loaded onto a microwell chip using the Singleron Matrix® Single Cell Processing System. GEXSCOPE® Single Cell RNA Library Kits (Singleron) were used for single-cell capture and library construction according to the manufacturer's specifications. Sequencing was performed on the Illumina HiSeq X and Illumina Novaseq 6000 platforms.

tag: tissue

value: Peripheral blood

tag: cell type

value: PBMCs, including T cells, B cells, NK cells, and monocytes

tag: disease

value: chronic thromboembolic pulmonary hypertension (CTEPH)


title: ZW2PLASMAB113A11

tag: adapter

tag: sample subgroup (condition)

tag: visit

value: no

tag: gender

value: M

tag: age

tag: age group


title: PBMCs from CTEPH patient, replicate 4, scRNAseq

description:
Primary Human PBMCs
GEXSCOPE


title: FPCP cells， WT，repeat1

tag: cell line

value: FPCP

value: Pancreatic tumor cell

tag: genotype


title: ZW2PLASMAB113A10

tag: cohort

value: Large cohort

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

tag: individual

tag: pregnant

tag: trimester

tag: race

value: Asian

tag: ethnicity

value: HiSeq


title: FPCP cells， Med12 sg2，repeat3

tag: cell type

value: Med12 Knockout


title: ZW2PLASMAB113A9

tag: anatomical location

tag: shortid

tag: batch

tag: adapter

tag: date of collection

value: F

value: Mixed

tag: sequencing technology


title: ZW2PLASMAB113A8

value: Entire cardiovascular system

tag: sample subgroup (condition)

tag: visit

tag: gender

tag: age

tag: age group


title: KPC1199 Med12 sg3，HP1A, Cut&Tag, repeat3

library_source: genomic

data_processing:
Sequenced reads were trimmed for adaptor sequence and to discard reads shorter than 50bp, then mapped to mm10 whole genome using Bowtie2 v. 2.4.2
Reads Per Kilobase of exon per Megabase of library size were calculated using homer annotatePeaks.pl
Peaks were called using MACS2 version 2.2.7.1 with the parameters -B  -t  --broad -g mm --broad-cutoff 0.05
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
Briefly, tumor cell were generated and collected .CUT&Tag assay was performed following the manual of hyperactive pG-Tn5/pA-Tn5 transposase for CUT&Tag kit (TD904, Vazyme).
DNA library were prepared according to manufacturer’s instructions of Trueprep index kit v2 (TD202, Vazyme)

tag: cell line

value: pancreatic tumor cell

tag: genotype

value: Med12 knockout


title: KPC1199 Med12 sg3，HP1A, Cut&Tag, repeat2


title: PBMCs from CTEPH patient, replicate 3, scRNAseq

description:
Primary Human PBMCs
10× Genomics

tag: tissue

value: Peripheral blood

tag: disease


title: ZW2PLASMAB113A7

tag: cohort

tag: rna source

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

value: Healthy volunteer

tag: individual

tag: pregnant

tag: trimester

tag: race

tag: ethnicity


title: ZW2PLASMAB113A6

tag: anatomical location

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

value: no

tag: date of collection

value: White

tag: sequencing technology


title: PBMCs from CTEPH patient, replicate 2, scRNAseq

description:
Primary Human PBMCs
10× Genomics

tag: tissue

tag: cell type

value: PBMCs, including T cells, B cells, NK cells, and monocytes

value: chronic thromboembolic pulmonary hypertension (CTEPH)


title: PBMCs from HC patient, replicate 1, scRNAseq

description:
Primary Human PBMCs
GEXSCOPE

tag: disease

value: healthy control


title: KPC1199 Med12 sg3，H3K27Ac, Cut&Tag, repeat2

tag: cell line

tag: genotype


title: KPC1199 Med12 sg3，HP1A, Cut&Tag, repeat1


title: ZW2PLASMAB113A5

tag: cohort

value: Large cohort

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

tag: individual

tag: visit

tag: gender

tag: age

tag: age group


title: FPCP cells， WT，repeat2

value: FPCP

value: Pancreatic tumor cell

value: WT


title: PBMCs from CTEPH patient, replicate 1, scRNAseq

description:
Primary Human PBMCs
10× Genomics


title: Bulk ATAC kidney cortex

city: San Francisco

first: Gabriel

last: Loeb

state: CA

address: 555 Mission Bay Blvd South, Rm 382H

department: Medicine

institute: UCSF

description: bulk ATAC-sequencing

data_processing:
Bulk atac-seq peak and bigwig files were generated with PEPATAC (Smith et al. NAR Genom Bioinform 2021, using the hg38 genome assembly).
Assembly: hg38
Supplementary files format and content: Bulk atac-seq peak and bigwig files were generated with PEPATAC (Smith et al. NAR Genom Bioinform 2021, using the hg38 genome assembly).

