title: AML_81

description: H

tag: tissue

value: AML patient bone marrow

tag: diagnosis

tag: vital status

tag: overall survival

value: 0.78 years

value: 69 years

value: intermediate risk

value: 83 percent

value: 78 percent

value: 35000 per uL

value: mutation-positive


title: I2_plate4_C_2

status: Public on Jan 19 2017

type: SRA

city: Barcelona

first: Lars

last: Velten

address: C. Dr. Aiguader 88, P05

department: Bioinformatics and Genomics

country: Spain

institute: CRG

library_source: transcriptomic

data_processing:
Demultiplexing. Perl 5.10.1
Trim off remaining poly-A tails, if applicable. Perl 5.10.1
Align reads to the human genome using GSNAP with default settings, expected paired-end length=400bp and allowable deviation from expected paired-end length=100bp. GSNAP version 2012-01-11
Count reads overlapping uniquely with mRNA genes. Python2.7/HTSeq
Remove cells with less than 750 genes at a minimum of 10 reads per gene. R-3.1.2
Remove genes with less than 10 reads in at least 5 cells. R-3.1.2
Fit error models to the readcount data for normalization. R-3.1.2 / scde
Remove cells with large overdispersion of the correlated component (theta_Corr < 0.45). R-3.1.2
Normalize data using posterior odds ratio, see manuscript. R-3.1.2
Genome_build: Homo Sapiens 37.68, with ERCC spike in sequences appended
Supplementary_files_format_and_content: Comma separated text file. First column: ENSEMBL Gene id. Second column: Raw read count.

molecule: polyA RNA

organism: Homo sapiens

source_name: Lin-CD34+CD38- bone marrow

extract_protocol:
Fresh bone marrow mononuclear cells were stained with fluorescence labeled antibodies against CD34, CD38, CD45RA, CD90, CD49f, CD135, CD10, CD7 and a lineage cocktail consisting of CD4, CD8, CD11b, CD14, CD19, CD20, CD56 and CD235a. Single Lin-CD34+CD38- and LinCD34+CD38+ HSPCs were sorted into lysis buffer.
Whole transcriptome amplifcation was performed using the QUARTZ-Seq protocol (Sasagawa et al., 2013). ERCC spike ins were included into the lysis buffer at a final dilution of 1:2,000,000. Libraries were constructed using Nextera Tn5 (Illumina) following the protocol provided, but using 1/4 of all volumes.

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: AML_69

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

country: USA

institute: Coriell Institute for Medical Research

library_source: genomic

data_processing:
Library strategy: DREAM
Sequencing reads were mapped to SmaI sites in the human genome (hg19) and signatures corresponding to methylated (starting with CCGGG) and unmethylated (starting with GGG) CpG were enumerated for each SmaI/XmaI site.
At each SmaI/XmaI site, let sm be the number of tags corresponding to methylated CpG (i.e., tags starting with CCGGG) and u be the number of tags corresponding to unmethylated CpG (i.e., tags starting with GGG), the methylation value was calculated as 100%*(c*sm/(c*sm+u)), where c is the correction factor based on observed vs expected methylation of spiked-in standards.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated plain text files

molecule: genomic DNA

source_name: AML patient bone marrow

extract_protocol:
DNA isolation: Red blood cells (RBCs) were lysed in the RBC lysis solution containing 155 mM ammonium chloride, 10 mM potassium bicarbonate and 1 mM EDTA. White blood cells (WBCs) were isolated as a pellet by centrifugation. The WBC pellet was then lysed in the solution containing 2% sodium dodecyl sulphate and 25 mM EDTA. Proteins were precipitated by adding 1/3 volume of 10 M ammonium acetate and removed as a pellet by centrifugation. DNA was precipitated from the supernatant with isopropanol, washed with 70% ethanol and dissolved in TE (10 mM TRIS pH 8.0, 1 mM EDTA).
Five micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels of 0, 25, 50, 75, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments.
Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

value: Acute myeloid leukemia (AML)

value: Dead

value: 2.91 years

tag: gender

value: M

tag: age

value: 44 years

tag: cytogenetic risk

value: adverse risk

tag: peripheral blasts

value: 0 percent

tag: bone marrow blasts

value: 53 percent

tag: wbc

value: 1800 per uL

tag: platelets

value: 34000 per uL

tag: dnmt3a mutation

value: wild-type

tag: idh mutation

tag: npm1 mutation


title: AML_70

tag: tissue

value: AML patient bone marrow

tag: diagnosis

tag: vital status

value: Alive

tag: overall survival

value: 6.16 years

value: 35 years

value: 22 percent

value: 93 percent

value: 2500 per uL

value: 58000 per uL


title: AML_71

value: Acute myeloid leukemia (AML)

value: Dead

value: 0.75 years

value: F

value: 54 years

value: intermediate risk

value: 52 percent

value: 81 percent

value: 4800 per uL

value: 92000 per uL


title: I2_plate4_B_11

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h


title: AML_68

value: AML patient bone marrow

value: 1.13 years

tag: gender

tag: age

value: 50 years

tag: cytogenetic risk

tag: peripheral blasts

value: 23 percent

value: 74 percent

value: 8000 per uL

value: 65000 per uL

value: wild-type

value: mutation-positive


title: AML_67

value: Acute myeloid leukemia (AML)

value: Dead

value: 0.02 years

value: 43 years

value: 17 percent

tag: bone marrow blasts

value: 38 percent

tag: wbc

value: 2000 per uL

tag: platelets

value: 25000 per uL

tag: dnmt3a mutation


title: AML_66

tag: tissue

value: AML patient bone marrow

tag: diagnosis

value: 0.7 years

value: M

value: 49 years

value: adverse risk

value: 31 percent

value: 55 percent

value: 16400 per uL

value: 90000 per uL

tag: idh mutation

tag: npm1 mutation


title: AML_76

value: Acute myeloid leukemia (AML)

tag: vital status

value: Alive

tag: overall survival

value: 5.43 years

value: 59 years

value: intermediate risk

value: 59 percent

value: 73 percent

value: 5300 per uL

value: 63000 per uL

value: mutation-positive

value: wild-type


title: I2_plate4_B_8

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: lin

tag: facs time


title: I2_plate4_B_10

tag: ssc-w

tag: ssc-h


title: AML_65

value: AML patient bone marrow

value: Dead

value: 0.82 years

tag: gender

value: F

tag: age

value: 35 years

tag: cytogenetic risk

tag: peripheral blasts

value: 18 percent

tag: bone marrow blasts

value: 65 percent

tag: wbc

value: 33400 per uL


title: I2_plate4_B_7


title: I2_plate4_B_6


title: AML_64

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

value: Alive

value: 2.88 years

value: 32 years

value: 4 percent

value: 39 percent

value: 2100 per uL

tag: platelets

tag: dnmt3a mutation

tag: idh mutation

tag: npm1 mutation


title: AML_61

tag: vital status

tag: overall survival

value: 5.87 years

value: 42 years

value: intermediate risk

value: 66 percent

value: 42 percent

value: 11800 per uL

value: mutation-positive


title: I2_plate4_B_4

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: lin

tag: facs time


title: I2_plate4_B_3

tag: ssc-w

tag: ssc-h


title: AML_59

value: AML patient bone marrow

value: Dead

value: 0.65 years

tag: gender

value: M

tag: age

value: 63 years

tag: cytogenetic risk

value: adverse risk

tag: peripheral blasts

value: 0 percent

tag: bone marrow blasts

value: 85 percent

tag: wbc

value: 19400 per uL

value: 59000 per uL

value: wild-type


title: AML_60

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

value: F

value: 57 years

value: 60 percent

value: 44 percent

value: 9000 per uL

tag: platelets

value: 26000 per uL

tag: dnmt3a mutation

tag: idh mutation

tag: npm1 mutation


title: I2_plate4_B_2

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a


title: I2_plate4_B_12

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: AML_58

value: AML patient bone marrow

tag: vital status

value: Dead

tag: overall survival

value: 0.14 years

tag: gender

tag: age

value: 49 years

tag: cytogenetic risk

tag: peripheral blasts

value: 1 percent

value: 22 percent

value: 4300 per uL


title: I2_plate4_B_1


title: AML_57

tag: tissue

tag: diagnosis

value: Alive

value: 3.33 years

value: 47 years

value: intermediate risk

value: 75 percent

tag: bone marrow blasts

value: 92 percent

tag: wbc

value: 64700 per uL

tag: platelets

value: 17000 per uL

tag: dnmt3a mutation


title: AML_63

value: Acute myeloid leukemia (AML)

