title: P11_L2_sc04

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L2_sc03

status: Public on Mar 31 2021

type: SRA

city: Tianjin

first: Caiying

last: Zhu

address: Heping District, Nanjing Road, 288

country: China

institute: Institute of Hematology and Blood Disease Hospital

description:
3' ends mRNA
AA_cells_counts.txt

library_source: transcriptomic

data_processing:
Sequencing data was demultiplexed based on barcodes in Read 2 (R2) of paired-end reads. UMI in R2 was added to the head of corresponding read 1 (R1), which was then trimmed to remove the template switch oligo (TSO) and polyA tail sequences; we also trimmed the reads with adaptor contaminants and low-quality bases (N> 10%).
The clean reads were aligned to the human GRCh38 genome using hisat2 (v2.1.0) with the known gene annotation (GENCODE release 27). Gene quantification was based on the UMIs after removing duplicated reads using modified HTSeq (version 0.9.1)
Gene expression level was normalized as log2 (TPM/10 + 1), in which TPM is short for Transcripts per million and adding one is to avoid negative expression values.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count values for each single cells.

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Fresh bone marrow and peripheral blood mononuclear cells were isolated by the Ficoll-PaqueTM PLUS (GE Healthcare) following the manufacturer’s instruction. Bone marrow samples were divided into two parts. One part was used for sorting HSPCs which were stained with human antibodies including lineage cocktail (CD3, CD14, CD16, CD19, CD20, CD56) (BV510, Biolegend), CD34 (APC, Clone 581, BD Biosciences), CD38 (PE-Cy™7, clone HIT2, BD Biosciences), CD90 (PerCP-Cy™5.5, clone5E10, BD Biosciences), CD45RA (FITC, clone HI100, BD Biosciences), CD49f (BV605, clone GoH3, BD Bioscience), CD10 (BV786, clone HI10a, BD Biosciences), CD135 (PE, clone 4G8, BD Biosciences). Another part of bone marrow and all peripheral blood were used for sorting T cells which were stained antibodies including CD3 (APC-Cy™7, clone SK7, BD Biosciences), CD4 (APC, clone RPA-T4, BD Biosciences), CD8 (PE-Cy™7, clone RPA-T8, BD Biosciences). All samples were incubated on ice for 30mins in the dark and washed with PBS. After cell suspension, DAPI (1 ug/ml, Sigma-Aldrich) was added to remove dead cells for FACS. Flow cytometry sorting was performed on a BD FACSAria III (BD Bioscience).
Fresh isolated cells were sorted directly into cell lysis buffer on a BD FACSAria III. The reverse transcription and template switch steps were performed following the modified Smart-seq2 protocol.(STRT-seq). Single cells with different barcodes were pooled for one library. The mixed cDNA was purified using DNA Clean and Concentration Kit (ZYMO, Cat.#D4014), and the small fragments and primers were removed by 0.8X AMPure XP beads (Beckman, Catt#A63882). A total of 30~40 ng purified products were amplified using biotinylated primers anchored with 8 nt sequences for library indexing. 300~450 ng cDNA was fragmented into 300 bp using Covaris S220 (Covaris). Dynabeads MyOne Streptavidin C1 (Invitrogen, Cat#65001) was used to enrich the 3' end of fragmented cDNA. The processes of end repair, polyA-tailing, adaptor ligation and library amplification were using KAPA Hyper Prep Kits (Kapa Biosystems, Cat#KK8504) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (NEB, Cat#E7335L).
Modified Smart-seq2

tag: Sex

value: Male

tag: treatment

value: untreated

tag: condition

value: SAA

tag: surface markers

tag: tissue

value: Peripheral blood

tag: age


title: P11_L2_sc01

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L2_sc05

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L2_sc21

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L2_sc02

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc95

description:
3' ends mRNA
AA_cells_counts.txt

value: Bone Marrow


title: P11_L1_sc93

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc92

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc91

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc89

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L2_sc09

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc87

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc90

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc84

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc88

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc83

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc85

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc80

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc82

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc94

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc81

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc79

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc78

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc77

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc75

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc72

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc96

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc73

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc74

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc69

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc68

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc67

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc71

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc70

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc66

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc86

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc65

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc61

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc64

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc63

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc60

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc58

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc57

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc56

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc54

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc62

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc49

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc55

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc51

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc50

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc52

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc47

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc44

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc43

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc42

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc46

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc45

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc40

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc41

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc38

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc39

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc37

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc36

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc59

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc35

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc33

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc30

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc31

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc28

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc29

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc48

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc26

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc25

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc32

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc22

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc19

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc27

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc17

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc15

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc16

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc14

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc12

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc13

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc11

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc07

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc09

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc10

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc08

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc05

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc06

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc04

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc03

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc02

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc21

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc74

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc01

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc18

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc70

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc73

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc24

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc72

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc69

description:
3' ends mRNA
AA_cells_counts.txt


title: P11_L1_sc20

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc61

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc67

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc66

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc59

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc60

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc58

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc62

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc57

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc55

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc56

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc51

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc53

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc50

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc49

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc71

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc48

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc68

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc47

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc46

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc41

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc45

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc40

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc38

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc63

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc43

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc42

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc37

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc36

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc39

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc29

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc27

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc31

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc28

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc52

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc26

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc25

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc24

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc21

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc22

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc20

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc19

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc44

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc18

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc17

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc15

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc14

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc33

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc32

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc16

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc13

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc11

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc10

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc08

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc04

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc06

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc03

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc93

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc94

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc01

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc91

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc05

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc88

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc89

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc87

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc84

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc92

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc12

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc82

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc81

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc86

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc80

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc85

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc83

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc79

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc02

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc77

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc74

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc90

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc73

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc78

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc75

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc72

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc71

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc70

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc68

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc69

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc64

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc61

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc65

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc63

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc60

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc59

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc58

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc57

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc56

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc53

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc51

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc52

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc50

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc54

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc48

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc49

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc46

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc44

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc42

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc45

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L3_sc07

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc40

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc67

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc47

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc66

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc43

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc38

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc36

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc37

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc41

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc33

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc35

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc32

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc31

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc55

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc30

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc29

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc26

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc27

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc22

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc21

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc24

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc25

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc20

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc39

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc15

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc18

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc17

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc19

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc14

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc16

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc10

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc12

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc13

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc11

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc05

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc09

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc06

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc04

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc02

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc08

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc07

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc03

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc01

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc94

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L2_sc28

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc93

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc92

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc86

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc87

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc88

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc91

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc83

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc85

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc84

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc82

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc77

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc79

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc75

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc89

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc78

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc74

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc81

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc72

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc70

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc71

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc69

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc67

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc64

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc66

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc65

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc62

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc63

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc90

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc61

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc80

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc60

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc59

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc55

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc56

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc73

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc58

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc51

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc52

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc57

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc68

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc49

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc53

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc54

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc47

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc45

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc43

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc42

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc46

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc38

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc39

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc50

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc40

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc41

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc37

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc36

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc35

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc33

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc32

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc31

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc29

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc48

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc30

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc27

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc28

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc26

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc44

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc19

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc22

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc21

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc20

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc11

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc24

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc12

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc18

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc16

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc17

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc10

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc14

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc13

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc09

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc06

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc02

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc03

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc01

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc25

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc07

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc08

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc05

description:
3' ends mRNA
AA_cells_counts.txt


title: P10_L1_sc04

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc64

description:
3' ends mRNA
AA_cells_counts.txt

value: Female

value: non-SAA


title: P10_L1_sc15

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc62

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc61

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc60

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc59

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc58

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc57

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc56

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc55

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc53

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc50

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc49

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc51

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc52

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc63

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc16

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc15

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc14

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc13

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc09

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc11

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc12

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc08

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc05

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc04

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc06

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc03

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc07

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc80

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc01

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc79

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc02

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc78

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc75

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc77

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc74

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L7_sc54

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc72

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc73

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc71

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc68

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc69

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc67

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc66

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc32

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc31

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc29

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc28

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc25

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc26

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc24

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc27

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc21

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc65

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc22

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc18

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc32

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc17

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc19

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc31

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc30

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc20

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc25

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc30

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc22

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc28

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L6_sc70

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc21

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc17

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc18

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc16

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc15

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc13

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc11

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc14

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc09

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc07

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc06

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc05

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc27

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc01

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc03

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc59

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc63

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc58

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc53

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc56

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc52

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc57

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc20

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc51

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc48

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc47

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc46

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc08

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc42

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc45

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc39

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc44

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc41

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc37

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc35

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc43

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L5_sc04

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc36

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc31

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc32

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc33

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc30

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc50

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc28

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc49

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc29

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc21

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc15

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc17

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc20

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc19

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc18

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc11

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc10

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc09

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc08

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L4_sc38

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc05

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc07

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc03

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc01

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc22

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc26

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc96

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc88

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc86

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc94

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc90

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc93

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc02

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc84

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc81

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc27

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc85

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc80

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc82

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc83

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc87

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc91

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L3_sc04

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc78

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc74

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc75

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc77

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc73

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc71

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc69

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc68

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc67

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc63

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc60

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc58

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc57

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc55

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc53

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc59

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc50

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc56

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc51

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc48

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc46

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc47

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc40

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc72

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc42

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc43

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc44

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc45

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc36

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc39

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc35

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc33

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc31

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc37

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc27

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc28

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc20

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc24

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc17

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc16

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc14

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc08

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc11

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc05

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc01

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc13

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc07

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc10

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc21

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc09

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L2_sc95

description:
3' ends mRNA
AA_cells_counts.txt


title: HDN4_sc89

description:
Full length mRNA
Full_length_SingleCell_counts.txt

data_processing:
Template switch oligo (TSO), ISPCR and Oligo(dT) primer were trimmed using Trimmomatic (v0.36), clean reads shorter than 36bp were removed.
The remained clean reads were aligned to the human GRCh38 genome using hisat2 (v2.1.0) with the known gene annotation (GENCODE release 27). Gene quantification was using HTSeq (version 0.9.1)
Gene expression level was normalized as log2 (TPM/10 + 1), in which TPM is short for Transcripts per million and adding one is to avoid negative expression values.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes count values for each single cells.