source_name: Kidney cortex

extract_protocol:
To isolate nuclei, 2g of fresh kidney cortex fragments were homogenized in buffer (250mM sucrose, 10mM Tris pH 7.5, 3mM MgCl2, 0.1% NP40) using a gentleMACS M Tube (Miltenyi Biotec, 130-093-237) and gentleMACS dissociator program E.01. The homogenate was filtered through a 200um filter, 100um filter, and pelleted by centrifugation.
The Omni-ATAC protocol was used (Corces et al. Nature Methods 2017), with minor modifications as follows. Nuclei from 2g of tissue were resuspended in 1ml of ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin and incubated on ice for 3 minutes. 15ml RSB with 0.1% Tween was added to the sample to dilute detergents. Nuclei were passed through a 40μm filter and subsequently counted. 100,000 nuclei were pelleted and resuspended in 95uL of transposition buffer (33uL PBS, 1uL 1% Digitonin, 1uL 10% Tween-20, 10uL Nuclease Free Water, 50uL 2x TD buffer: 20mM Tris pH 7.5, 10mM MgCl2, 20% Dimethyl Formamide) with 10μl of transposase (Illumina, 20034197).

value: Kidney cortex


title: ZW2PLASMAB113A1

tag: anatomical location

value: Entire cardiovascular system

tag: shortid

tag: batch

tag: adapter

tag: pregnant

tag: trimester

value: F

tag: race

tag: ethnicity

value: HiSeq


title: ZW2PLASMAB113A3

tag: sample subgroup (condition)

tag: date of collection

value: M

tag: sequencing technology


title: ZW2PLASMAB112A24

tag: cohort

tag: rna source

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.


title: CLDN11_OE3, human iPSC-derived oligodendrocyte

city: Beijing

first: Yibo

last: Wang

state: Beijin

address: 167 Beilishi Road, Xicheng District, Beijing

institute: Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Hisat2 (version:2.0.4)
Adaptor sequences contained in reads were removed using trimadap, bases with a mass Q below 20 at the 3 'end were removed by seqtk trimfq (version: 1.0), i.e., the base error rate was less than 0.01, (Q = -10 logerrorratio).
Reads less than 25 in length were removed using lengthsort.pl. Ribosome RNA reads of the species to which they belonged were removed by bowtie2 (version: 2.2.6).
Genome mapping of pre-processed reads was performed applying the spliced mapping algorithm of Hisat2 (version: 2.0.4).
Stringtie (version: 1.3.0) was applied to count the number of Fragments per gene after Hisat2 alignment, then the TMM (trimmed mean of M values) method was used to normalize, and finally the FPKM value of each gene was calculated using a perl script.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for all samples.

source_name: Human iPSC-derived oligodendrocyte

growth_protocol: The human iPSC-derived oligodendrocytes were cultured at oligodendrocyte medium after processing by 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 mg/ml streptomycin at 37 °C in 5% CO2.

extract_protocol:
Total RNA was extracted using the MJzol Animal RNA Isolation Kit (Majorivd) and purified using RNAClean XP Kit (Beckman Coulter) and RNase-Free DNase Set (QIAGEN) according to standard operating procedures provided by the manufacturer. The mRNA was enriched using VAHTS® mRNA Capure Beads (Human/Mouse/Rat).
The mRNA sequencing libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme) according to standard operating procedures provided by the manufacturer.

treatment_protocol: The iPSC-derived oligodendrocytes were grown on 6 well cell culture plates (Costar, 3516), and transfected with 2 µg plasmid DNA per well using Lipofectamine TM 3000 (Invitrogen, L3000008) according to the manufacturer’s protocol.