value: 0.99 years

value: M

value: 63 years

value: adverse risk

value: 18 percent

value: 20 percent

value: 1800 per uL

value: 37000 per uL

value: wild-type

tag: idh mutation

tag: npm1 mutation


title: I2_plate4_A_12

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h


title: I2_plate4_B_9

tag: lin

tag: facs time


title: I2_plate4_A_11


title: AML_56

value: AML patient bone marrow

tag: vital status

value: Dead

tag: overall survival

value: 5.15 years

tag: gender

value: F

tag: age

value: 37 years

tag: cytogenetic risk

tag: peripheral blasts

value: 87 percent

value: 84 percent

value: 47100 per uL

value: mutation-positive


title: AML_55

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

value: 0.29 years

value: M

value: 61 years

value: intermediate risk

value: 47 percent

tag: bone marrow blasts

value: 24 percent

tag: wbc

value: 6800 per uL

tag: platelets

value: 46000 per uL

tag: dnmt3a mutation


title: I2_plate4_A_9

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a


title: I2_plate4_A_8

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: AML_54

value: AML patient bone marrow

tag: vital status

value: Alive

tag: overall survival

value: 1.29 years

tag: gender

tag: age

value: 58 years

value: 62 percent

value: 10100 per uL

value: 66000 per uL

value: wild-type

tag: idh mutation

tag: npm1 mutation


title: AML_53

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

value: Dead

value: 0.74 years

value: F

value: 57 years

tag: cytogenetic risk

tag: peripheral blasts

value: 40 percent

tag: bone marrow blasts

value: 57 percent

tag: wbc

value: 14800 per uL

value: mutation-positive


title: I2_plate4_A_6

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a


title: I2_plate4_A_7

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: AML_52

value: AML patient bone marrow

tag: vital status

tag: overall survival

value: 2.56 years

tag: gender

value: M

tag: age

value: 45 years

value: intermediate risk

value: 20 percent

value: 38 percent

value: 54100 per uL

tag: platelets

value: 15000 per uL

tag: dnmt3a mutation


title: AML_51

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

value: Alive

value: 3.27 years

value: 43 years

tag: cytogenetic risk

tag: peripheral blasts

value: 4 percent

value: 30 percent

value: 7800 per uL

value: 71000 per uL

value: wild-type

tag: idh mutation

tag: npm1 mutation


title: I2_plate4_B_5

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a


title: I2_plate4_A_10

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: I2_plate4_A_4


title: AML_49

value: AML patient bone marrow

tag: vital status

value: Dead

tag: overall survival

value: 1.51 years

tag: gender

value: F

tag: age

value: 37 years

value: adverse risk

value: 3 percent

tag: bone marrow blasts

tag: wbc

value: 2400 per uL

value: 72000 per uL


title: AML_62

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

value: 1.17 years

value: 22 years

tag: cytogenetic risk

tag: peripheral blasts

value: 46.5 percent

value: 91 percent

value: 7700 per uL

tag: platelets

value: 17000 per uL

tag: dnmt3a mutation


title: AML_50

value: 1.88 years

value: M

value: 60 years

value: intermediate risk

value: 25 percent

value: 4400 per uL

value: 70000 per uL

value: mutation-positive

tag: idh mutation

value: wild-type

tag: npm1 mutation


title: AML_48

value: AML patient bone marrow

value: Dead

value: 1.54 years

value: F

value: 20 years

value: 95 percent

value: 86 percent

value: 73200 per uL

value: 63000 per uL


title: I2_plate4_A_2

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h


title: islet_single_cell_artemether_36

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Trimming of adapter sequences was performed with trimmomatic (v 0.32) minimum read length after trimming: 25
Alignment of the trimmed reads to the human transcriptome (hg19 GRCh37 ftp://ftp.ensembl.org/pub/release-74/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.74.cdna.all.fa.gz) was performed with bowtie1 (v 1.1)
Calculation of normalized transcript-wise expression estimates (RPKM values) was performed based on the transcriptome alignments using the R (v 3.1.2) package BitSeq (v 1.10.0). Function: getExpression() with uniform=FALSE
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include transcript-wise RPKM values or read counts for each sample

source_name: pancreatic islet

extract_protocol:
To disassociate islets into single cells, islets were incubated in Accutase (Life technology) in 37 °C for 20 min, neutralized by CMRL medium. Purification of single cells was performed by flow cytometry cell sorting on a Moflo AstriosEQ (Beckman Coulter, Miami)
cDNA synthesis and enrichment was performed following the Smart-seq2 protocol as described (Picelli et al., 2014).

treatment_protocol: Islets were cultured in CMRL medium (Life technology) supplemented with 10% FBS, 2 mM glutamine, 100 U/mL penicillin, and 100 µg/mL streptomycin. Artemether treatment was administered for the indicated period of time.

tag: assigned cell type

value: acinar

tag: treatment length

tag: cell count


title: I2_plate4_A_3

tag: lin

tag: facs time


title: AML_47

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

tag: vital status

value: Alive

tag: overall survival

value: 2.68 years

tag: gender

value: M

tag: age

value: 53 years

tag: cytogenetic risk

value: 41 percent

tag: bone marrow blasts

value: 82 percent

tag: wbc

value: 22000 per uL

value: 76000 per uL


title: I2_plate4_A_1

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a


title: AML_46

value: AML patient bone marrow

value: 3.33 years

value: 27 years

value: intermediate risk

tag: peripheral blasts

value: 5 percent

value: 2100 per uL

tag: platelets

tag: dnmt3a mutation

value: wild-type

tag: idh mutation

tag: npm1 mutation


title: I2_plate3_H_12

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: AML_45

tag: tissue

tag: diagnosis

tag: vital status

value: Dead

tag: overall survival

value: 0.16 years

tag: gender

value: F

tag: age

value: 51 years

value: 27 percent

value: 16400 per uL


title: islet_single_cell_artemether_34

tag: assigned cell type

value: alpha

tag: treatment length

tag: cell count


title: I2_plate3_H_11

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a


title: islet_single_cell_artemether_33

value: acinar


title: I2_plate3_H_10

tag: ssc-w


title: I2_plate3_H_9

tag: ssc-h


title: islet_single_cell_artemether_32

value: duct


title: AML_43

value: Acute myeloid leukemia (AML)

value: 0.96 years

value: 59 years

tag: cytogenetic risk

tag: peripheral blasts

value: 88 percent

tag: bone marrow blasts

value: 92 percent

tag: wbc

value: 52900 per uL

tag: platelets

value: 48000 per uL

tag: dnmt3a mutation

tag: idh mutation

tag: npm1 mutation


title: I2_plate3_H_8

tag: lin

tag: facs time


title: I2_plate4_A_5


title: AML_42

tag: tissue

value: AML patient bone marrow

tag: diagnosis

tag: vital status

tag: overall survival

value: 0.13 years

tag: gender

value: M

tag: age

value: 55 years

value: intermediate risk

value: 25 percent

value: 90 percent

value: 29600 per uL

value: wild-type

value: mutation-positive


title: islet_single_cell_artemether_31

tag: assigned cell type

value: undefined

tag: treatment length

tag: cell count


title: AML_41

value: Acute myeloid leukemia (AML)