extract_protocol:
Fresh bone marrow mononuclear cells were isolated by the Ficoll-PaqueTM PLUS (GE Healthcare) following the manufacturer’s instruction. Ten mononuclear cells were stained with human antibodies including lineage cocktail (CD3, CD14, CD16, CD19, CD20, CD56) (BV510, Biolegend), CD34 (APC, Clone 581, BD Biosciences), CD38 (PE-Cy™7, clone HIT2, BD Biosciences), CD90 (PerCP-Cy™5.5, clone5E10, BD Biosciences), CD45RA (FITC, clone HI100, BD Biosciences), CD49f (BV605, clone GoH3, BD Bioscience), CD10 (BV786, clone HI10a, BD Biosciences), CD135 (PE, clone 4G8, BD Biosciences). All samples were incubated on ice for 30mins in the dark and washed with PBS. After cell suspension, DAPI (1 ug/ml, Sigma-Aldrich) was added to remove dead cells for FACS.
Fresh isolated cells were transferred directly into cell lysis buffer and the reverse transcription and template swithc steps were performed following the Smart-seq2 protocol with minor modifications. The number of cycles for PCR amplification was 24. After purifying the PCR products, 4 cycles of PCR were added in order to obtain sufficient cDNA. The cDNA was fragmented using Covaris S220 instead of Tn5 transposase. The processes of end repair, polyA-tailing, adaptor ligation and library amplification were using KAPA Hyper Prep Kits (Kapa Biosystems, cat.No: KK8504) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (NEB, cat.No: E7335L)
Smart-seq2

tag: individual

value: donor Ctrl3

value: male

tag: disease state

value: Ctrl

tag: cell type

value: hematopoietic stem and progenitor cells (HSPCs)


title: HDN4_sc87


title: HDN4_sc86


title: P1_L1_sc38

description:
3' ends mRNA
AA_cells_counts.txt


title: HDN4_sc90


title: HDN4_sc88


title: P1_L1_sc04

description:
3' ends mRNA
AA_cells_counts.txt


title: P1_L1_sc06

description:
3' ends mRNA
AA_cells_counts.txt


title: HDN4_sc71


title: HDN4_sc72


title: HDN4_sc73


title: HDN4_sc96


title: P1_L1_sc03

description:
3' ends mRNA
AA_cells_counts.txt


title: HDN4_sc94


title: HDN4_sc92


title: HDN4_sc91


title: HDN4_sc93


title: HDN4_sc67


title: HDN4_sc53


title: HDN4_sc54


title: HDN4_sc65


title: HDN4_sc51


title: HDN4_sc39


title: P1_L1_sc15

description:
3' ends mRNA
AA_cells_counts.txt


title: HDN4_sc83


title: HDN4_sc81


title: HDN4_sc38


title: HDN4_sc79


title: HDN4_sc75


title: HDN4_sc35


title: HDN4_sc74


title: P1_L3_sc06

description:
3' ends mRNA
AA_cells_counts.txt


title: HDN4_sc26


title: HDN4_sc68


title: HDN4_sc69


title: HDN4_sc20


title: HDN4_sc66


title: HDN4_sc80


title: HDN4_sc55


title: HDN4_sc23


title: HDN4_sc49


title: HDN4_sc50


title: HDN1_sc58


title: HDN4_sc37


title: HDN1_sc57


title: HDN4_sc36


title: HDN4_sc34


title: HDN4_sc33


title: HDN4_sc52


title: HDN1_sc46


title: HDN4_sc27


title: HDN1_sc45


title: HDN1_sc63


title: HDN1_sc62


title: HDN1_sc39


title: HDN1_sc37


title: HDN1_sc43


title: HDN1_sc41


title: HDN1_sc53


title: HDN1_sc59


title: HDN1_sc51


title: HDN1_sc49


title: HDN4_sc31


title: HDN1_sc31


title: HDN1_sc52


title: HDN1_sc34


title: HDN4_sc21


title: HDN1_sc28


title: HDN1_sc22


title: HDN1_sc23


title: HDN1_sc19


title: HDN1_sc21


title: HDN1_sc18


title: HDN4_sc77


title: HDN1_sc36


title: HDN1_sc42


title: HDN1_sc35


title: HDN1_sc30


title: HDN1_sc24


title: HDN1_sc38


title: HDN1_sc13


title: HDN1_sc12


title: HDN1_sc11


title: HDN1_sc09


title: HDN1_sc14


title: HDN1_sc10


title: HDN1_sc03


title: HDN1_sc08


title: HDN1_sc29


title: HDN1_sc04


title: HDN1_sc27


title: HDN1_sc01


title: HDN1_sc05


title: HDN1_sc06


title: nonSAA_L2_sc31

value: donor P17


title: HDN1_sc20


title: nonSAA_L2_sc29


title: nonSAA_L2_sc18


title: nonSAA_L2_sc30


title: nonSAA_L2_sc15


title: nonSAA_L2_sc20


title: nonSAA_L2_sc27


title: nonSAA_L2_sc25


title: nonSAA_L2_sc24


title: HDN1_sc17


title: nonSAA_L2_sc23


title: nonSAA_L2_sc22


title: nonSAA_L2_sc13


title: nonSAA_L2_sc21


title: nonSAA_L2_sc17


title: HDN1_sc15


title: nonSAA_L2_sc12


title: nonSAA_L2_sc11


title: nonSAA_L2_sc07


title: nonSAA_L2_sc02


title: nonSAA_L2_sc09


title: nonSAA_L1_sc92


title: nonSAA_L1_sc85


title: nonSAA_L1_sc93


title: nonSAA_L1_sc89


title: nonSAA_L1_sc88


title: nonSAA_L2_sc05


title: nonSAA_L1_sc87


title: nonSAA_L2_sc04


title: nonSAA_L2_sc08


title: nonSAA_L1_sc83


title: nonSAA_L1_sc84


title: nonSAA_L1_sc80


title: nonSAA_L1_sc78


title: nonSAA_L1_sc82


title: nonSAA_L1_sc77


title: nonSAA_L1_sc76


title: nonSAA_L1_sc75


title: nonSAA_L1_sc74


title: nonSAA_L1_sc73


title: nonSAA_L1_sc70


title: nonSAA_L1_sc67


title: nonSAA_L1_sc94


title: nonSAA_L1_sc65


title: nonSAA_L1_sc71


title: nonSAA_L1_sc62


title: nonSAA_L1_sc72


title: nonSAA_L1_sc66


title: nonSAA_L1_sc60


title: nonSAA_L1_sc64


title: nonSAA_L1_sc58


title: nonSAA_L1_sc56


title: nonSAA_L1_sc52


title: nonSAA_L1_sc51


title: nonSAA_L1_sc54


title: nonSAA_L1_sc53


title: nonSAA_L1_sc49


title: nonSAA_L1_sc50


title: nonSAA_L1_sc40


title: nonSAA_L1_sc35


title: nonSAA_L1_sc34


title: nonSAA_L1_sc33


title: nonSAA_L1_sc38


title: nonSAA_L1_sc30


title: nonSAA_L1_sc32


title: nonSAA_L1_sc29


title: nonSAA_L1_sc27


title: nonSAA_L1_sc24


title: nonSAA_L1_sc23


title: nonSAA_L1_sc26


title: nonSAA_L1_sc28


title: nonSAA_L1_sc22


title: nonSAA_L1_sc19


title: nonSAA_L1_sc20


title: nonSAA_L1_sc18


title: nonSAA_L1_sc08


title: nonSAA_L1_sc25


title: nonSAA_L1_sc13


title: nonSAA_L1_sc07


title: nonSAA_L1_sc15


title: nonSAA_L1_sc11


title: nonSAA_L1_sc16


title: nonSAA_L1_sc06


title: P23

data_processing:
TSO primer, polyA tail, adaptor, and low-quality sequence (N > 10%) were trimmed using Trimmomatic (version 0.36).
Clean reads were aligned against the human GRCh38 genome using STAR (version 2.7)). Duplicate reads were identified and removed by using Picard(version 2.17.6). MATS(version 4.0.2) and DaPars(version 0.9.0) to perform alternative splicing and alternative polyadenylation analysis, respectively.
Gene quantification was using HTSeq (version 0.9.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count values for eachsamples.