tag: cell type

value: Human iPSC-derived oligodendrocyte

tag: genotype

value: CLDN11 overexpression

tag: treatment

value: CLDN11 plasmid transfected for 48 hours


title: ZW2PLASMAB113A2

tag: anatomical location

value: Healthy volunteer

tag: individual

tag: visit

value: no

tag: gender

tag: age

tag: age group

value: Mixed


title: ZW2PLASMAB113A12

value: Large cohort

tag: shortid

tag: batch

tag: adapter

tag: pregnant

tag: trimester

tag: race

value: Asian


title: ZW2PLASMAB113A4

tag: cohort

tag: rna source

value: total cell-free biofluid RNA

tag: sample subgroup (condition)

value: Pregnant individual

value: yes

tag: date of collection

value: White

tag: ethnicity

value: Latin

tag: sequencing technology


title: KPC1199 Med12 sg3，H3K27Ac, Cut&Tag, repeat1

tag: cell line

tag: cell type

value: pancreatic tumor cell

tag: genotype

value: Med12 knockout


title: KPC1199 Med12 sg3，Med12, Cut&Tag, repeat3


title: CLDN11_OE2, human iPSC-derived oligodendrocyte

tag: treatment


title: ZW2PLASMAB112A23

tag: anatomical location

value: Entire cardiovascular system

tag: rna isolation kit

tag: individual

tag: visit

value: unknown

tag: gender

value: F

tag: age

tag: age group

value: HiSeq


title: ZW2PLASMAB112A22

tag: cohort

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: batch

tag: adapter

tag: pregnant

tag: trimester

tag: race


title: ZW2PLASMAB112A21

tag: rna source

tag: sample subgroup (condition)

value: Healthy volunteer

tag: date of collection

tag: ethnicity

tag: sequencing technology


title: KPC1199 Med12 sg3，Med12, Cut&Tag, repeat2

tag: cell line

tag: cell type

tag: genotype


title: CLDN11_OE1, human iPSC-derived oligodendrocyte

value: Human iPSC-derived oligodendrocyte

value: CLDN11 overexpression

tag: treatment

value: CLDN11 plasmid transfected for 48 hours


title: ZW2PLASMAB112A19

value: Large cohort

tag: anatomical location

tag: rna isolation kit

tag: individual

tag: visit

value: no

tag: gender

tag: age

tag: age group


title: KPC1199 Med12 sg3，Med12, Cut&Tag, repeat1


title: Vector_3, human iPSC-derived oligodendrocyte

value: control

value: vector control plasmid transfected for 48 hours


title: KPC1199 Med12 sg3，Setdb1, Cut&Tag, repeat3


title: ZW2PLASMAB112A17

tag: cohort

value: total cell-free biofluid RNA

tag: shortid

tag: batch

tag: adapter

tag: pregnant

tag: trimester

value: M

tag: race

value: White


title: Vector_2, human iPSC-derived oligodendrocyte

tag: cell type


title: ZW2PLASMAB112A15

tag: rna source

tag: sample subgroup (condition)

tag: date of collection

tag: ethnicity

tag: sequencing technology


title: KPC1199 Med12 sg3，Setdb1, Cut&Tag, repeat2

tag: cell line

value: pancreatic tumor cell

tag: genotype

value: Med12 knockout


title: ZW2PLASMAB112A13

tag: anatomical location

value: Entire cardiovascular system

tag: rna isolation kit

tag: individual

tag: visit

tag: gender

tag: age


title: Vector_1, human iPSC-derived oligodendrocyte

tag: treatment


title: ZW2PLASMAB112A12

tag: cohort

tag: shortid

tag: batch

tag: adapter

tag: pregnant

tag: trimester

value: F

tag: age group

value: Latin


title: ZW2PLASMAB112A9

tag: rna source

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: sample subgroup (condition)

tag: date of collection

tag: race

tag: ethnicity

tag: sequencing technology

value: HiSeq


title: ZW2PLASMAB112A14

tag: anatomical location

tag: rna isolation kit

value: Healthy volunteer

tag: individual

tag: visit


title: KPC1199 Med12 sg3，Setdb1, Cut&Tag, repeat1

tag: cell line

tag: cell type

tag: genotype


title: KPC1199 Med12 sg3，H3K9me3, Cut&Tag, repeat2


title: AsPC1 cells, Med12 sg5,repeat3

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to hg38 with orientation mode using HISAT2  software
The mapped reads of each sample were assembled by StringTie  in a reference-based approach
differential expression analysis was performed using the DESeq2
Assembly: GRCh38
Supplementary files format and content: excel sheet includs tpm of each sample

value: Pancreatic tumor cell

value: Med12 Knockout


title: ZW2PLASMAB112A8

tag: cohort

value: Large cohort

tag: shortid

tag: batch

tag: adapter

tag: gender

tag: age


title: ZW2PLASMAB112A11

tag: rna source

tag: sample subgroup (condition)