value: Alive

value: 3.31 years

value: F

value: 56 years

tag: cytogenetic risk

tag: peripheral blasts

value: 22 percent

tag: bone marrow blasts

value: 42 percent

value: 5100 per uL

value: 23000 per uL


title: AML_40

value: AML patient bone marrow

value: Dead

value: 0.02 years

value: M

value: 49 years

value: 80 percent

tag: wbc

value: 32300 per uL

tag: platelets

value: 13000 per uL

tag: dnmt3a mutation


title: islet_single_cell_artemether_30

value: undefined


title: islet_single_cell_artemether_28


title: I2_plate3_H_7

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h

tag: lin


title: islet_single_cell_artemether_35

value: alpha


title: I2_plate3_H_6

tag: facs time


title: AML_39

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

tag: vital status

tag: overall survival

value: 0.64 years

tag: gender

tag: age

value: 58 years

value: adverse risk

value: 12 percent

value: 21 percent

value: 14800 per uL

value: 79000 per uL

value: wild-type

tag: idh mutation

tag: npm1 mutation


title: islet_single_cell_artemether_29

tag: assigned cell type

value: acinar

tag: treatment length

tag: cell count


title: AML_38

value: AML patient bone marrow

value: Alive

value: 4.18 years

value: M

value: 17 years

tag: cytogenetic risk

value: intermediate risk

tag: peripheral blasts

value: 97 percent

tag: bone marrow blasts

value: 96 percent

tag: wbc

tag: platelets

value: 40000 per uL

tag: dnmt3a mutation

value: mutation-positive


title: I2_plate3_H_5

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: AML_37

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

tag: vital status

value: Dead

tag: overall survival

value: 2.03 years

tag: gender

value: F

tag: age

value: 62 years

value: 0 percent

value: 41 percent

value: 2700 per uL

tag: idh mutation

tag: npm1 mutation


title: I2_plate3_H_4


title: islet_single_cell_artemether_26

tag: assigned cell type

value: duct

tag: treatment length

tag: cell count


title: I2_plate3_H_3

tag: fsc-a

tag: fsc-w

tag: fsc-h


title: AML_44

value: AML patient bone marrow

value: 0.58 years

tag: cytogenetic risk

value: adverse risk

tag: peripheral blasts

value: 6 percent

tag: bone marrow blasts

value: 42 percent

tag: wbc

value: 5000 per uL

tag: platelets

value: 42000 per uL

tag: dnmt3a mutation

value: wild-type


title: AML_36

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

tag: vital status

value: Alive

tag: overall survival

value: 1.77 years

value: 54 years

value: intermediate risk

value: 50 percent

value: 45 percent

value: 7500 per uL

value: 22000 per uL

value: mutation-positive


title: islet_single_cell_artemether_24

value: acinar


title: AML_35

value: AML patient bone marrow

value: Dead

value: 2.49 years

tag: gender

value: F

tag: age

value: 59 years

value: 15 percent

value: 69 percent

value: 21000 per uL

value: 85000 per uL

tag: idh mutation

tag: npm1 mutation


title: islet_single_cell_artemether_25

tag: assigned cell type

value: alpha

tag: treatment length

tag: cell count


title: islet_single_cell_artemether_23

value: pp


title: AML_34

value: Acute myeloid leukemia (AML)

value: 0.84 years

value: 65 years

tag: cytogenetic risk

value: adverse risk

value: 5 percent

value: 22 percent

value: 3900 per uL

value: 14000 per uL

value: wild-type


title: I2_plate3_G_11

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: I2_plate3_H_1


title: islet_single_cell_artemether_22


title: islet_single_cell_artemether_21

value: undefined


title: AML_33

tag: tissue

value: AML patient bone marrow

tag: diagnosis

tag: vital status

value: Alive

tag: overall survival

value: 1.74 years

value: M

value: 52 years

value: intermediate risk

tag: peripheral blasts

value: 92 percent

tag: bone marrow blasts

value: 94 percent

tag: wbc

value: 91700 per uL

tag: platelets

value: 33000 per uL

tag: dnmt3a mutation

value: mutation-positive


title: I2_plate3_G_9

tag: fsc-a


title: islet_single_cell_artemether_27

tag: assigned cell type

value: beta

tag: treatment length

tag: cell count


title: islet_single_cell_artemether_19


title: AML_31

value: Acute myeloid leukemia (AML)

value: Dead

value: 1.05 years

tag: gender

value: F

tag: age

value: 56 years

tag: cytogenetic risk

value: 7 percent

value: 99 percent

value: 2500 per uL

value: 47000 per uL

tag: idh mutation

tag: npm1 mutation


title: AML_32

tag: tissue

value: AML patient bone marrow

tag: diagnosis

value: Alive

value: 1.97 years

value: M

value: 29 years

value: 0 percent

value: 55 percent

value: 2000 per uL

value: 57000 per uL

value: wild-type


title: Normal_04

source_name: Normal peripheral blood leukocytes

value: Normal peripheral blood leukocytes

value: Healthy

tag: vital status

tag: overall survival

value: unknown


title: I2_plate3_G_12

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: AML_29

value: Acute myeloid leukemia (AML)

value: Dead

value: 2.54 years

value: 55 years

value: intermediate risk

tag: peripheral blasts

value: 17 percent

tag: bone marrow blasts

value: 86 percent

tag: wbc

value: 9400 per uL

tag: platelets

value: 14000 per uL

tag: dnmt3a mutation

value: mutation-positive


title: I2_plate3_H_2

tag: fsc-a


title: islet_single_cell_artemether_18

tag: assigned cell type

value: alpha

tag: treatment length

tag: cell count


title: islet_single_cell_artemether_17


title: I2_plate3_G_6


title: islet_single_cell_artemether_20


title: islet_single_cell_artemether_16

value: delta


title: I2_plate3_G_8


title: islet_single_cell_artemether_15


title: AML_30

tag: tissue

value: AML patient bone marrow

tag: diagnosis

tag: vital status

value: Alive

tag: overall survival

value: 2.35 years

tag: gender

value: M

tag: age

value: 57 years

tag: cytogenetic risk

value: 14 percent

value: 40 percent

value: 32200 per uL

tag: idh mutation

tag: npm1 mutation


title: I2_plate3_G_5

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: AML_26

value: Acute myeloid leukemia (AML)

value: Dead

value: 0.7 years

value: 54 years

tag: peripheral blasts

value: 35 percent

tag: bone marrow blasts

value: 30 percent

tag: wbc

value: 5000 per uL

tag: platelets

value: 48000 per uL

tag: dnmt3a mutation

value: wild-type


title: I2_plate3_G_4

tag: fsc-a


title: AML_25

tag: tissue

value: AML patient bone marrow

tag: diagnosis

tag: vital status

tag: overall survival

value: 2.08 years

tag: gender

value: F

tag: age

value: 47 years

value: intermediate risk

value: 50 percent

value: 58 percent

value: 800 per uL

value: 6000 per uL

value: mutation-positive


title: I2_plate3_G_10

tag: fsc-w

tag: fsc-h

tag: ssc-a


title: AML_24

value: Acute myeloid leukemia (AML)

value: Alive

value: 3.17 years

value: 49 years

tag: cytogenetic risk

value: 0 percent

value: 60 percent

value: 39000 per uL

tag: idh mutation

tag: npm1 mutation


title: islet_single_cell_artemether_14

tag: assigned cell type

value: beta

tag: treatment length

tag: cell count


title: I2_plate3_G_2

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: I2_plate3_G_3

tag: fsc-a


title: AML_23

tag: tissue

value: AML patient bone marrow

tag: diagnosis

tag: vital status

value: Dead

tag: overall survival

value: 0.03 years

value: 29 years

tag: peripheral blasts

value: 81 percent

tag: bone marrow blasts

value: 92 percent

tag: wbc

value: 37000 per uL

tag: platelets

value: 47000 per uL

tag: dnmt3a mutation

value: wild-type


title: SH5_YZ5_KO2_1345_06_19_14

city: Boston

first: Susan

middle: J

last: Hagen

state: Massachusetts

address: 330 Brookline Avenue, E/RW-871

department: Surgery

institute: Beth Israel Deaconess Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mouse genome (mm10) using STAR alignerhttp://bioinformatics.oxfordjournals.org/content/early/2012/10/25/bioinformatics.bts635), quantified by feature Counts (http://www.ncbi.nlm.nih.gov/pubmed/24227677), and analyzed by DESeq (http://www.ncbi.nlm.nih.gov/pubmed/20979621) for differential expression.
P-values were adjusted using the Benjamini-Hochberg procedure (J R Statist Soc B  1995;57:289-300).
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated values format; one file contains the complete gene list and the other file contains the gene expression data for each sample

molecule: total RNA

organism: Mus musculus

source_name: Stomach corpus-neck region

extract_protocol:
The somach was removed, frozen (unfixed) in OCT with isopentane cooled with liquid nitrogen, sectioned, and the neck region captured by laser capture microdissection.  RNA was made using the RNeazy microkit (Qiagen; #74004).  RNA quantity was determined on the Qubit using the RNA BR Assay kit (ThermoFisher; #Q10210)).  RNA quality was determined on the Bioanalyzer using the RNA pico kit (Agilent; #5067-1513).  100 ng of RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: age