molecule: polyA RNA

extract_protocol:
Mononuclear cells from 3 healthy donors and untreated aplastic anemia patients' bone marrow aspirates were isolated using Ficoll density gradient separation and cryopreserved in 90% FBS/ 10% DMSO for storage in liquid nitrogen. The thawing frozen cells were stained with human antibodies including lineage cocktail (CD3, CD14, CD16, CD19, CD20, CD56) (BV510, Biolegend) and CD34 (APC, Clone 581, BD Biosciences) antibodies. Lin-CD34+ HSPCs (cell count ranges from 130 to 2000) were sorted directly into cell lysis buffer on a BD FACSAria III.
The reverse transcription and template switch steps were performed following the full-length Smart-seq2 protocol with some modifications. Concentration of oligd(T30VN) and template switch oligo (TSO) primers used for mRNA reverse transcription were double. The cDNA was fragmented using Covaris S220 instead of Tn5 transposase. The processes of end repair, polyA-tailing, adaptor ligation and library amplification were using KAPA Hyper Prep Kits (Kapa Biosystems, Cat# KK8504) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (NEB, Cat# E7335L).The 150bp paired-end reads were generated from Illumina NovaSeq6000 platform.
A modified Smart-seq2

value: female


title: P22


title: P21


title: nonSAA_L1_sc21


title: P19


title: nonSAA_L1_sc05


title: nonSAA_L1_sc02


title: P18


title: P20


title: nonSAA_L1_sc14


title: Ctrl8


title: Ctrl7


title: Pulp2

status: Public on Feb 16 2021

city: Basel

first: Andreas

last: Moor

address: Mattenstrasse 26

department: Department of Biosystems Science and Engineering

country: Switzerland

institute: ETH

description: Age 18-35yo, healthy dental pulp

data_processing:
The quality and concentration of the single cell preparations were evaluated using an haemocytometer in a Leica DM IL LED microscope and adjusted to 1,000 cells/µl
10,000 cells per sample were loaded in to the 10X Chromium controller and library preparation was performed according to the manufacturer’s indications (single cell 3’ v2 or v3 protocol)
The resulting libraries were sequenced in an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=26, i7=8, R2=98) to a depth of around 50,000 reads per cell
Genome_build: Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26
Supplementary_files_format_and_content: cell ranger output

source_name: Human dental pulp

extract_protocol:
PULP: Teeth (third molars) were collected immediately after extraction and preserved in sterile NaCl 0.9%, on ice for the time needed to transfer them from the clinic to the processing laboratory (< 10 minutes).  Periodontium was carefully removed (see below). The cleansed tooth was then carefully wiped with 70% ethanol. The tooth was then cracked with a press, and carefully opened with forceps. The dental pulp was then removed from the tooth with a separate set of instruments, placed in a Petri dish filled with cold HBSS and minced into small pieces (< 2 mm diameter). Dental pulp pieces were transferred in falcon tubes filled with HBSS, centrifuged at 4°C, 300g, for 10 minutes. Tissues were digested in 10 mL Collagenase P 5 U/mL (11 213 873 001, Sigma Aldrich, Buchs, Switzerland) for 40 minutes at 37°C. After digestion, samples were disaggregated by pipetting, filtered through a 70 um cell strainer, and resuspended in HBSS + 0.002% Bovine Serum Albumin (BSA; 0163.2, Roth AG, Arlesheim, Switzerland).
library preparation was performed according to the manufacturer’s indications (single cell 3’ v2 or v3 protocol)

tag: cell types

value: Single cells, heterogeneous

tag: 10x kit


title: nonSAA_L1_sc04


title: rna_37C_2

status: Public on Dec 10 2020

city: San Antonio

first: David

last: Kadosh

state: Texas

address: 7703 Floyd Curl Dr., MC: 7758

department: Department of Microbiology, Immunology & Molecular Genetics

country: USA

data_processing:
Adaptor sequences and low-quality score (phred quality score < 5) bases were trimmed from RNA-Seq and Ribo-Seq datasets with TrimGalore (v 0.4.3) (Krueger, 2012). Only reads that were at least 20 nucleotide long were retained.
Trimmed sequences from RNA-seq and Ribo-seq were both mapped using STAR (v.2.5.2b) (Dobin, 2013) using Assembly 22 fasta as the reference and GTF s07-m01-r27 from CGD allowing a mismatch of at most two positions (--outFilterMismatchNmax 2). Only uniquely mapping reads were retained (-outFilterMultimapNmax 1). All the reads mapping to non-mRNA sequences were filtered out before downstream analysis. The corresponding non-mRNA sequences were also obtained from CGD (C_albicans_SC5314_version  _A22-s07-m01-r27_other_features_no_introns.fasta). The periodicity analysis of Ribo-seq data was performed using ribotricer (v1.3.2) (Choudhary, 2020). Gene level counting was performed using featureCounts (v1.6.4) (Liao, 2014). Since Assembly 22 is a diploid assembly, the reads were counted for each copy of the gene separately (hapA and hapB) and then merged into a single read count per gene.
Differential expression analysis was performed using DESeq2 (Love, et al, 2014). Only genes with at least one read per replicate were selected for performing the library size normalization step and running the moderated t-statistic test. Genes were defined to be differentially expressed (DE) if the transcripts per million (TPM) was greater than 1 in at least 2 replicates and if their absolute fold-change on log2 scale is at least 1 with an FDR adjusted p-value of less than or equal to 0.05.
Differential translational efficiency was performed using riborex (Li, 2017) by retaining genes that had at least one read count in one replicate across the two conditions in both Ribo-seq and RNA-seq samples. Only genes that had a read count of at least one per replicate were used as input to riborex. We define genes to be exhibiting differential translational efficiency if their TPM was greater than 1 in at least 2 replicates while the absolute fold-change on log2 scale was at least 1 and the corresponding non-adjusted p-value less than or equal to 0.05. Gene ontology (GO) analysis was performed using clusterProfiler (Yu, 2012) using GO slim ontology file available from CGD.
Genome_build: ASM18296v3
Supplementary_files_format_and_content: raw counts table

organism: Candida albicans

source_name: fungal cells

growth_protocol: Serum inductions were carried out in YEPD (yeast extract peptone dextrose) medium as  described previously using C. albicans wild-type strain DK 318 (Banerjee et al. 2008) with the following exceptions: 1)  the initial starting overnight culture volume was 150 mL and overnight cultures were diluted at OD600 ~ 4.0, 2) cells were diluted into a final culture volume of 450 mL of YEPD at 30°C or YEPD + 10% serum at 37°C. Cells were harvested at the 1-hour post-induction time point and recovered by rapid filtration.

extract_protocol:
Lysates were prepared as described previously (Spealman et al. 2016) with a few modifications.  Flash frozen cells were thawed on an ice water slurry and cell suspensions were transferred into tubes with 0.5 mm diameter acid-washed glass beads and placed on ice for 5 min. The samples were lysed by vortexing 8 times for 30 sec. each with a 30 sec. rest on ice between each vortex. Samples were further processed according to instructions for the Illumina TrueSeq Ribo Profile (Yeast) Kit. Briefly, lysates were pre-cleared by centrifugation at 3000g for 5 min. at 4°C to remove cell debris and further clarified by centrifugation at 20000g for 10 min. at 4°C. The lysates were treated for 10 min. on ice with 10U/mL DNase I (Illumina) and quantified by measuring absorbance at 260 nm (A260). Finally, 100 uL aliquots were frozen in liquid nitrogen and stored at -80°C until further use.
Ribosome profiling and library preparation were carried out according to the protocol described for the True Seq Ribo Profile (Yeast) Kit (Illumina). Lysates were digested with 15 U RNase I (Ambion) per A260 unit and incubated at room temperature for 45 min. with gentle rotation. The reactions were stopped by the addition of 1000U/mL SUPERase-IN (Ambion). 80S monosome fractions were purified from the cell lysate using MicroSpin S-400 HR columns (GE Healthcare). Ribosome protected fragments (RPFs) were further purified using the RNA Clean & Concentrator-25 Kit (Zymo Research) method. This kit was also used for total RNA purification. rRNA depletion was carried out using a Ribo-Zero Magnetic Gold (Yeast) kit (Illumina). An additional subtraction step was included to remove rRNA sequences from circularized cDNA as described previously (Spealman et al. 2016) with slight modifications.  Subtractions were carried out in a 30 uL reaction volume, with 10 uL sample, 2 uL 20X SSC and 2 uL of a rRNA subtraction pool containing custom-designed biotinylated oligonucleotides (Dataset S8). The circularized DNA was next used as a template for amplification of library PCR products. PCR products of 140-160 bp were recovered from excised gel slices, quantified by Agilent  Bioanalyzer/Fragment analyzer and deep sequencing was performed using an Illumina Hiseq3000 machine at the Greehey Children’s Cancer Research Institute Genome Sequencing Facility (University of Texas Health Science Center at San Antonio). All ribosome profiling experiments were performed in biological triplicate.