value: Pregnant individual

tag: pregnant

value: yes

tag: trimester

tag: date of collection

tag: age group


title: AsPC1 cells, Med12 sg5,repeat2


title: KPC1199 Med12 sg3，H3K9me3, Cut&Tag, repeat3


title: AsPC1 cells, Med12 sg5,repeat1


title: ZW2PLASMAB112A7

tag: anatomical location

tag: rna isolation kit

tag: individual

value: no

tag: race

tag: ethnicity

tag: sequencing technology


title: ZW2PLASMAB112A6

tag: cohort

value: total cell-free biofluid RNA

tag: shortid

tag: visit

value: Asian


title: ZW2PLASMAB112A10

tag: batch

tag: adapter

tag: gender

value: M

value: White


title: KPC1199 Med12 sg3，H3K9me3, Cut&Tag, repeat1

tag: cell line

tag: cell type

value: pancreatic tumor cell

tag: genotype

value: Med12 knockout


title: ZW2PLASMAB112A20

value: Entire cardiovascular system

tag: rna source

tag: sample subgroup (condition)

tag: pregnant

tag: trimester

tag: date of collection

value: F

tag: age


title: AsPC1 cells, Med12 sg4,repeat3


title: ZW2PLASMAB112A5

tag: anatomical location

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: individual

tag: age group

tag: race

tag: ethnicity


title: KPC1199 Med12 sg3 treated with JQ1 0.2uM，H3K27Ac, Cut&Tag, repeat2

tag: treatment


title: AsPC1 cells, Med12 sg4,repeat2


title: ZW2PLASMAB112A3

tag: cohort

tag: shortid

tag: batch

tag: adapter

tag: visit

tag: gender

tag: sequencing technology

value: HiSeq


title: KPC1199 Med12 sg3 treated with JQ1 0.2uM，H3K27Ac, Cut&Tag, repeat1

tag: cell line

tag: cell type

tag: genotype


title: ZW2PLASMAB112A4

tag: anatomical location

tag: rna source

tag: sample subgroup (condition)

value: Healthy volunteer

tag: pregnant

tag: trimester

tag: date of collection

tag: age


title: ZW2PLASMAB112A16

tag: cohort

tag: rna isolation kit

tag: individual

value: unknown

tag: age group

tag: race

tag: ethnicity


title: ZW2PLASMAB112A2

tag: shortid

tag: batch

tag: adapter

tag: visit

tag: gender

tag: sequencing technology


title: ZW2PLASMAB111A24

tag: anatomical location

tag: rna source

tag: sample subgroup (condition)


title: AsPC1 cells, WT,repeat3

tag: cell line

tag: cell type

value: Pancreatic tumor cell

tag: genotype

value: WT


title: KPC1199 WT，HP1A, Cut&Tag, repeat3


title: ZW2PLASMAB112A1

tag: cohort

value: Large cohort

tag: rna isolation kit

tag: pregnant

tag: trimester

tag: date of collection

tag: age


title: ZW2PLASMAB111A23

tag: shortid

tag: batch

tag: individual

tag: age group

tag: race

tag: ethnicity


title: KPC1199 WT，HP1A, Cut&Tag, repeat2


title: KPC1199 WT，HP1A, Cut&Tag, repeat1


title: ZW2PLASMAB111A21

tag: anatomical location

tag: rna source

tag: adapter

tag: visit

tag: gender

tag: sequencing technology


title: ZW2PLASMAB111A22

tag: cohort

tag: rna isolation kit

tag: sample subgroup (condition)


title: ZW2PLASMAB111A19

value: Pregnant individual

tag: pregnant

value: yes

tag: trimester

tag: date of collection

value: Latin


title: AsPC1 cells, WT,repeat1

tag: cell line

tag: cell type

tag: genotype


title: ZW2PLASMAB111A20

value: total cell-free biofluid RNA

tag: shortid

tag: batch

tag: individual

value: no

tag: age

tag: age group

tag: race


title: AsPC1 cells, WT,repeat2


title: Patu8988T cells, Med12 sg5,repeat3

value: Med12 Knockout


title: ZW2PLASMAB111A18

tag: anatomical location

tag: rna source

tag: adapter

tag: visit

tag: gender

value: M

value: White

tag: ethnicity


title: KPC1199 WT，Setdb1, Cut&Tag, repeat2

value: pancreatic tumor cell


title: ZW2PLASMAB111A17

tag: cohort

value: Entire cardiovascular system

tag: rna isolation kit

tag: sample subgroup (condition)