value: 7 weeks after birth

tag: genotype

value: Knockout, CLDN18-/-


title: SH6_YZ6_KO3_1346_06_19_14


title: I2_plate3_G_1

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w


title: I2_plate3_F_12

tag: fsc-a

tag: ssc-h

tag: lin

tag: facs time


title: AML_28

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

tag: vital status

tag: overall survival

value: 1.04 years

tag: gender

value: F

value: 45 years

tag: cytogenetic risk

value: adverse risk

value: 42 percent

value: 20 percent

value: 5200 per uL

value: 91000 per uL

tag: idh mutation

tag: npm1 mutation


title: I2_plate3_F_11


title: AML_21

value: AML patient bone marrow

value: Dead

value: 2.18 years

tag: age

value: 62 years

value: intermediate risk

tag: peripheral blasts

value: 16 percent

tag: bone marrow blasts

value: 31 percent

tag: wbc

value: 4400 per uL

tag: platelets

value: 60000 per uL

tag: dnmt3a mutation


title: AML_22

value: Acute myeloid leukemia (AML)

value: 0.59 years

value: M

value: 55 years

value: 0 percent

value: 85 percent

value: 1200 per uL

value: wild-type


title: SH4_YZ4_KO1_1344_06_19_14

tag: strain

value: 7 weeks after birth

tag: genotype

value: Knockout, CLDN18-/-


title: SH3_YZ3_C3_1353_06_19_14

value: wild-type, CLDN18+/+


title: AML_20

description: E

value: AML patient bone marrow

value: Dead

value: 0.99 years

value: F

value: 32 years

value: 46 percent

value: 52 percent

value: 66600 per uL

value: 45000 per uL

value: mutation-positive


title: AML_19

description: D

value: Acute myeloid leukemia (AML)

value: Alive

value: 16.83 years

value: 19 years

value: intermediate risk

value: 71 percent

value: 8900 per uL

value: 68000 per uL


title: I2_plate3_F_10

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: I2_plate3_F_9


title: AML_18

description: C

tag: tissue

value: AML patient bone marrow

tag: diagnosis

tag: vital status

tag: overall survival

value: 16.17 years

tag: gender

value: 44 years

tag: cytogenetic risk

value: 96 percent

value: 94 percent

value: 25800 per uL

value: 26000 per uL

value: wild-type

tag: idh mutation

tag: npm1 mutation


title: AML_27

value: Dead

value: 1.44 years

value: F

tag: age

value: 49 years

tag: peripheral blasts

value: 8 percent

tag: bone marrow blasts

value: 32 percent

tag: wbc

value: 1400 per uL

tag: platelets

value: 20000 per uL

tag: dnmt3a mutation


title: AML_17

description: B

value: Acute myeloid leukemia (AML)

value: 18 years

value: M

value: 52 years

value: intermediate risk

value: 74 percent

value: 79 percent

value: 59300 per uL

value: 23000 per uL

value: mutation-positive


title: RNA-seq WT B-1a [19720]

first: Maria

last: Fischer

address: Campus-Vienna-Biocenter 1

institute: Research Institute of Molecular Pathology

description: Cells sorted from an individual mouse (low cell numbers) for V segment usage analysis; SuperScript® VILO™ cDNA Synthesis, strand-specific

data_processing:
For analysis of differential gene expression, the number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode set to ‘union’. The datasets were analyzed using the R package DESeq2 version 1.4.1. Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings.
For ChIP-seq, the reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using the Bowtie program version 12.5. Peaks were called with a P value of < 10-10 by using the MACS program version 1.3.6.1 with default parameters, a genome size of 2,654,911,517 bp (mm9) and a pro-B cell input sample. The identified peaks were then assigned to target genes as described previously.
For alignment of ATAC-seq reads, the Bowtie version 2.1.0 was used with the additional parameter -sensitive -X 5000.
Genome_build: MM9
Supplementary_files_format_and_content: text tab delim = TPM values in ASCII text format tab delimited; bigwig = bigWig Track format of read density coverage in reads per million (in some cases after extension to 150 base pairs)

source_name: RNA-seq WT B-1a

extract_protocol:
Rneasy Plus Mini Kit, Dynabeads mRNA purification kit
For strand specific RNA-sequencing, RNA was isolated with an RNeasy Plus Mini Kit (Qiagen), and mRNA was obtained by poly(A) selection with a Dynabeads mRNA purification kit (Invitrogen), followed by fragmentation by heating at 94 °C for 3 min (in fragmentation buffer). The fragmented mRNA was used as template for first-strand cDNA synthesis with random hexamers and a Superscript VILO cDNA Synthesis kit (Invitrogen). The second-strand cDNA was synthesized with 100 mM dATP, dCTP, dGTP and dUTP in the presence of RNase H, E. coli DNA polymerase I and DNA ligase (Invitrogen). Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module. For strandspecific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-Nglycosylase (New England Biolabs) as described10 followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems). Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS Library Quantification kit. For analysis of Bhlhe41 binding, Chromatin from 6x107 B-1a cells was prepared using a lysis buffer containing 0.25% SDS. The cells were subjected to ChIP as described11 with minor modifications. Anti-V5 agarose beads (Sigma- Aldrich) were used for precipitation. Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems) and Illumina deep sequencing.  Open chromatin regions were mapped in sorted Vh12/Vk4 transgenic WT and DKO B-1a cells from the spleen of bone marrow chimeras by ATAC-seq, as described by Buenrostro et. al. with the following modification. The nuclei were prepared by incubation of cells with nuclear preparation buffer (0.30 M sucrose, 10 mM Tris, pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.1% NP40, 0.15 mM spermine, 0.5 mM spermidine and 2 mM 6AA) before the Tn5 treatment (3 × 104 cells with 4 ?l of the Nextera Tn5 transposase).

tag: strain background

tag: genotype/variation

value: Wild-type

tag: cell type

value: peritoneal cavity B-1a cells

tag: cell preparation

value: Ex-vivo, FACS sorted

tag: cell sorting strategy


title: I2_plate3_F_7

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: AML_16

description: aP

tag: tissue

value: AML patient bone marrow

tag: diagnosis

tag: vital status

value: Alive

tag: overall survival

value: 12.67 years

tag: gender

value: F

tag: age

value: 32 years

tag: cytogenetic risk

tag: peripheral blasts

value: 58 percent

tag: bone marrow blasts

value: 76 percent

value: 16900 per uL

value: wild-type

tag: idh mutation

tag: npm1 mutation


title: RNA-seq DKO B-1b [19719]

source_name: RNA-seq DKO B-1b

tag: strain background

tag: genotype/variation

value: Bhlhe41-/- Bhlhe40-/-

tag: cell type

value: peritoneal cavity B-1b cells

tag: cell preparation

tag: cell sorting strategy


title: AML_15

description: aO

value: Acute myeloid leukemia (AML)

value: Dead

value: 0.37 years

value: M

value: 65 years

value: intermediate risk

value: 62 percent

value: 78 percent

tag: wbc

value: 45100 per uL

tag: platelets

tag: dnmt3a mutation


title: SH2_YZ2_C2_1352_06_19_14

tag: strain

value: 7 weeks after birth

tag: genotype

value: wild-type, CLDN18+/+


title: I2_plate3_F_5

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: I2_plate3_F_6


title: I2_plate3_G_7


title: AML_14

description: aN

tag: tissue

value: AML patient bone marrow

tag: diagnosis

tag: vital status

value: Alive

tag: overall survival

value: 15.5 years

tag: gender

tag: age

value: 21 years

tag: cytogenetic risk

tag: peripheral blasts

value: 84 percent

tag: bone marrow blasts

value: 73 percent

value: 99400 per uL

value: 19000 per uL

tag: idh mutation

tag: npm1 mutation


title: RNA-seq WT B-1b [19718]

source_name: RNA-seq WT B-1b

tag: strain background

tag: genotype/variation

value: Wild-type

tag: cell type

value: peritoneal cavity B-1b cells

tag: cell preparation

value: Ex-vivo, FACS sorted

tag: cell sorting strategy


title: SH1_YZ1_C1_1351_06_19_14

tag: strain

tag: genotype


title: RNA-seq WT B-1a [19717]

value: peritoneal cavity B-1a cells


title: I2_plate3_F_8

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: AML_13

description: aM

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

tag: vital status

value: Dead

tag: overall survival

value: 0.5 years

tag: gender

value: M

tag: age

value: 58 years

tag: cytogenetic risk

value: adverse risk

tag: peripheral blasts

value: 33 percent

tag: bone marrow blasts

value: 52 percent

tag: wbc

value: 1400 per uL

tag: platelets

value: 24000 per uL

tag: dnmt3a mutation

value: mutation-positive

tag: idh mutation

value: wild-type


title: I2_plate3_F_3

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w


title: AML_12

description: aL

tag: tissue

value: AML patient bone marrow

tag: diagnosis

value: 0.22 years

value: F

value: 55 years

value: intermediate risk

value: 76 percent

value: 79 percent

value: 78200 per uL

tag: npm1 mutation


title: RNA-seq DKO B-1a [19715]