treatment_protocol: Next, cells were scraped off the filter paper with a cell scraper, placed in ice-cold lysis buffer (1x yeast polysome buffer (Illumina), 1%Triton X-100 (Illumina), 50 ug/mL GMPPNP (Sigma), 10 ug/mL Blasticidin S (InvivoGen)) and homogeneously mixed prior to snap freezing in liquid nitrogen.

value: YEPD + serum at 37°C

tag: assay

value: RNA

value: fungal cells


title: rna_30C_1

institute: University of Texas Health Science Center at San Antonio

value: YEPD at 30°C


title: Ctrl2


title: ribo_37C_1

data_processing:
Library strategy: Ribo-seq
Adaptor sequences and low-quality score (phred quality score < 5) bases were trimmed from RNA-Seq and Ribo-Seq datasets with TrimGalore (v 0.4.3) (Krueger, 2012). Only reads that were at least 20 nucleotide long were retained.
Trimmed sequences from RNA-seq and Ribo-seq were both mapped using STAR (v.2.5.2b) (Dobin, 2013) using Assembly 22 fasta as the reference and GTF s07-m01-r27 from CGD allowing a mismatch of at most two positions (--outFilterMismatchNmax 2). Only uniquely mapping reads were retained (-outFilterMultimapNmax 1). All the reads mapping to non-mRNA sequences were filtered out before downstream analysis. The corresponding non-mRNA sequences were also obtained from CGD (C_albicans_SC5314_version  _A22-s07-m01-r27_other_features_no_introns.fasta). The periodicity analysis of Ribo-seq data was performed using ribotricer (v1.3.2) (Choudhary, 2020). Gene level counting was performed using featureCounts (v1.6.4) (Liao, 2014). Since Assembly 22 is a diploid assembly, the reads were counted for each copy of the gene separately (hapA and hapB) and then merged into a single read count per gene.
Differential expression analysis was performed using DESeq2 (Love, et al, 2014). Only genes with at least one read per replicate were selected for performing the library size normalization step and running the moderated t-statistic test. Genes were defined to be differentially expressed (DE) if the transcripts per million (TPM) was greater than 1 in at least 2 replicates and if their absolute fold-change on log2 scale is at least 1 with an FDR adjusted p-value of less than or equal to 0.05.
Differential translational efficiency was performed using riborex (Li, 2017) by retaining genes that had at least one read count in one replicate across the two conditions in both Ribo-seq and RNA-seq samples. Only genes that had a read count of at least one per replicate were used as input to riborex. We define genes to be exhibiting differential translational efficiency if their TPM was greater than 1 in at least 2 replicates while the absolute fold-change on log2 scale was at least 1 and the corresponding non-adjusted p-value less than or equal to 0.05. Gene ontology (GO) analysis was performed using clusterProfiler (Yu, 2012) using GO slim ontology file available from CGD.
Genome_build: ASM18296v3
Supplementary_files_format_and_content: raw counts table

value: Ribo


title: Pulp3

description: Age 18-35yo, healthy dental pulp


title: rna_30C_3


title: rna_37C_1


title: rna_37C_3


title: rna_30C_2


title: ribo_30C_3


title: ribo_37C_3


title: ribo_30C_2


title: CMP_sc18

status: Public on Jun 25 2020

data_processing:
Raw reads were first separated by specific cell barcode information attached in read 2 (R2) of the pair-ended reads.UMI information was aligned to the corresponding read 1 (R1), which was then trimmed to remove the template switch oligo (TSO) sequence and polyA tail sequence, we also removed reads with adaptor contaminants and low-quality bases (N > 10%).
The clean reads were aligned to the mm10 mouse transcriptome (UCSC) using TopHat (version 2.0.12). Uniquely mapped reads were then counted using htseq-count in the HTSeq package and grouped by the cell-specific barcodes. Based on the UMI information,duplicated transcripts with the same UMI sequences of each gene were removed.
Log2 (TPM/10+1) was used as expression values.
Differential expression genes between IL4Rα high and IL4Rα low single-cell groups were identified by FindMarkers function of Seurat(Version 2.0).
Canonical pathway analyses were performed by Ingenuity Pathway Analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each single cells.

organism: Mus musculus

source_name: bone marrow

extract_protocol:
RNA libraries were prepared for sequencing using a modified Smart-seq2 protocols. Each single LT-HSC or CMP was placed into the lysis buffer by mouth pipette,The reverse transcription reaction was performed with 25 nt oligo(dT) primer anchored with an 8 nt cell-specific barcode and 8 nt unique molecular identifiers (UMIs).After the first-strand synthesis, the second-strand cDNAs were synthesized, and the cDNAs were amplified by 17 cycles of PCR. The amplified cDNAs of the single cells were then pooled together for the following steps. Biotinylated pre-indexed primers were used to further amplify the PCR product by an additional 4 cycles of PCR to introduce biotin tags to the 30 ends of the amplified cDNAs. Approximately 300 ng cDNA was sheared to approximately 300 bp by Covaris S2, and the 30 terminal of the cDNA was captured by Dynabeads MyOne Streptavidin C1 beads. The RNA-seq library was constructed using a Kapa Hyper Prep Kit and subjected to 150 bp paired-end sequencing on an Illumina HiSeq 4000 platform.
Single cell RNA-seq

tag: strain

value: BM-derived CMP

tag: passages

tag: genotype

value: Wild type


title: CMP_sc19


title: CMP_sc20


title: CMP_sc17


title: CMP_sc23


title: CMP_sc22


title: CMP_sc15


title: CMP_sc21


title: CMP_sc16


title: CMP_sc13


title: ribo_30C_1


title: CMP_sc24


title: CMP_sc14


title: CMP_sc11


title: CMP_sc12


title: CMP_sc7


title: ribo_37C_2


title: CMP_sc8


title: CMP_sc5


title: CMP_sc4


title: CMP_sc3


title: CMP_sc1


title: CMP_sc2


title: LT-HSC_sc33

value: BM-derived LT-HSC


title: LT-HSC_sc32


title: LT-HSC_sc27


title: LT-HSC_sc28


title: LT-HSC_sc30


title: LT-HSC_sc26


title: CMP_sc10


title: LT-HSC_sc23


title: LT-HSC_sc22


title: LT-HSC_sc25


title: LT-HSC_sc24


title: CMP_sc9


title: CMP_sc6


title: LT-HSC_sc20


title: LT-HSC_sc21


title: LT-HSC_sc19


title: LT-HSC_sc34


title: CON_MK2: megakaryocytes, control, biological rep2

type: RNA

hyb_protocol: Following labeling, cDNA was hybridized on a Clariom™ D Assay, mouse.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Command Console installed in the GeneChip® Scanner 3000 7G.

data_processing: The data was analyzed with the Robust Multichip Analysis (RMA) algorithm, using the Affymetrix default analysis settings.

label: biotin

source_name: Megakaryocytes from healthy control mice bone marrow

label_protocol: Biotinylated cDNA was prepared from 250 ng total RNA according to the manufacturer’s standard protocol (Affymetrix).

growth_protocol: Megakaryocytes (SSChigh CD41high, DNA content ≧ 8N) were isolated from MLL-AF9 induced AML mice and healthy control mice bone marrow by flow cytometry.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Megakaryocytes were directly sorted into Trizol

tag: gender


title: AML_MK2: megakaryocytes, AML, biological rep2

source_name: Megakaryocytes from AML mice bone marrow


title: CON_MK3: megakaryocytes, control, biological rep3

value: Megakaryocytes from healthy control mice bone marrow


title: CON_MK1: megakaryocytes, control, biological rep1


title: AML_MK1: megakaryocytes, AML, biological rep1

value: Megakaryocytes from AML mice bone marrow


title: AML_MK3: megakaryocytes, AML, biological rep3


title: LT-HSC_sc18


title: LT-HSC_sc17


title: LT-HSC_sc29


title: LT-HSC_sc16


title: LT-HSC_sc11


title: LT-HSC_sc15


title: LT-HSC_sc5


title: LT-HSC_sc3


title: LT-HSC_sc1


title: LT-HSC_sc13


title: LT-HSC_sc9


title: LT-HSC_sc12


title: PDGFB-MSC3

status: Public on Jun 22 2020

description:
human cord blood CD34+ cells by direct reprogramming with episomal vector-mediated transient OCT4 expression
TPM_matrix.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
RNA-seq reads for each library were mapped independently using Salmon （version 0.8.2） against the transcript sequences of human genome build hg38, downloaded via GENCODE.Transcripts per million (TPM) of each sample was analyzed.
Differentially expressed genes from RNA-Seq data were detected in the method of DESeq2
Those significant genes were analyzed with DAVID (http://david.niaid.nih.gov) and commercial software of  IPA (Interpretative phenomenological analysis)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: human iMSCs

extract_protocol:
GFP-MSCs and PDGFB-MSCs were collected and total RNA was extracted using RNA isolation kits (EXIQON).
RNA-seq libraries were constructed using the NEBNext UltraTM RNA Library Prep Kit (NEB, USA) and sequenced 150-bp paired-end on an Illumina HiSeq X10 platform.