tag: pregnant

tag: trimester

value: F

value: Asian

tag: sequencing technology


title: KPC1199 WT，Setdb1, Cut&Tag, repeat3

tag: cell line

tag: cell type

tag: genotype


title: Patu8988T cells, Med12 sg5,repeat2


title: ZW2PLASMAB111A16

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: batch

value: Healthy volunteer

tag: individual

tag: date of collection

tag: age

tag: age group

value: HiSeq


title: ZW2PLASMAB111A15

tag: anatomical location

tag: rna source

tag: adapter

tag: visit

tag: gender

tag: race


title: ZW2PLASMAB111A14

tag: cohort

tag: rna isolation kit

tag: sample subgroup (condition)

tag: pregnant

tag: trimester

tag: ethnicity


title: Patu8988T cells, Med12 sg5,repeat1

tag: cell line

tag: cell type

value: Pancreatic tumor cell

tag: genotype


title: AsPC1 cells, Med12 sg4,repeat1


title: ZW2PLASMAB111A12

value: Large cohort

tag: shortid

tag: batch

tag: individual

tag: date of collection

tag: age

tag: sequencing technology


title: ZW2PLASMAB111A13

tag: anatomical location

tag: rna source

tag: adapter

tag: visit

tag: gender

tag: age group


title: KPC1199 WT，Setdb1, Cut&Tag, repeat1

value: WT


title: KPC1199 WT，Med12, Cut&Tag, repeat3


title: Patu8988T cells, Med12 sg3,repeat3


title: ZW2PLASMAB111A11

tag: cohort

tag: rna isolation kit

tag: sample subgroup (condition)

tag: pregnant

tag: trimester

tag: race


title: KPC1199 WT，Med12, Cut&Tag, repeat2

tag: cell line

tag: cell type

tag: genotype


title: Patu8988T cells, Med12 sg3,repeat2


title: ZW2PLASMAB111A8

tag: shortid

tag: batch

tag: individual

tag: date of collection

tag: age

tag: ethnicity


title: ZW2PLASMAB111A10

tag: anatomical location

tag: rna source

tag: adapter

tag: visit

tag: gender

tag: sequencing technology


title: KPC1199 WT，Med12, Cut&Tag, repeat1


title: KPC1199 WT，H3K27Ac, Cut&Tag, repeat2


title: ZW2PLASMAB111A5

tag: cohort

tag: rna isolation kit

tag: sample subgroup (condition)

tag: pregnant

tag: trimester

tag: age group


title: Patu8988T cells, WT,repeat3

tag: cell line

tag: cell type

tag: genotype


title: ZW2PLASMAB111A6

tag: shortid

tag: batch

tag: individual

tag: date of collection

tag: age

tag: race


title: ZW2PLASMAB111A3

tag: anatomical location

tag: rna source

tag: adapter

tag: visit

tag: gender

tag: ethnicity


title: ZW2PLASMAB111A4

tag: cohort

tag: rna isolation kit

tag: sample subgroup (condition)

tag: pregnant

tag: trimester

tag: sequencing technology


title: KPC1199 WT，H3K27Ac, Cut&Tag, repeat1

tag: cell line

tag: cell type

tag: genotype


title: Patu8988T cells, WT,repeat2


title: Patu8988T cells, WT,repeat1


title: ZW2PLASMAB111A1

tag: shortid

tag: batch

tag: individual

tag: date of collection

tag: age

tag: age group


title: ZW2PLASMAB110A22

tag: anatomical location

tag: rna source

tag: adapter

tag: visit

tag: gender

tag: race


title: ZW2PLASMAB111A2

tag: cohort

tag: rna isolation kit

tag: sample subgroup (condition)

tag: pregnant

tag: trimester

tag: ethnicity


title: KPC1199 WT，H3K9me3, Cut&Tag, repeat3

tag: cell line

tag: cell type

tag: genotype


title: FU-UR-1_TFE3KD_dox_rep2

city: Boston

first: Dipanjan

last: Chowdhury

state: MA

address: 4 Blackfan Circle

institute: Dana-Farber Cancer Institute

data_processing:
Paired-end RNA-seq reads were aligned to a Bowtie2 indexed human genome (hg38 sourced from UCSC) using STAR with default settings. For better alignment, the first aligned splicing junctions detected by STAR (SJ.out.tab) were used for STAR alignment again with parameters “--sjdbFileChrStartEnd SJ.out.tab --readFilesIn $R1 $R2 --quantMode TranscriptoomeSAM GeneCounts --sjdbGTFfile $GTF_file --outSAMtype BAM Unsorted SortedByCoordinate”. Then the aligned to transcriptome bam files (AlignedtoTranscriptome.out.bam) were used to quantify gene expression levels by rsem-calculate-expression function from RSEM. Tag per million reads (TPM) from gene expression results files (.genes.results) were extracted and assembled for subsequent differential gene expression analysis by DESeq2.
Assembly: hg38
Supplementary files format and content: genes.results.gz