source_name: RNA-seq DKO B-1a

tag: strain background

tag: genotype/variation

value: Bhlhe41-/- Bhlhe40-/-

tag: cell type

value: peritoneal cavity B-1a cells

tag: cell preparation

value: Ex-vivo, FACS sorted

tag: cell sorting strategy


title: RNA-seq WT B-1a [17253]

value: Wild-type


title: AML_10

description: aJ

value: Acute myeloid leukemia (AML)

tag: vital status

value: Dead

tag: overall survival

value: 0.99 years

tag: gender

value: M

tag: age

value: 56 years

tag: cytogenetic risk

tag: peripheral blasts

value: 18 percent

tag: bone marrow blasts

value: 44 percent

tag: wbc

value: 22200 per uL

value: 19000 per uL


title: I2_plate3_F_1

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: RNA-seq WT B-1a [17251]

tag: strain background

tag: genotype/variation

tag: cell type

tag: cell preparation

tag: cell sorting strategy


title: AML_09

description: aI

tag: tissue

value: AML patient bone marrow

tag: diagnosis

tag: vital status

value: Alive

tag: overall survival

value: 17.92 years

tag: gender

tag: age

value: 55 years

tag: cytogenetic risk

value: favorable risk

value: 54 percent

value: 58 percent

value: 17200 per uL

tag: platelets

value: 78000 per uL

tag: dnmt3a mutation

value: wild-type

tag: idh mutation

tag: npm1 mutation


title: I2_plate3_E_12

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: RNA-seq DKO B-1a [17250]

tag: strain background

tag: genotype/variation

value: Bhlhe41-/- Bhlhe40-/-

tag: cell type

value: peritoneal cavity B-1a cells

tag: cell preparation

value: Ex-vivo, FACS sorted

tag: cell sorting strategy


title: AML_08

description: aH

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

tag: vital status

tag: overall survival

value: 15 years

tag: gender

value: F

tag: age

value: 44 years

tag: cytogenetic risk

tag: peripheral blasts

value: 87 percent

tag: bone marrow blasts

value: 72 percent

tag: wbc

tag: platelets

value: 35000 per uL


title: RNA-seq DKO B-1a [17249]


title: I2_plate3_E_10

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: AML_07

description: aG

tag: tissue

value: AML patient bone marrow

tag: diagnosis

tag: vital status

value: Dead

value: 0.47 years

value: 32 years

value: intermediate risk

value: 84 percent

value: 70 percent

value: 36000 per uL

tag: dnmt3a mutation

tag: idh mutation

value: mutation-positive

tag: npm1 mutation


title: AML_06

description: aF

tag: overall survival

value: 1.41 years

tag: gender

tag: age

value: 24 years

tag: cytogenetic risk

value: adverse risk

tag: peripheral blasts

value: 92 percent

tag: bone marrow blasts

value: 93 percent

value: 56600 per uL

value: 21000 per uL

value: wild-type


title: RNA-seq DKO B-1a [19716]

tag: strain background

tag: genotype/variation

value: Bhlhe41-/- Bhlhe40-/-

tag: cell type

value: peritoneal cavity B-1a cells

tag: cell preparation

value: Ex-vivo, FACS sorted

tag: cell sorting strategy


title: AML_05

description: aD

tag: tissue

value: AML patient bone marrow

value: Acute myeloid leukemia (AML)

value: Dead

value: 1.08 years

value: M

value: 72 years

value: 81 percent

value: 79 percent

tag: wbc

tag: platelets

value: 41000 per uL


title: I2_plate3_F_2

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: I2_plate3_E_9


title: Thymus Satb1 ChIP-seq, b

city: San Francisco

first: Hunter

last: Richards

state: CA

address: 513 Parnassus Ave., HSW 863

department: Orofacial Sciences

institute: UCSF

data_processing:
Raw ChIP-seq data was aligned to mouse reference genome release mm9 using bowtie v1.0.0 with the following parameters set: --chunkmbs 1024 --best --strata -n 3 -m 1
Candidate peaks were called using MACS (v1.4.3) keeping peaks ranked below a p-value threshold of 1x10^-5. For downstream analysis only peaks having an FDR < 1% and Fold Enrichment > 4 were kept.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: bigWig tracks of coverage profiles were generated using the wigToBigWig utility from UCSC.

source_name: thymus

extract_protocol:
For ChIP-seq using anti-SATB1 (abcam, ab109122), 4x10^7 C57BL/6J thymocytes were freshly prepared and washed with PBS containing 0.5 mM PMSF and were subjected to crosslinking by incubation for 10 min in 5 mM HEPES pH 7.5, 10 mM NaCl, 0.1 mM EDTA, 0.05 mM EGTA, 1% formaldehyde at 23 °C. The reaction was stopped by addition of glycine to 0.125 M. Cells were then immediately washed in ice-cold PBS containing 0.5 mM PMSF and lysed by incubation for 10 min on ice in 1 ml of 50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% TritonX-100 containing protease inhibitor (Roche). Nuclei were pelleted and lysed by resuspending in 10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA containing protease inhibitor (Roche). Pelleted chromatin was resuspended in 400 μl of 10 mM Tris pH 8.0, 300 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% TritonX-100, 0.1% sodium deoxycholate and 0.5% N-laurylsarcosine, and was sonicated using a model XL2000 ultrasonic cell disruptor (MICROSON) so that relatively large fragments (1-10 kbp) were included. Sonicated chromatin was incubated overnight at 4 °C with anti-SATB1 antibody that was preconjugated with magnetic beads (Dynabeads). Immunoprecipitated DNA was then purified after vigorous washing of immunoprecipitates and reversal of crosslinks by overnight incubation at 65 °C in 50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS.
Input DNA and ChIP DNA (10-20 ng) were subjected to sonication (Bioruptor, UCD-200) on low power for 20 cycles (30 sec. on and 30 sec. off). Libraries were constructed using the ThruPlex DNA-seq kit (Rubicon Genomics) according to the manufacture's protocol, followed by purification using SPRI beads (Thermo Fisher). Libraries were sequenced to 50 bp read length on a HiSeq2000 (Illumina).

tag: strain

value: total thymocyte

tag: chip antibody

value: Satb1 (AbCam ab109122)


title: I2_plate3_E_8


title: I2_plate3_E_5


title: AML_04

description: aC

tag: diagnosis

tag: vital status

tag: overall survival

value: 0.39 years

tag: gender

tag: age

value: 67 years

tag: cytogenetic risk

value: adverse risk

tag: peripheral blasts

value: 75 percent

tag: bone marrow blasts

value: 67 percent

value: 42000 per uL

value: 91000 per uL

tag: dnmt3a mutation

tag: idh mutation

value: mutation-positive

tag: npm1 mutation


title: Thymus Satb1 ChIP-seq, a

tag: cell type


title: Thymus input control ChIP-seq


title: AML_11

description: aK

tag: tissue

value: AML patient bone marrow

value: Acute myeloid leukemia (AML)

value: Alive

value: 6.76 years

value: 33 years

value: intermediate risk

value: 34 percent

value: 32 percent

tag: wbc

value: 7100 per uL

tag: platelets

value: 40000 per uL

value: wild-type


title: I2_plate3_E_7

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: AML_02

description: aA

tag: diagnosis

tag: vital status

value: Dead

tag: overall survival

value: 10.56 years

tag: gender

value: M

tag: age

value: 39 years

tag: cytogenetic risk

tag: peripheral blasts

value: 79 percent

value: 49 percent

value: 52800 per uL

value: 30000 per uL


title: AML_03

description: aB

tag: tissue

value: AML patient bone marrow

value: Acute myeloid leukemia (AML)