value: iMSCs overexpressed PDGFB


title: LT-HSC_sc14


title: LT-HSC_sc7


title: LT-HSC_sc8


title: LT-HSC_sc4


title: LT-HSC_sc2


title: PDGFB-MSC1


title: LT-HSC_sc6


title: LT-HSC_sc10


title: PDGFB-MSC2


title: GFP-MSC3

value: iMSCs overexpressed GFP


title: GFP-MSC2


title: L85

status: Public on May 05 2020

description: 3' ends mRNA

data_processing:
Raw reads were separated by specific cell barcode information attached in read 2 (R2) of the pair-ended reads.UMI information was aligned to the corresponding read 1 (R1),which was then trimmed to remove the template switch oligo (TSO) and ployA tail sequences;we also trimmed the reads with adaptor contaminants and low-quality bases (N> 10%)
The clean reads were aligned to the mm10 mouse transcriptome (UCSC) using TopHat (verson 2.0.12).Mapping reads were then counted using htseq-count in the HTSeq package. Based on the UMI information,duplicated transcripts with the same UMI sequences of each gene were removed.
Gene expression level was normalized as log2 (TPM/10 + 1), in which TPM is short for Transcripts per million and adding one is to avoid negative expression values.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each single cells.

source_name: Day3 collected cells

extract_protocol:
Fresh isolated cells were transferred directly into cell lysis buffer and the reverse transcription and template swithc steps were performed following the Smart-seq2 protocol
The cDNA libraries were prepared for sequencing using a KAPA Hyper Prep Kit for Illumina
Modified Smart-seq2

value: 8-10 weeks

value: Bone marrow and spleen

value: Day3 collected cells


title: L89

description: 3' ends mRNA


title: L86

description: 3' ends mRNA

source_name: Day5 collected cells

value: Day5 collected cells


title: L83

description: 3' ends mRNA

source_name: Day1 collected cells

value: Day1 collected cells


title: L87

description: 3' ends mRNA

value: Bone marrow


title: L88

description: 3' ends mRNA

source_name: Day1 and Day3 collected cells

value: Day1 and Day3 collected cells


title: L84

description: 3' ends mRNA


title: GFP-MSC1


title: L80

description: 3' ends mRNA


title: L79

description: 3' ends mRNA


title: L76

description: 3' ends mRNA

source_name: iHSC2 and iHSC3

value: iHSC2 and iHSC3


title: L73

description: 3' ends mRNA

source_name: iHSC4 and iHSC5

value: iHSC4 and iHSC5


title: L74

description: 3' ends mRNA

source_name: iHSC1 and iMPP7

value: iHSC1 and iMPP7


title: L71

description: 3' ends mRNA


title: L70

description: 3' ends mRNA

value: Spleen


title: L81

description: 3' ends mRNA


title: L66

description: 3' ends mRNA


title: L77

description: 3' ends mRNA

source_name: Day5 and Day7 collected cells

value: Day5 and Day7 collected cells


title: L72

description: 3' ends mRNA


title: L69

description: 3' ends mRNA


title: L63

description: 3' ends mRNA

source_name: Day7 collected cells

value: Day7 collected cells


title: L62

description: 3' ends mRNA


title: L68

description: 3' ends mRNA


title: L61

description: 3' ends mRNA


title: L59

description: 3' ends mRNA


title: L60

description: 3' ends mRNA


title: L58

description: 3' ends mRNA


title: L54

description: 3' ends mRNA

source_name: iHSC3, B and NK

value: iHSC3, B and NK


title: L51

description: 3' ends mRNA

source_name: iMPP3, iMPP4 and iHSC2

value: iMPP3, iMPP4 and iHSC2


title: L53

description: 3' ends mRNA

source_name: CD4+T, CD8+T and iMPP6

value: CD4+T, CD8+T and iMPP6


title: L52

description: 3' ends mRNA

source_name: iMPP4, iMPP5 and iMPP6

value: iMPP4, iMPP5 and iMPP6


title: L49

description: 3' ends mRNA

source_name: Day7 collected cells, iMPP1, iMPP2 and iHSC3

value: 8-10 weeks


title: L43

description: 3' ends mRNA

source_name: Monocyte, Granulocyte and CLP

value: Monocyte, Granulocyte and CLP


title: L78

description: 3' ends mRNA

value: Bone marrow and spleen


title: L50

description: 3' ends mRNA

source_name: iMPP9, iHSC5 and iHSC3

value: iMPP9, iHSC5 and iHSC3


title: L42

description: 3' ends mRNA

source_name: iMPP2, EryA and EryB

value: iMPP2, EryA and EryB


title: L28

description: 3' ends mRNA

source_name: iMPP9, MK and CLP

value: Bone marrow

value: iMPP9, MK and CLP


title: L26

description: 3' ends mRNA

source_name: iMPP8 and iMPP9

value: iMPP8 and iMPP9


title: L37

description: 3' ends mRNA


title: L23

description: 3' ends mRNA


title: L17

description: 3' ends mRNA

source_name: GMP and CMP

value: GMP and CMP


title: L38

description: 3' ends mRNA


title: L39

description: 3' ends mRNA


title: L14

description: 3' ends mRNA

source_name: iMPP1 and iHSC1

value: iMPP1 and iHSC1


title: L4

description: 3' ends mRNA


title: L15

description: 3' ends mRNA

source_name: MEP and iHSC4

value: MEP and iHSC4


title: L2

description: 3' ends mRNA

source_name: CD4+T and CD8+ T

value: Spleen

value: CD4+T and CD8+ T


title: L40

description: 3' ends mRNA


title: L55

description: 3' ends mRNA

source_name: MK, iHSC3 and Day7 collected cells

value: MK, iHSC3 and Day7 collected cells


title: L12

description: 3' ends mRNA

source_name: Macrophage

value: Macrophage


title: Treatment day 5 rep 2

status: Public on Aug 13 2019

city: Houston

first: Robert

last: Britton

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
day 5
HCFJWADXX-2-ID12
condition6r2

data_processing:
Reads were aligned to mm9 using TopHat2
SAMtools was used to index mapped reads
Count tables were generated with Bioconductor packages, Rsamtools and Genomicalignments
Differentially expressed genes were identified using DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: counts

source_name: RAW264.7 cell line

growth_protocol: RAW264.7 cells were grown in RPMI 1640 (Invitrogen, Cat#11875-093) or MEM-alpha (Invitrogen, Cat#41061-029) plus 10% fetal bovine serum (Invitrogen, Cat#10100-147)

extract_protocol:
RAW264.7 cells were isolated in Trizol reagent and RNA was harvested. Illumina TruSeq RNA Sample Prep Kit (Cat#RSS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RAW264.7 cells were stimulated for differentiation with RANKL (100 ug/ml) and treated with vehicle or treatment (L. reuteri cell culture supernatant); RNA harvested on days 1,3, and 5

value: Balb/c

value: monocyte/macrophage

value: immortalized


title: L47

description: 3' ends mRNA

source_name: Day7 collected cells

value: 8-10 weeks

value: Day7 collected cells


title: Treatment day 5 rep 1

description:
day 5
HCFJWADXX-2-ID11
condition6r1


title: Vehicle day 5 rep 1

description:
day 5
HCFJWADXX-2-ID09
condition5r1


title: Treatment day 3 rep 2

description:
day 3
HCFJWADXX-2-ID08
condition4r2


title: Treatment day 1 rep 2

description:
day 1
HCFJWADXX-2-ID04
condition2r2


title: Vehicle day 5 rep 2

description:
day 5
HCFJWADXX-2-ID10
condition5r2


title: Vehicle day 3 rep 1

description:
day 3
HCFJWADXX-2-ID05
condition3r1


title: Vehicle day 3 rep 2

description:
day 3
HCFJWADXX-2-ID06
condition3r2


title: L16

description: 3' ends mRNA

source_name: EryA and iMPP2

value: EryA and iMPP2


title: Treatment day 3 rep 1

description:
day 3
HCFJWADXX-2-ID07
condition4r1


title: L3

description: 3' ends mRNA

source_name: B and NK

value: B and NK


title: in 1x3hr GMP +TNFα rep3

status: Public on Jul 01 2019

city: Memphis

first: Masayuki

last: Yamashita

state: TN

address: 262 Danny Thomas Place

department: Division of Experimental Hematology, Department of Hematology

institute: St. Jude Children's Research Hospital

data_processing:
Data quality was verified on Sequencing Analysis Viewer (Illumina) and demultiplexing was performed with CASAVA 1.8.2 (Illumina).
Adapter trimming, alignment, and gene-level expression quantification was performed using STAR (Dobin et al., 2013).
Normalization was performed in R using the DESeq2 package (Love et al., 2014)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text files include normalized read count values

source_name: Bone marrow GMPs (Lin-/cKit+/Sca1-/FcγR+/CD34+)

extract_protocol:
RNA was extracted using RNeasy Plus Micro Kit (Qiagen). RNA integrity number (RIN) was determined by Bioanalyzer (Agilent Technologies) and RNA samples with RIN > 8.0 were subjected to further processing.
The double-stranded cDNA was generated using Ovation RNA-Seq System V2 (Nugen), and the sequencing libraries were prepared using LTP Library Preparation Kit (Kapa Biosystems). Different adaptors were used for multiplexing samples in one lane.