source_name: cell line

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomyicin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini Kit (QIAGEN, #74136)
After the QC procedures, mRNA is enriched using oligo(dT) beads. Then, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. After a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: ccRCC cell line (786-O) and tRCC cell line (FU-UR-1) were transduced with lentivirus expressing doxycycline shRNA against wild type TFE3 and ASPSCR1-TFE3 and selected with 500 mg/mL of G418. Subsequently, the cells were treated with doxycycline at a concentration of 1mg/mL for 5 days. s-TFE tRCC cells were transduced with control sgRNA or sgRNA targeting ASPSCR1-TFE3 for 5 days

tag: tissue

value: cell line

value: Cancer cell

value: ASPSCR1-TFE3 knockdown

tag: treatment

value: dox


title: cortex,WT,OLIG1,P1-2, CUT&Tag

city: SHANGHAI

first: YU

last: TIAN

state: SHANGHAI

address: 131 DONGAN ROAD

institute: FUDAN UNIVERSITY

data_processing:
scRNA-seq: High quality sequences (clean reads) were obtained by removing low quality sequences and joints. The clean reads were then processed with Cell Ranger software to obtain quantitative information on gene expression.
CUT&Tag: Basecells were performed using bcl2fastq v2.17 for Novaseq outut
Assembly: mm10 (scRNA-seq); mm39 (Cut&Tag)
Supplementary files format and content: Tab-separated value files and matrix files
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: Cortex

extract_protocol:
ScRNA-seq were performed on FACS sorted tdT+ cells from the P1 Olig1/2f/f;IS-reporter mice cortex which were electroporated of pCAG-Cre plasmid at E15.5.Emx1-CRE;Olig1/2f/f mice cortex were dissected out at P7 and immediately submerged in fresh ice-cold Hanks balanced salt solution. The cortex was then cut into pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit according to the manufacturer’s instructions.
The CUT&Tag assay was conducted on FACS-sorted GFP+ cells, using the cortex dissected from hGFAP-GFP at P1
The Chromium dropletbased sequencing platform (10X Genomics) was used to generate scRNA-Seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina NovaSeq 6000 or Illumina Hiseq4000.
CUT&Tag liabraries were prepared using the Vazyme#TD901 complemented with TruePrep® Index Kit V2 for Illumina  10 ng of DNA was used as starting material for CUT&Tag simples.Liabraries were amplified using 18 cycles on the thermocycler.

value: Cortex


title: ZW2PLASMAB110A18

tag: anatomical location

value: total cell-free biofluid RNA

tag: shortid

tag: batch

tag: individual

value: no

tag: date of collection

tag: age

tag: age group

tag: sequencing technology


title: ZW2PLASMAB111A7

tag: cohort

tag: rna source

tag: rna isolation kit

tag: adapter

tag: sample subgroup (condition)

tag: visit

tag: gender

tag: race


title: FU-UR-1_TFE3KD_dox_rep1

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: FU-UR-1_TFE3KD_dox_rep3


title: ZW2PLASMAB110A15

tag: anatomical location

tag: shortid

tag: batch

tag: individual

tag: pregnant

tag: trimester

tag: date of collection

value: White

tag: ethnicity


title: KPC1199 WT，H3K9me3, Cut&Tag, repeat1

value: pancreatic tumor cell


title: Patu8988T cells, Med12 sg3,repeat1

value: Med12 Knockout


title: ZW2PLASMAB110A16

tag: cohort

value: Entire cardiovascular system

tag: rna source

tag: rna isolation kit

tag: adapter

tag: sample subgroup (condition)

value: F

tag: age

tag: age group

value: Latin

tag: sequencing technology


title: ZW2PLASMAB110A21

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

value: Healthy volunteer

tag: visit

tag: gender

tag: race

value: HiSeq


title: FU-UR-1_TFE3KD_nodox_rep3

tag: tissue

tag: cell line

tag: cell type

tag: genotype

value: Control

tag: treatment


title: ZW2PLASMAB110A11

value: Large cohort

tag: anatomical location

tag: shortid

tag: batch

tag: individual

tag: pregnant

tag: trimester

tag: date of collection

tag: ethnicity


title: cortex,WT,OLIG2,P1-1, CUT&Tag

value: WT


title: cortex,WT,OLIG1,P1-1, CUT&Tag


title: ZW2PLASMAB110A14

tag: cohort

tag: rna source

tag: rna isolation kit

tag: adapter

tag: sample subgroup (condition)