value: 0.64 years

value: F

value: 57 years

value: 81 percent

tag: bone marrow blasts

value: 75 percent

tag: wbc

value: 26500 per uL

value: 93000 per uL

tag: dnmt3a mutation

tag: idh mutation

value: mutation-positive

tag: npm1 mutation


title: I2_plate3_E_4

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w


title: I2_plate3_E_1

tag: ssc-h

tag: lin

tag: facs time


title: I2_plate3_E_11


title: I2_plate3_D_12


title: I2_plate3_F_4


title: I2_plate3_E_3


title: AML_01

description: A

tag: diagnosis

tag: vital status

value: Alive

tag: overall survival

value: 21.67 years

tag: gender

tag: age

value: 46 years

value: intermediate risk

value: 77 percent

value: 72 percent

tag: platelets

value: 44000 per uL

value: wild-type


title: I2_plate3_E_2


title: I2_plate3_D_11


title: I2_plate3_D_9


title: I2_plate3_D_8


title: I2_plate3_D_7


title: I2_plate3_D_10


title: I2_plate3_D_6


title: I2_plate3_E_6


title: I2_plate3_D_1


title: I2_plate3_C_12


title: I2_plate3_C_11


title: I2_plate3_D_5


title: I2_plate3_D_4


title: I2_plate3_C_9


title: I2_plate3_D_2


title: I2_plate3_C_6


title: I2_plate3_C_5


title: I2_plate3_C_7


title: I2_plate3_C_8


title: I2_plate3_C_10


title: I2_plate3_C_4


title: esa1∆ sds3∆ rep3

city: La Jolla

first: Lorraine

last: Pillus

address: 9500 Gilman Drive

department: Biological Sciences

institute: UCSD

data_processing:
Library adaptors were trimmed computationally with Cutadapt
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Reads were mapped to Repbase, and any reads mapping to Repbase were removed from further analysis.
The remaining reads were mapped to SacCer3 with STAR.
Genome_build: SacCer3
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample.

organism: Saccharomyces cerevisiae

source_name: MATα W303 esa1∆::HIS3 sds3∆::natMX

growth_protocol: Cells were grown in SC media at 24˚ until reaching in mid- log-phase.

extract_protocol:
RNA was prepared in biological triplicate using hot-phenol extraction. RNA was DNase treated (Ambion) and quality was evaluated by both agarose-gel electrophoresis and bioanalyzer (Agilent).
Samples were depleted of rRNA (Ribo-zero Magnetic Gold Yeast, Epibio), and libraries prepared using standard Illumina methods (Tru-seq Stranded total RNA, Illumina)

tag: strain background

tag: genotype

value: esa1delta sds3delta


title: I2_plate3_C_2


title: esa1∆ epl1∆ sds3∆ rep3

source_name: MATα W303 esa1∆::^HIS3 epl1∆::kanMX sds3∆::natMX

value: esa1delta  epl1delta sds3delta


title: esa1∆ sds3∆ rep1


title: I2_plate3_C_1


title: esa1∆ sds3∆ rep2


title: esa1∆ epl1∆ sds3∆ rep1


title: I2_plate3_C_3


title: epl1∆ sds3∆ rep3

source_name: MATα W303 epl1∆::kanMX sds3∆::natMX

value: epl1delta sds3delta


title: I2_plate3_B_12


title: I2_plate3_B_11


title: epl1∆ sds3∆ rep1


title: I2_plate3_B_10


title: I2_plate3_D_3


title: epl1∆ sds3∆ rep2


title: WT rep3

value: WT


title: I2_plate3_B_9


title: I2_plate3_B_7


title: WT rep1


title: I2_plate3_B_8


title: esa1∆ epl1∆ sds3∆ rep2


title: Three-cell-type-3

city: Raleigh

first: Vincent

middle: L

last: Chiang

state: NC

address: 840 Main Campus Drive

department: Forestry and Environmental Resources

institute: North Carolina State University

description: Processed data file: Tissue_LCM_rawcount.txt

data_processing:
Twelve libraries with different index numbers were pooled by mixing equal quantities of DNA from each library and applied as one lane for HiSeq 2000 sequencing.
100 bp average read lengths were obtained after removing the library sequence index sequences from each read, reads were mapped to the reference P. trichocarpa genome release V3.0 (JGI Phytozome V11, https://phytozome.jgi.doe.gov/pz/portal.html) using the program "TOPHAT".
Genome_build: Populus trichocarpa v3.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa)
Supplementary_files_format_and_content: Tissue_LCM_rawcount.txt: Tab-delimited text file with Phytozome Populus trichocarpa gene model names (version 3) and the read counts.

organism: Populus trichocarpa

source_name: Combination of xylem fiber, vessel and ray cells

growth_protocol: P. trichocarpa trees were grown in ½ Mircle-Gro Soil (Scotts Miracle-Gro products, Maysville, OH, USA) and ½ Metro-Mix 200 (Sun Gro, Bellevue, WA, USA) in the greenhouse for 6 months (16 h light/8 h dark cycle with supplemental light of ~300 µE m-2 s-1) before tissue was harvested for characterization.

extract_protocol:
Total RNA was isolated using RNeasy Plant RNA isolation kit (Qiagen), and RNAs of LCM samples were amplified using Arcrurus RiboAmp HS PLUS kit (Life Technology).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Shoot tip samples were obtained from the first to third internode, leaf samples were fully expanded young leaves, phloem was scraped from inner part of the bark, and xylem samples were stem secondary developing xylem collected by scraping from surface of debarked stems as we did previously (Shi et al., 2010). Root samples were primary roots collected from young seedlings rooted in water. Cell samples containing fiber cells, vessel cells, or a mixture of three different cell types (fiber, vessel, and ray) were collected from 6-month-old greenhouse grown P. trichocarpa by using a LMD7000 (Leica).

tag: tissue

value: Xylem

tag: cell type

value: Combination of fiber, vessel and ray cells

value: 6 months


title: Vessel-3

source_name: Xylem vessel cells

value: Vessel cell


title: Three-cell-type-1


title: I2_plate3_B_5

tag: fsc-a

tag: fsc-w


title: I2_plate3_B_4

tag: fsc-h

tag: ssc-a


title: I2_plate3_B_6

tag: ssc-w

tag: ssc-h


title: I2_plate3_B_3

tag: lin

tag: facs time


title: Vessel-2


title: Fiber-3

source_name: Xylem fiber cells

value: Fiber cell


title: I2_plate3_B_1


title: I2_plate3_A_12


title: Vessel-1


title: Fiber-2


title: I2_plate3_A_11


title: I2_plate3_A_10


title: Xylem-2

source_name: Stem differentiating xylem

value: Stem differentiating xylem


title: Fiber-1


title: Xylem-3


title: I2_plate3_A_9

source_name: Lin-CD34+CD38- bone marrow


title: WT rep2


title: I2_plate3_A_8


title: I2_plate3_A_7


title: Root-2

source_name: Primary root

value: Primary root


title: I2_plate3_A_6


title: Root-1


title: I2_plate3_A_5


title: Three-cell-type-2


title: I2_plate3_A_3


title: Phloem-3

source_name: Phloem

value: Phloem


title: I2_plate3_A_4


title: Phloem-2


title: I2_plate3_A_2


title: Phloem-1


title: I2_plate3_B_2


title: I2_plate3_A_1


title: Leaf-3

source_name: Leaf

value: Leaf


title: Leaf-2


title: Leaf-1


title: Shoot-3

source_name: Shoot tip

value: Shoot tip


title: Shoot-2


title: Shoot-1


title: Xylem-1


title: Root-3


title: S-24

status: Public on Jan 18 2017

city: Lanzhou

first: Jinlin

last: Zhang

address: Tianshui South Road No.222

country: China

institute: Lanzhou Univeisity

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using release-20130225 with parameters--seqType fq --min_contig_length 100 --min_glue 3 --group_pairs_distance 250 --path_reinforcement_distance 85 --min_kmer_cov 3
Assembly and cluster were calculated by Trinity release-20130225 with parameters --seqType fq --min_contig_length 100  --min_glue 3 --group_pairs_distance 250 --path_reinforcement_distance 85 --min_kmer_cov 3 from Grabherr MG et al, Nature biotechnology.
Fragments Per kb per Million (FPKM) fragments were calculated by using SOAP Release 2.21 software with parameters -m 0 -x 500 -s 40 -l 35 -v 5 -r 2 from Ali Mortazavi et al. Nature Methods, 2008.
For gene expression analysis, the number of clean tags for each gene was calculated and normalized to the number of transcripts per million (TPM) tags (Xue et al, 2010).