treatment_protocol:
For ex vivo TNFα treatment, FACS-purified HSCs and GMPs were cultured in Iscove’s modified Dulbecco’s media (IMDM) containing 5% FBS (StemCell Technology), 50 U/ml penicillin, 50 μg/ml streptomycin, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate and 50 μM 2-mercaptoethanol, supplemented with the following cytokines unless otherwise indicated (all from PeproTech except for TNFα): SCF (25 ng/ml), TPO (25 ng/ml), Flt3-L (25 ng/ml), IL-11 (25 ng/ml), IL-3 (10 ng/ml), GM-CSF (10 ng/ml) and EPO (4 U/ml) ± TNFα (1 μg/ml; Genentech).
For in vivo TNFα treatment, C57BL/6 mice were injected retro-orbitally with a single dose of 2 μg TNFα (Genentech) in 100 μl PBS or 100 μl PBS alone (untreated animals) 3 hours prior to BM harvest.

value: GMPs

value: in vivo 1x3hr +TNFα

value: Bone marrow

value: 6-12 weeks old


title: Treatment day 1 rep 1

description:
day 1
HCFJWADXX-2-ID03
condition2r1


title: in 1x3hr GMP -TNFα rep2

value: in vivo 1x3hr -TNFα


title: Vehicle day 1 rep 2

description:
day 1
HCFJWADXX-2-ID02
condition1r2


title: L5

description: 3' ends mRNA

source_name: Granulocyte and Monocyte

value: Granulocyte and Monocyte


title: in 1x3hr GMP +TNFα rep2


title: in 1x3hr GMP +TNFα rep1


title: in 1x3hr GMP -TNFα rep1


title: ex 12hr GMP +TNFα rep1

value: ex vivo 12hr +TNFα


title: ex 12hr GMP +TNFα rep3


title: LT-HSC_sc31

source_name: bone marrow

value: BM-derived LT-HSC

value: Wild type


title: ex 12hr GMP +TNFα rep2


title: ex 12hr GMP -TNFα rep1

value: ex vivo 12hr -TNFα


title: ex 12hr GMP -TNFα rep3


title: ex 12hr GMP -TNFα rep2


title: ex 3hr GMP +TNFα rep2

value: ex vivo 3hr +TNFα


title: ex 3hr GMP +TNFα rep3


title: ex 3hr GMP -TNFα rep3

value: ex vivo 3hr -TNFα


title: ex 3hr GMP -TNFα rep1


title: Vehicle day 1 rep 1

description:
day 1
HCFJWADXX-2-ID01
condition1r1

value: Balb/c

value: monocyte/macrophage

value: immortalized


title: in 1x3hr in vivo +TNFα rep2

source_name: Bone marrow HSCs (Lin-/cKit+/Sca1+/Flk2-/CD48-/CD150+)

value: HSCs

value: in vivo 1x3hr in vivo +TNFα


title: ex 3hr GMP -TNFα rep2

value: GMPs


title: in 1x3hr in vivo +TNFα rep3


title: in 1x3hr in vivo -TNFα rep3

value: in vivo 1x3hr in vivo -TNFα


title: in 1x3hr in vivo -TNFα rep1

value: Bone marrow


title: in 1x3hr GMP -TNFα rep3

value: 6-12 weeks old


title: ex 12hr in vivo +TNFα rep3

value: ex vivo 12hr in vivo +TNFα


title: ex 12hr in vivo -TNFα rep1

value: ex vivo 12hr in vivo -TNFα


title: ex 3hr in vivo +TNFα rep3

value: ex vivo 3hr in vivo +TNFα


title: in 1x3hr in vivo -TNFα rep2


title: ex 3hr in vivo +TNFα rep2


title: ex 12hr in vivo -TNFα rep2


title: L1

description: 3' ends mRNA

value: 8-10 weeks


title: ex 12hr in vivo +TNFα rep1


title: ex 3hr in vivo -TNFα rep1

value: ex vivo 3hr in vivo -TNFα


title: ex 12hr in vivo +TNFα rep2


title: ex 12hr in vivo -TNFα rep3


title: ex 3hr in vivo -TNFα rep2


title: ex 3hr in vivo +TNFα rep1


title: K562_Max_(20190121_MM_HsSc_0113MPM866)

status: Public on Jun 25 2019

city: Chapel Hill

first: Michael

last: Meers

state: NC

address: 250 Bell Tower Dr.

institute: UNC Chapel Hill

description: CUT&RUN for Max in K562 cells using Standard CUT&RUN

library_source: genomic

data_processing:
Genome_build: UCSC hg19
1. We used Bowtie2 2.2.5 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> (Supplementary file .bed).

molecule: genomic DNA

source_name: CUT&Run

tag: antibody

value: Rb anti-Max Proteintech cat# 10426-1-AP

value: K562, human immortalised myelogenous leukemia cell line


title: ex 3hr GMP +TNFα rep1

value: ex vivo 3hr +TNFα


title: H1_T_(20181220_MM_HsSc_1213MPM848)

description: CUT&RUN for T in 1 day (H1) cells using Standard CUT&RUN; Rb anti-Gt 2* ab

value: Gt anti-T RAF2085;D Systems cat# AF2085

value: H1 (WA01) human embryonic stem cell line (WiCell)

tag: Stage

value: 1 day


title: K562_Myc_(20190121_MM_HsSc_0113MPM864)

description: CUT&RUN for Myc in K562 cells using Standard CUT&RUN

value: Rb anti-c-Myc Cell Signaling cat# D38NF


title: in 1x3hr in vivo +TNFα rep1

value: HSCs

tag: treatment

value: in vivo 1x3hr in vivo +TNFα


title: H1_SUZ12_(20181004_MPM_HsSc_696_0926)

description: CUT&RUN for SUZ12 in 1 day (H1) cells using AutoCUT&RUN

extract_protocol:
Janssens_protocols.docx
PMID 25827087

value: Rb anti-SUZ12 Abcam cat# ab12073


title: H1_Sox2_std_(20171222_MM_HsSc_1208MPM091)

description: CUT&RUN for Sox2 in 1 day (H1) cells using Standard CUT&RUN

value: Rb anti-Sox2 Abcam cat# ab92494


title: H1_Sox2_auto_(20180605_MM_HsSc_385_0413)

description: CUT&RUN for Sox2 in 1 day (H1) cells using AutoCUT&RUN


title: H1_Nanog_(20181004_MPM_HsSc_702_0926)

description: CUT&RUN for Nanog in 1 day (H1) cells using AutoCUT&RUN

value: Rb anti-Nanog Abcam cat# ab109250


title: H1_POU5F1_hiCa_(20180723_MM_HsSc_0709MPM514S)

description: CUT&RUN for POU5F1 in 1 day (H1) cells using HpA-MN CUT&RUN High Ca2+

value: Rb anti-POU5F1 Abcam cat# ab109183


title: H1_Sox17_(20181121_MM_HsSc_780_1113)

description: CUT&RUN for SOX17 in 1 day (H1) cells using AutoCUT&RUN; Rb anti-Gt 2* ab

value: Gt anti-Sox17 RAF1924;D Systems cat# AF1924


title: H1_IgG_B_auto_(20181121_MM_HsSc_781_1113)

description: CUT&RUN for IgG in 1 day (H1) cells using AutoCUT&RUN

value: Rb anti-Ms IgG Abcam cat# ab46540


title: H1_IgG_std_(20181220_MM_HsSc_1213MPM849)

description: CUT&RUN for IgG in 1 day (H1) cells using Standard CUT&RUN


title: H1_IgG_A_auto_(20180605_MM_HsSc_388_0413)

value: Gp anti-Rb IgG Antibodies Online cat# ABIN101961


title: H1_H3K4me2_(20180605_MM_HsSc_391_0413)

description: CUT&RUN for H3K4me2 in 1 day (H1) cells using AutoCUT&RUN

value: Rb anti-H3K4me2 Upstate (Millipore) cat# 07-030


title: H1_GATA4_(20181121_MM_HsSc_778_1113)

description: CUT&RUN for GATA4 in 1 day (H1) cells using AutoCUT&RUN; Rb anti-Ms 2* ab

value: Ms anti-GATA4 Santa Cruz cat# sc-25310X


title: H1_H3.3_(20181004_MPM_HsSc_701_0926)