tag: age

tag: age group

tag: sequencing technology


title: ZW2PLASMAB110A8

tag: visit

tag: gender

tag: race


title: ZW2PLASMAB110A17

tag: anatomical location

tag: shortid

tag: batch

value: Pregnant individual

value: yes


title: ZW2PLASMAB110A13

tag: individual

tag: pregnant

tag: trimester


title: UOK146_rep2

tag: tissue

value: cell line

tag: cell line

tag: cell type

value: Cancer cell

tag: genotype

tag: treatment


title: cortex,WT,OLIG2,P1-2, CUT&Tag

value: Cortex


title: ZW2PLASMAB110A12

tag: cohort

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

tag: adapter

tag: sample subgroup (condition)

value: no

tag: date of collection

value: M

tag: age

value: Not specified

tag: ethnicity


title: ZW2PLASMAB110A23

tag: anatomical location

value: Entire cardiovascular system

tag: shortid

tag: batch

tag: visit

tag: gender

value: F

tag: age group

tag: race

value: White

tag: sequencing technology


title: Islets_ndLN_TCR

city: Pittsburgh

first: Jian

last: Cui

state: PA

address: 5051 Centre Avenue

department: Immunology

institute: University of Pittsburgh

description: TCR library, read 1 contains barcode and UMI information, and read 2 containsTCR sequences

library_source: other

data_processing:
*library strategy: CITE-seq, TCR-seq
CellRanger v6.0.1, along with its count and vdj functions, and cite-seq-count v1.4.3 were utilized to aggregate reads across sequencing samples, resulting in unified sets of corresponding readouts.
Assembly: mm10
Supplementary files format and content: CellRanger output files:  GEX_barcodes.tsv.gz,GEX_features.tsv.gz, GEX_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: TCR_filtered_contig_annotations.csv
Supplementary files format and content: cite-seq-count output files:  HTO_barcodes.tsv.gz, HTO_features.tsv.gz, HTO_matrix.mtx.gz

molecule: other

source_name: islet and lymph nodes

extract_protocol:
Regulatory T cells and conventional CD4 T cells (Tconvs) were isolated from the islets and ndLN 6 Foxp3CRE-GFP.NOD and 6 Rosa26+/LSL-Ametrine-Nrp1Foxp3CRE-GFP.NOD (6-week females).
Cells were loaded into Single Cell Chip at a a goal of 50:50 ratio of Tregs:Tconvs. Cells were then processed through 10X controller for droplet generation and Library preparation.
The CITE-seq and hashing protocol were employed to produce a hashtag oligo library and a 5' gene expression library.

tag: tissue

value: islet and lymph nodes

tag: genotype

value: wild type and Rosa^Nrp1^L/+

tag: cell type

value: CD4 Tconv and Treg

tag: library type

value: TCR


title: ZW2PLASMAB110A4

tag: cohort

value: Large cohort

tag: rna source

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: adapter

value: Healthy volunteer

tag: individual

tag: pregnant

tag: trimester

value: HiSeq


title: UOK146_rep1

value: cell line

tag: cell line

value: Cancer cell

value: Control

tag: treatment


title: FU-UR-1_TFE3KD_nodox_rep1


title: UOK109_rep3


title: ZW2PLASMAB110A9

tag: anatomical location

value: total cell-free biofluid RNA

tag: shortid

tag: batch

tag: sample subgroup (condition)

tag: visit

value: no

tag: date of collection

tag: gender

tag: age

tag: ethnicity

value: Latin


title: Islets_ndLN_GEX

description: GEX (5' mRNA) library,Read 1 contains the cell barcode and UMI, and Read 2 contains the transcript

molecule: polyA RNA

tag: tissue

tag: genotype

tag: cell type

tag: library type

value: mRNA


title: UOK146_rep3


title: ZW2PLASMAB110A2

tag: cohort

value: Entire cardiovascular system

tag: rna source

tag: rna isolation kit

tag: adapter

tag: individual

tag: pregnant

value: M

tag: age group

tag: race

value: Not specified

tag: sequencing technology


title: ZW2PLASMAB110A7

tag: anatomical location

tag: shortid

tag: batch

tag: sample subgroup (condition)