organism: Haloxylon ammodendron

source_name: Plant shoot

growth_protocol: Seeds of Haloxylon ammodendron, collected from Alxa League, Inner Mongolia, China, were surface sterilized for 5 min with 75% (v/v) ethanol solution followed by 5 times of rinsing with sterile water and then placed on the filter paper, with 25± 2°C in the dark for 12h. After germination, uniform seedlings were transplanted to plugged holes (5 × 5×5 cm; one seedling/hole) in plastic containers containing heat-sterilized vermiculite and 1/2 Hoagland nutrient solution for growth in a greenhouse with temperature of 28 ± 2°C/23 ± 2°C (day/night), the daily photoperiod of 16h/d, the flux density of 1200 µmolm−2s−1 and the relative humidity of 50-70%. Solutions were changed once every three days to maintain constant nutrient concentrations.

extract_protocol:
Total RNA was extracted three times from the six samples (shoot and root treated with sorbitol for 0, 6h and 24h), respectively, using the RNeasy Plant Mini Kit (Qiagen). The quality of total RNA was checked using the Nano Drop Spectrometer (ND-1000 Spectrophotometer, Peqlab).
To acquire a global overview of transcriptome in Haloxylon ammodendron, equivalent amount of total RNA isolated from shoots and roots were pooled, respectively. The two pooled mRNA were used to create the final two cDNA library in shoots and root. Finally, the cDNA libraries was sequenced on the Illumina HiSeq™2000 platform in BGI Shenzhen, respectively.

treatment_protocol: Eight-week-old Haloxylon ammodendron seedlings were treated with 1/2 Hoagland nutrient solution supplemented with 0.4% sorbitol to maintain the osmotic potential as −0.75 MPa or no sorbitol for control. Shoot and root samples were harvested 0, 6h and 24h after treatments, frozen in liquid nitrogen and stored at -80 °C for RNA-seq, qRT-PCR and physiological analyses.

value: shoot

tag: treatment

value: with 0.4% sorbitol  treatment for 24h


title: R-6

source_name: Plant root

value: root

value: with 0.4% sorbitol treatment for 6h


title: S-0

value: with 0.4% sorbitol  treatment for 0h


title: S1

value: mix of shoot samples treated with 0.4% sorbitol treatment for 0, 6 and 24 h


title: R1

value: mix of root samples treated with 0.4% sorbitol treatment for 0, 6 and 24 h


title: Bulk_unstimulated_ZAP70_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA ZAP70_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz

data_processing:
Single-cell sequencing: Data were processed using the Drop-seq Tools v1.12 software (Macosko et al, 2015). Briefly, each transcriptome Read 2 was tagged with the cell barcode (bases 1 to 12) and UMI (unique molecular identifier) barcode (bases 13 to 20) obtained from Read 1, trimmed for sequencing adapters and poly-A sequences, and aligned using STAR v2.4.0 15 to the human reference genome assembly (Ensembl GRCm38/GRCh38 release) containing artificial chromosomes that represent the CROPseq-Guide-Puro plasmid construct (250 bp common U6 promoter sequence, one gRNA sequence per artificial chromosome (20 bp), and the remaining 260 bp downstream plasmid backbone until the poly-A sequence). Cell barcodes were corrected for possible bead synthesis errors, allowing the removal of up to 4 bases using the DetectBeadSynthesisErrors tool from the Drop-seq Tools v1.12 software. Reads aligning to exons were tagged with the respective gene name, and counts of unique UMIs per gene within each cell were used to build a digital gene expression matrix for cells with counts for at least 500 genes. This matrix was converted to transcripts per million and log-transformed for further analysis. We excluded genes coding from ribosomal proteins from the analysis as we suspect their widespread detection is caused by solubilization of their mRNAs as noted previously (Macosko et al, 2015). For the assignment of gRNAs to cells, we quantified the overlap of reads to the specific gRNA sequence within the CROPseq-Guide-Puro plasmid chromosomes and assigned the most abundant gRNA to the respective cell.
Bulk RNA sequencing data: Reads were trimmed with Trimmomatic and aligned to the GRCh38 assembly of the human genome using Bowtie1 with the following parameters: -q -p 6 -a -m 100 -minins 0 maxins 5000 –fr –sam -chunkmbs 200. Duplicate reads were removed with Picard’s MarkDuplicates utility with standard parameters before transcript quantification with BitSeq 18 using the Markov chain Monte Carlo method and standard parameters. To obtain gene-level quantifications, we assigned the expression values of its highest expressed transcript to each gene.
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated values (CSV) files with genes as rows and samples/cells as columns. For the file with the single-cell expression values, we added 4 metadata header rows (stimulation condition, microfluidics run ("replicate"), cell barcode, assigned gRNA, targeted gene), which refer to the respective cells. The "replicate" field indicates the run referenced in the sample title.

source_name: Jurkat cells

growth_protocol: Jurkat cells stably expressing SpCas9 (after transduction with lentiCas9-Blast, Addgene #52962) were kept in RPMI medium + 10% FCS + penicillin/streptomycin containing 25 μg/ml blasticidin. After transduction with gRNA-encoding lentiviral particles (CROPseq-Guide-Puro), cells were selected with 2 μg/ml puromycin for 10 days, while keeping up the selection for blasticidin, and then used in T cell receptor stimulation experiments followed by CROP-seq (or bulk RNA-seq on single knockout lines for validation).

extract_protocol:
CROP-seq: Adherent cells were detached using Trypsin-EDTA (Gibco #25300-054), following standard cell culture practices. Cells were collected by centrifugation at 300 rcf for 5 min, washed once with PBS-0.01% BSA (freshly prepared on the day of the run), and resuspended in 1 ml of PBS-0.01% BSA. Cells were filtered through a 40 µm cell strainer to obtain a suspension of single-cells, which were counted using a CASY device. Single cells were then co-encapsulated with barcoded beads (ChemGenes #Macosko-2011-10) using an Aquapel-coated PDMS microfluidic device (FlowJEM), connected to syringe pumps (kdScientific) via polyethylene tubing with an inner diameter of 0.38 mm (Scicominc #BB31695-PE/2). Cells were supplied in PBS-0.01% BSA at a concentration of 220 cells/µl, barcoded beads were resuspended in Drop-seq lysis buffer at a concentration of 150 beads/µl. The flow rates for cells and beads were set to 1.6 ml/hour, while Droplet Generation Oil (BioRad #1864006) was run at 8 ml/hour. During the run, the barcoded bead solution was mixed by magnetic stirring with a mixing disk set to 1 jump/s. A typical run lasted between 35 and 40 min. In case of multiple runs per day, droplets were intermittently stored at 4 °C and processed together. Our most important modification to the protocol is an alternative way to break droplets, which recovers beads much more efficiently than in the original publication of Drop-seq (Macosko et al., 2015). After removing as much oil below the droplet layer as possible, we added 30 ml of 6x SSC buffer (Promega #V4261) and 1 ml of Perfluoroctanol (Sigma Aldrich #370533-25G) and shook the tube forcefully 6 times to break the droplets. Based on their large diameter, beads were then collected by syringe-filtering the solution through a 0.22 µm filter unit (Merck #SLGV033RS), washing 2x with 20 ml of 6x SSC buffer and eluting by turning the filter upside down and rinsing it with 3x 10 ml of 6x SSC buffer. Beads were then collected by centrifugation at 1,250 rcf for 2 min, setting the brake speed to 50%. After washing a second time with 10 ml 6x SSC, the pellet was taken up in 200 µl of 5x RT buffer and transferred to a 1.5 ml tube. Bulk RNA-seq: Total RNA was extracted using the Qiagen AllPrep Kit (Qiagen #80311).
CROP-seq: Reverse transcription and Exonuclease I treatment were performed as described in the original publication, and the number of barcoded beads was estimated using a Fuchs-Rosenthal counting chamber (mixing the bead suspension with 6x DNA loading dye). Depending on the performance of the experiment, we prepared up to 24 PCR reactions per Drop-seq run, adding 4,400 beads (~220 cells) per PCR and enriching the cDNA for 4 + 10 cycles, using the already described reagents. We then prepared Drop-seq libraries using the Nextera XT kit (Illumina #15032350), starting from 1 ng of cDNA pooled in equal amounts from all PCR reactions for a given run. We typically required an additional 10 enrichment cycles, using the Illumina Nextera XT i7 primers along with the Drop-seq New-P5 SMART-PCR hybrid oligo. The slightly increased cDNA input typically results in an average size distribution of about 575 bp. After quality control, libraries were sequenced with paired-end SBS chemistry on Illumina HiSeq 3000/4000 instruments. Drop-seq Custom Read1 Primer was spiked into the HP10 primer solution, located in column 11 of the cBot Reagent Plate at 1µM final concentration. High sequence complexity needed for optimal base calling performance was achieved by adding 20-30% PhiX as spike-in. Cluster generation and Read 1 primer hybridization were completed using cBot protocol ‘HiSeq_3000_4000_HD_Exclusion_Amp_v1.0’. Alternatively, libraries were sequenced on an Illumina NextSeq 550 instrument using the 75 cycle High Output Kit. We loaded 1.8 pM library and provided Drop-seq Custom Read1 Primer at 0.3 µM in position 7 of the reagent cartridge. On NextSeq machines, we sequenced without PhiX spike-in, using a read configuration of 20 bases (Read1), 8 bases (Index) and 64 bases (Read2); Bulk RNA-seq: Bulk RNA-seq libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen #015.96) according to the manufacturer's instructions.