description: CUT&RUN for H3.3 in 1 day (H1) cells using AutoCUT&RUN

value: Ms anti-H3.3 Abnova cat# H0000302-M01


title: ex 3hr in vivo -TNFα rep3

value: ex vivo 3hr in vivo -TNFα

value: Bone marrow

value: 6-12 weeks old


title: H1_FoxA2_auto_(20180605_MM_HsSc_387_0413)

description: CUT&RUN for FoxA2 in 1 day (H1) cells using AutoCUT&RUN

value: Rb anti-FoxA2 Millipore cat# 07-633

value: H1 (WA01) human embryonic stem cell line (WiCell)

value: 1 day


title: H1_FoxA2_hiCa_(20180723_MM_HsSc_0709MPM513S)

description: CUT&RUN for FoxA2 in 1 day (H1) cells using HpA-MN CUT&RUN High Ca2+


title: H1_FoxA1_std_(20181220_MM_HsSc_1213MPM846)

description: CUT&RUN for FoxA1 in 1 day (H1) cells using Standard CUT&RUN

value: Rb anti-FoxA1 Abcam cat# ab23738


title: H1_FoxA1_auto_(20180605_MM_HsSc_386_0413)

description: CUT&RUN for FoxA1 in 1 day (H1) cells using AutoCUT&RUN


title: DE_Sox2_(20180511_MM_HsSc_357_0413)

description: CUT&RUN for Sox2 in 5 day (DE) cells using AutoCUT&RUN differentiated for 5 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: 5 days


title: H1_POU5F1_std_(20171122_MM_HsSc_1113MPM036)

description: CUT&RUN for POU5F1 in 1 day (H1) cells using Standard CUT&RUN


title: DE_POU5F1_(20180723_MM_HsSc_0709MPM474S)

description: CUT&RUN for POU5F1 in 5 day (DE) cells using HpA-MN CUT&RUN High Ca2+ differentiated for 5 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: H1_ATACseq_(20181017_MM_Hs_0705MPM516)

description: ATAC-seq in 1 day (H1) cells

source_name: ATAC-Seq

extract_protocol:
MeersEtAl2019.ATACseq.txt
PMID 25827087


title: DE_IgG_B_auto_(20181120_MM_HsSc_741_1113)

description: CUT&RUN for IgG in 5 day (DE) cells using AutoCUT&RUN differentiated for 5 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: H1_CTCF_(20181004_MPM_HsSc_697_0926)

description: CUT&RUN for CTCF in 1 day (H1) cells using AutoCUT&RUN

value: Rb anti-CTCF Millipore cat# 07-729


title: DE_H3K4me2_(20180511_MM_HsSc_363_0413)

description: CUT&RUN for H3K4me2 in 5 day (DE) cells using AutoCUT&RUN differentiated for 5 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: DE_Nanog_(20181003_MPM_HsSc_626_0926)

description: CUT&RUN for Nanog in 5 day (DE) cells using AutoCUT&RUN differentiated for 5 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Rb anti-Nanog Abcam cat# ab109250


title: DE_IgG_A_auto_(20180511_MM_HsSc_360_0413)


title: DE_H3K27me3_(20180511_MM_HsSc_361_0413)

description: CUT&RUN for H3K27me3 in 5 day (DE) cells using AutoCUT&RUN differentiated for 5 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Rb anti-H3K27me3 Cell Signaling cat# CST9733S


title: DE_FoxA2_hiCa_(20180723_MM_HsSc_0709MPM465S)

description: CUT&RUN for FoxA2 in 5 day (DE) cells using HpA-MN CUT&RUN High Ca2+ differentiated for 5 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: DE_FoxA2_auto_(20180511_MM_HsSc_359_0413)

description: CUT&RUN for FoxA2 in 5 day (DE) cells using AutoCUT&RUN differentiated for 5 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: DE_GATA4_(20181120_MM_HsSc_738_1113)

description: CUT&RUN for GATA4 in 5 day (DE) cells using AutoCUT&RUN; Rb anti-Ms 2* ab differentiated for 5 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: DE_FoxA1_hiCa_(20180723_MM_HsSc_0709MPM475S)

description: CUT&RUN for FoxA1 in 5 day (DE) cells using HpA-MN CUT&RUN High Ca2+ differentiated for 5 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: DE_H3K27ac_(20180511_MM_HsSc_362_0413)

description: CUT&RUN for H3K27ac in 5 day (DE) cells using AutoCUT&RUN differentiated for 5 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Rb anti-H3K27ac Abcam cat# ab4729


title: DE_FoxA1_auto_(20180511_MM_HsSc_358_0413)

description: CUT&RUN for FoxA1 in 5 day (DE) cells using AutoCUT&RUN differentiated for 5 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: H1_H3K27me3_(20180605_MM_HsSc_389_0413)

description: CUT&RUN for H3K27me3 in 1 day (H1) cells using AutoCUT&RUN


title: DE_EOMES_(20181003_MPM_HsSc_637_0926)

description: CUT&RUN for EOMES in 5 day (DE) cells using AutoCUT&RUN differentiated for 5 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Rb anti-EOMES Abcam cat# ab23345


title: DE_CTCF_hiCa_(20180829_MM_HsSc_0817MPM541S)

description: CUT&RUN for CTCF in 5 day (DE) cells using HpA-MN CUT&RUN High Ca2+ differentiated for 5 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: H1_H3K27ac_(20180605_MM_HsSc_390_0413)

description: CUT&RUN for H3K27ac in 1 day (H1) cells using AutoCUT&RUN


title: 4d_Sox2_(20180511_MM_HsSc_364_0413)

description: CUT&RUN for Sox2 in 4 day cells using AutoCUT&RUN differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Rb anti-Sox2 Abcam cat# ab92494

value: 4 days


title: H1_EOMES_(20181004_MPM_HsSc_713_0926)

description: CUT&RUN for EOMES in 1 day (H1) cells using AutoCUT&RUN


title: DE_ATACseq_(20181017_MM_Hs_0705MPM476)

description: ATAC-seq in 5 day (DE) cells


title: 4d_POU5F1_std_(20181220_MM_HsSc_1213MPM823)

description: CUT&RUN for POU5F1 in 4 day cells using Standard CUT&RUN differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Rb anti-POU5F1 Abcam cat# ab109183


title: DE_CTCF_auto_(20181003_MPM_HsSc_621_0926)

description: CUT&RUN for CTCF in 5 day (DE) cells using AutoCUT&RUN differentiated for 5 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: DE_Sox17_(20181120_MM_HsSc_740_1113)

description: CUT&RUN for SOX17 in 5 day (DE) cells using AutoCUT&RUN; Rb anti-Gt 2* ab differentiated for 5 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Gt anti-Sox17 RAF1924;D Systems cat# AF1924


title: 4d_POU5F1_hiCa_(20180723_MM_HsSc_0709MPM486S)

description: CUT&RUN for POU5F1 in 4 day cells using HpA-MN CUT&RUN High Ca2+ differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 4d_Sox17_(20181120_MM_HsSc_750_1113)

description: CUT&RUN for SOX17 in 4 day cells using AutoCUT&RUN; Rb anti-Gt 2* ab differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 4d_Nanog_(20181003_MPM_HsSc_645_0926)

description: CUT&RUN for Nanog in 4 day cells using AutoCUT&RUN differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 4d_IgG_std_(20181220_MM_HsSc_1213MPM825)

description: CUT&RUN for IgG in 4 day cells using Standard CUT&RUN differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Rb anti-Ms IgG Abcam cat# ab46540


title: 4d_H3K4me2_(20180511_MM_HsSc_370_0413)

description: CUT&RUN for H3K4me2 in 4 day cells using AutoCUT&RUN differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Rb anti-H3K4me2 Upstate (Millipore) cat# 07-030


title: 4d_IgG_B_auto_(20181120_MM_HsSc_751_1113)

description: CUT&RUN for IgG in 4 day cells using AutoCUT&RUN differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 4d_IgG_A_auto_(20180511_MM_HsSc_367_0413)

value: Gp anti-Rb IgG Antibodies Online cat# ABIN101961


title: 4d_H3K27ac_(20180511_MM_HsSc_369_0413)

description: CUT&RUN for H3K27ac in 4 day cells using AutoCUT&RUN differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 4d_H3K27me3_(20180511_MM_HsSc_368_0413)

description: CUT&RUN for H3K27me3 in 4 day cells using AutoCUT&RUN differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 4d_GATA4_(20181120_MM_HsSc_748_1113)

description: CUT&RUN for GATA4 in 4 day cells using AutoCUT&RUN; Rb anti-Ms 2* ab differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Ms anti-GATA4 Santa Cruz cat# sc-25310X


title: 4d_FoxA2_hiCa_(20180723_MM_HsSc_0709MPM477S)

description: CUT&RUN for FoxA2 in 4 day cells using HpA-MN CUT&RUN High Ca2+ differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Rb anti-FoxA2 Millipore cat# 07-633