tag: visit

tag: trimester

tag: date of collection

value: F

value: White


title: ZW2PLASMAB110A10

tag: gender

tag: age

tag: ethnicity


title: cortex,Olig1/2,P7, scRNA-seq

description: 10x Genomics

data_processing:
scRNA-seq: High quality sequences (clean reads) were obtained by removing low quality sequences and joints. The clean reads were then processed with Cell Ranger software to obtain quantitative information on gene expression.
CUT&Tag: Basecells were performed using bcl2fastq v2.17 for Novaseq outut
Assembly: mm10 (scRNA-seq); mm39 (Cut&Tag)
Supplementary files format and content: Tab-separated value files and matrix files
Supplementary files format and content: bigWig

tag: tissue

value: Cortex

tag: genotype


title: Islets_ndLN_HTO

description: HTO library, Read 1 contains cell barcode and UMI.Read 2 contains the15 bp hashtag.

molecule: protein

value: islet and lymph nodes

value: wild type and Rosa^Nrp1^L/+

tag: cell type

value: CD4 Tconv and Treg

tag: library type

value: HTO

tag: hto


title: ZW2PLASMAB109A23

tag: cohort

value: Large cohort

tag: rna source

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: adapter

value: Healthy volunteer

tag: individual

tag: pregnant

tag: age group

tag: race

value: HiSeq


title: UOK109_rep1

value: cell line

tag: cell line

value: Cancer cell

value: Control

tag: treatment


title: ZW2PLASMAB109A24

tag: anatomical location

value: Entire cardiovascular system

value: total cell-free biofluid RNA

tag: shortid

tag: batch

tag: sample subgroup (condition)

tag: visit

value: no

tag: trimester

tag: date of collection

tag: gender

tag: age

value: Latin

tag: sequencing technology


title: FU-UR-1_TFE3KD_nodox_rep2

tag: tissue

tag: cell type

tag: genotype


title: ZW2PLASMAB109A22

tag: cohort

tag: rna source

tag: rna isolation kit

tag: adapter

tag: individual

tag: pregnant

value: F

tag: age group

tag: ethnicity


title: ZW2PLASMAB110A1

tag: anatomical location

tag: shortid

tag: batch

tag: sample subgroup (condition)

tag: visit

value: M

tag: race

value: White


title: ZW2PLASMAB110A6

tag: trimester

tag: date of collection

tag: gender

tag: age

value: Asian

tag: sequencing technology


title: ZW2PLASMAB110A5

tag: cohort

tag: rna source

tag: rna isolation kit


title: sgPtk2 tumor 3

city: Toronto

first: Graham

last: MacLeod

state: ON

address: 144 College Street

department: Pharmaceutical Sciences

country: Canada

institute: University of Toronto

description: tumor_rnaseq_counts.txt | ko1

data_processing:
FASTQ files were aligned to the mouse genome (GRCm39) using STAR.
Read counts were extracted and normalized using DESeq2.
Assembly: GRCm39 primary assembly
Supplementary files format and content: tab delimited text file containing DESEQ2 normalized RNA-seq counts from STAR alignment.

source_name: brain tumor

extract_protocol:
RNA was extracted using the Trizol reagent (invitrogen) and cleaned using the Qiagen RNeasy kit.
50 ng per sample was used for library preparation with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina after the total RNA was depleted using NEBNExt rRNA depletion kit

tag: tissue

value: brain tumor

tag: genotype

tag: treatment


title: UOK109_rep2

tag: cell line

tag: cell type


title: sgPtk2 tumor 2

description: tumor_rnaseq_counts.txt | ko3


title: ZW2PLASMAB109A20

tag: anatomical location

tag: shortid

tag: batch

tag: adapter

tag: individual

tag: pregnant

tag: age group

tag: ethnicity


title: ZW2PLASMAB110A3

tag: sample subgroup (condition)

tag: visit

tag: trimester

tag: date of collection

tag: gender

tag: age

tag: race

tag: sequencing technology


title: 786-O_TFE3KD_dox_rep3

tag: tissue

tag: cell line

tag: cell type

tag: genotype

value: TFE3 knockdown

tag: treatment

value: dox


title: ZW2PLASMAB109A19

tag: cohort

value: Large cohort

tag: anatomical location

tag: rna source

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: batch

tag: adapter

tag: individual


title: sgPtk2 tumor 1

description: tumor_rnaseq_counts.txt | ko2