value: H1 (WA01) human embryonic stem cell line (WiCell)


title: 4d_FoxA2_auto_(20180511_MM_HsSc_366_0413)

description: CUT&RUN for FoxA2 in 4 day cells using AutoCUT&RUN differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 4d_FoxA1_hiCa_(20180723_MM_HsSc_0709MPM487S)

description: CUT&RUN for FoxA1 in 4 day cells using HpA-MN CUT&RUN High Ca2+ differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Rb anti-FoxA1 Abcam cat# ab23738


title: 4d_EOMES_(20181003_MPM_HsSc_647_0926)

description: CUT&RUN for EOMES in 4 day cells using AutoCUT&RUN differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 4d_CTCF_auto_(20181003_MPM_HsSc_640_0926)

description: CUT&RUN for CTCF in 4 day cells using AutoCUT&RUN differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 4d_CTCF_hiCa_(20180829_MM_HsSc_0817MPM553S)

description: CUT&RUN for CTCF in 4 day cells using HpA-MN CUT&RUN High Ca2+ differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 4d_ATACseq_(20181017_MM_Hs_0705MPM488)

description: ATAC-seq in 4 day cells


title: 4d_FoxA1_auto_(20180511_MM_HsSc_365_0413)

description: CUT&RUN for FoxA1 in 4 day cells using AutoCUT&RUN differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 3d_T_(20181220_MM_HsSc_1213MPM836)

description: CUT&RUN for T in 3 day cells using Standard CUT&RUN; Rb anti-Gt 2* ab differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Gt anti-T RAF2085;D Systems cat# AF2085

value: 3 days


title: 3d_Sox17_(20181121_MM_HsSc_760_1113)

description: CUT&RUN for SOX17 in 3 day cells using AutoCUT&RUN; Rb anti-Gt 2* ab differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 4d_FoxA1_std_(20181220_MM_HsSc_1213MPM822)

description: CUT&RUN for FoxA1 in 4 day cells using Standard CUT&RUN differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 4d_T_(20181220_MM_HsSc_1213MPM824)

description: CUT&RUN for T in 4 day cells using Standard CUT&RUN; Rb anti-Gt 2* ab differentiated for 4 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 3d_POU5F1_std_(20181220_MM_HsSc_1213MPM835)

description: CUT&RUN for POU5F1 in 3 day cells using Standard CUT&RUN differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 3d_Sox2_(20180511_MM_HsSc_371_0413)

description: CUT&RUN for Sox2 in 3 day cells using AutoCUT&RUN differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 3d_POU5F1_hiCa_(20180723_MM_HsSc_0709MPM498S)

description: CUT&RUN for POU5F1 in 3 day cells using HpA-MN CUT&RUN High Ca2+ differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 3d_IgG_std_(20181220_MM_HsSc_1213MPM837)

description: CUT&RUN for IgG in 3 day cells using Standard CUT&RUN differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 3d_IgG_A_auto_(20180511_MM_HsSc_374_0413)

description: CUT&RUN for IgG in 3 day cells using AutoCUT&RUN differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 3d_H3K27ac_(20180511_MM_HsSc_376_0413)

description: CUT&RUN for H3K27ac in 3 day cells using AutoCUT&RUN differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 3d_H3K4me2_(20180511_MM_HsSc_377_0413)

description: CUT&RUN for H3K4me2 in 3 day cells using AutoCUT&RUN differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 3d_Nanog_(20181004_MPM_HsSc_664_0926)

description: CUT&RUN for Nanog in 3 day cells using AutoCUT&RUN differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Rb anti-Nanog Abcam cat# ab109250


title: 3d_H3K27me3_(20180511_MM_HsSc_375_0413)

description: CUT&RUN for H3K27me3 in 3 day cells using AutoCUT&RUN differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Rb anti-H3K27me3 Cell Signaling cat# CST9733S


title: 3d_IgG_B_auto_(20181121_MM_HsSc_761_1113)


title: 3d_FoxA2_auto_(20180511_MM_HsSc_373_0413)

description: CUT&RUN for FoxA2 in 3 day cells using AutoCUT&RUN differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 3d_FoxA1_std_(20181220_MM_HsSc_1213MPM834)

description: CUT&RUN for FoxA1 in 3 day cells using Standard CUT&RUN differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 3d_GATA4_(20181120_MM_HsSc_758_1113)

description: CUT&RUN for GATA4 in 3 day cells using AutoCUT&RUN; Rb anti-Ms 2* ab differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 3d_FoxA1_hiCa_(20180723_MM_HsSc_0709MPM499S)

description: CUT&RUN for FoxA1 in 3 day cells using HpA-MN CUT&RUN High Ca2+ differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 3d_EOMES_(20181004_MPM_HsSc_666_0926)

description: CUT&RUN for EOMES in 3 day cells using AutoCUT&RUN differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 3d_FoxA1_auto_(20180511_MM_HsSc_372_0413)

description: CUT&RUN for FoxA1 in 3 day cells using AutoCUT&RUN differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 3d_FoxA2_hiCa_(20180723_MM_HsSc_0709MPM489S)

description: CUT&RUN for FoxA2 in 3 day cells using HpA-MN CUT&RUN High Ca2+ differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 3d_ATACseq_(20181017_MM_Hs_0705MPM500)

description: ATAC-seq in 3 day cells


title: 3d_CTCF_auto_(20181003_MPM_HsSc_659_0926)

description: CUT&RUN for CTCF in 3 day cells using AutoCUT&RUN differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Rb anti-CTCF Millipore cat# 07-729


title: 3d_CTCF_hiCa_(20180829_MM_HsSc_0817MPM565S)

description: CUT&RUN for CTCF in 3 day cells using HpA-MN CUT&RUN High Ca2+ differentiated for 3 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 2d_Sox2_(20180511_MM_HsSc_378_0413)

description: CUT&RUN for Sox2 in 2 day cells using AutoCUT&RUN differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: 2 days


title: 2d_T_(20181220_MM_HsSc_1213MPM844)

description: CUT&RUN for T in 2 day cells using Standard CUT&RUN; Rb anti-Gt 2* ab differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 2d_H3K4me2_(20180605_MM_HsSc_384_0413)

description: CUT&RUN for H3K4me2 in 2 day cells using AutoCUT&RUN differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 2d_IgG_B_auto_(20181121_MM_HsSc_771_1113)

description: CUT&RUN for IgG in 2 day cells using AutoCUT&RUN differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 2d_POU5F1_hiCa_(20180723_MM_HsSc_0709MPM510S)

description: CUT&RUN for POU5F1 in 2 day cells using HpA-MN CUT&RUN High Ca2+ differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 2d_H3K27ac_(20180605_MM_HsSc_383_0413)

description: CUT&RUN for H3K27ac in 2 day cells using AutoCUT&RUN differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Rb anti-H3K27ac Abcam cat# ab4729


title: 2d_H3K27me3_(20180605_MM_HsSc_382_0413)

description: CUT&RUN for H3K27me3 in 2 day cells using AutoCUT&RUN differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 2d_Sox17_(20181121_MM_HsSc_770_1113)

description: CUT&RUN for SOX17 in 2 day cells using AutoCUT&RUN; Rb anti-Gt 2* ab differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 2d_IgG_A_auto_(20180605_MM_HsSc_381_0413)


title: 2d_IgG_std_(20181220_MM_HsSc_1213MPM845)

description: CUT&RUN for IgG in 2 day cells using Standard CUT&RUN differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 2d_Nanog_(20181004_MPM_HsSc_683_0926)

description: CUT&RUN for Nanog in 2 day cells using AutoCUT&RUN differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 2d_FoxA2_auto_(20180511_MM_HsSc_380_0413)

description: CUT&RUN for FoxA2 in 2 day cells using AutoCUT&RUN differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 2d_FoxA1_auto_(20180511_MM_HsSc_379_0413)

description: CUT&RUN for FoxA1 in 2 day cells using AutoCUT&RUN differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 2d_FoxA1_std_(20181220_MM_HsSc_1213MPM842)

description: CUT&RUN for FoxA1 in 2 day cells using Standard CUT&RUN differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 2d_FoxA1_hiCa_(20180723_MM_HsSc_0709MPM511S)

description: CUT&RUN for FoxA1 in 2 day cells using HpA-MN CUT&RUN High Ca2+ differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 2d_EOMES_(20181004_MPM_HsSc_694_0926)

description: CUT&RUN for EOMES in 2 day cells using AutoCUT&RUN differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Rb anti-EOMES Abcam cat# ab23345


title: 2d_CTCF_hiCa_(20180829_MM_HsSc_0817MPM577S)

description: CUT&RUN for CTCF in 2 day cells using HpA-MN CUT&RUN High Ca2+ differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 2d_FoxA2_hiCa_(20180723_MM_HsSc_0709MPM501S)

description: CUT&RUN for FoxA2 in 2 day cells using HpA-MN CUT&RUN High Ca2+ differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)