treatment_protocol: Jurkat cells were serum-starved for 3 hours prior to stimulation. They were stimulated with 1 µg/ml anti-CD3 (eBioscience #16-0037) and 1 µg/ml anti-CD28 antibody (eBioscience #16-0289-81) for 4 hours while under starvation and then subjected to CROP-seq. The unstimulated (naïve) control was subjected to continued starvation.

tag: cell line

value: Jurkat

tag: library

value: RNA-seq

tag: experiment

tag: condition

value: naive

tag: knockout

tag: grna


title: CROP-seq_HEK293T

description: Single-cell RNA-seq on HEK293T cell lines mixed in equal proportions knocked out for MBD1, TET2 and DNMT3B

data_processing:
Single-cell sequencing: Data were processed using the Drop-seq Tools v1.12 software (Macosko et al, 2015). Briefly, each transcriptome Read 2 was tagged with the cell barcode (bases 1 to 12) and UMI (unique molecular identifier) barcode (bases 13 to 20) obtained from Read 1, trimmed for sequencing adapters and poly-A sequences, and aligned using STAR v2.4.0 15 to the human reference genome assembly (Ensembl GRCm38/GRCh38 release) containing artificial chromosomes that represent the CROPseq-Guide-Puro plasmid construct (250 bp common U6 promoter sequence, one gRNA sequence per artificial chromosome (20 bp), and the remaining 260 bp downstream plasmid backbone until the poly-A sequence). Cell barcodes were corrected for possible bead synthesis errors, allowing the removal of up to 4 bases using the DetectBeadSynthesisErrors tool from the Drop-seq Tools v1.12 software. Reads aligning to exons were tagged with the respective gene name, and counts of unique UMIs per gene within each cell were used to build a digital gene expression matrix for cells with counts for at least 500 genes. This matrix was converted to transcripts per million and log-transformed for further analysis. We excluded genes coding from ribosomal proteins from the analysis as we suspect their widespread detection is caused by solubilization of their mRNAs as noted previously (Macosko et al, 2015). For the assignment of gRNAs to cells, we quantified the overlap of reads to the specific gRNA sequence within the CROPseq-Guide-Puro plasmid chromosomes and assigned the most abundant gRNA to the respective cell.
Bulk RNA sequencing data: Reads were trimmed with Trimmomatic and aligned to the GRCh38 assembly of the human genome using Bowtie1 with the following parameters: -q -p 6 -a -m 100 -minins 0 maxins 5000 –fr –sam -chunkmbs 200. Duplicate reads were removed with Picard’s MarkDuplicates utility with standard parameters before transcript quantification with BitSeq 18 using the Markov chain Monte Carlo method and standard parameters. To obtain gene-level quantifications, we assigned the expression values of its highest expressed transcript to each gene.
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated values (CSV) files with genes as rows and samples/cells as columns. For the file with the single-cell expression values, we added 4 metadata header rows (stimulation condition, microfluidics run, cell barcode, assigned gRNA, targeted gene), which refer to the respective cells.

source_name: HEK293T cells

value: CROP-seq


title: Bulk_unstimulated_RUNX2_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA RUNX2_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_RUNX2_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA RUNX2_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_RELA_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA RELA_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz

value: RELA


title: Bulk_unstimulated_RELA_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA RELA_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_PTPN6_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA PTPN6_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_PTPN11_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA PTPN11_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_PTPN6_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA PTPN6_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_NR4A1_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA NR4A1_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_NFKB2_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA NFKB2_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_NFKB2_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA NFKB2_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: R-24

tag: tissue


title: S-6

value: with 0.4% sorbitol  treatment for 6h


title: Bulk_unstimulated_NFAT5_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA NFAT5_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_NFKB1_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA NFKB1_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_NFATC1_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA NFATC1_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_NFKB1_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA NFKB1_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_NFAT5_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA NFAT5_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_LCK_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA LCK_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz

value: LCK


title: Bulk_unstimulated_LAT_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA LAT_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz

value: LAT


title: Bulk_unstimulated_LAT_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA LAT_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_JUND_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA JUND_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz

value: JUND


title: Bulk_unstimulated_PTPN11_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA PTPN11_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_JUND_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA JUND_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_JUN_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA JUN_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz

value: JUN


title: Bulk_unstimulated_EGR4_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA EGR4_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_FOS_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA FOS_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz

value: FOS


title: Bulk_unstimulated_EGR2_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA EGR2_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_EGR3_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA EGR3_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_EGR4_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA EGR4_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_EGR3_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA EGR3_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: R-0


title: Bulk_unstimulated_EGR2_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA EGR2_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_NFATC1_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA NFATC1_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_LCK_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA LCK_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_EGR1_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA EGR1_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_EGR1_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA EGR1_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_DOK2_2

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA DOK2_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_DOK2_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA DOK2_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_CTRL00320

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA CTRL00320
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_CTRL00196

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA CTRL00196
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_CTRL00275

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA CTRL00275
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_CTRL00080

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA CTRL00080
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_CTRL00096

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA CTRL00096
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_CTRL00022

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA CTRL00022
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_CTRL00018

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA CTRL00018
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_FOS_1

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA FOS_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_RUNX2_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA RUNX2_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_RELA_1

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA RELA_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_RELA_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA RELA_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_PTPN11_1

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA PTPN11_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_NR4A1_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA NR4A1_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_PTPN6_1

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA PTPN6_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_NFKB2_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA NFKB2_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_NFKB1_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA NFKB1_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_NFATC1_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA NFATC1_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_NR4A1_1

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA NR4A1_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_NFKB2_1

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA NFKB2_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_NFATC1_1

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA NFATC1_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_NFAT5_1

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA NFAT5_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_LCK_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA LCK_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_unstimulated_CTRL00087

description:
RNA-seq on a bulk population of Jurkat cells transduced with gRNA CTRL00087
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_LCK_1

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA LCK_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_LAT_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA LAT_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_LAT_1

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA LAT_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_JUND_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA JUND_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_JUN_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA JUN_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_JUND_1

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA JUND_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_JUN_1

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA JUN_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_FOS_1

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA FOS_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_FOS_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA FOS_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_PTPN6_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA PTPN6_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_EGR3_1

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA EGR3_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_EGR2_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA EGR2_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Drop-seq_HEK293T-3T3

description: Single-cell RNA-seq on Human HEK293T and Mouse 3T3 cell lines mixed in equal proportions

organism:
Homo sapiens
Mus musculus

source_name: Human HEK293T and Mouse 3T3 cells mixed 1:1

value: HEK293T and 3T3

value: Drop-seq


title: Bulk_stimulated_EGR3_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA EGR3_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_EGR1_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA EGR1_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_EGR2_1

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA EGR2_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_PTPN11_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA PTPN11_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_EGR1_1

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA EGR1_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_NFAT5_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA NFAT5_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: MEP_M34_KO_15

city: Martinsried

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

country: Germany

institute: Ludwig-Maximilians University Munich

description: processed data file: MEP.counts.txt

data_processing:
Sequencing reads were demultiplexed from the Nextera (i5 and i7) indices using deML (Renaud 2014, Bioinformatics)
Demultiplexed reads were aligned to the mouse genome mm10 and ERCC reference using NextGenMap (Sedlazeck et al., 2013)
Count data was generated from mapped reads using featureCounts (Liao et al., 2014) on ENSEMBL gene models (GRCm38.74)
Genome_build: mm10
Supplementary_files_format_and_content: gene-wise count data in tab delimited text file, available on the series record.

source_name: MEP hematopoetic stem cell

extract_protocol:
Liver single cell suspensions by homogenization of fetal liver tissue with a 1ml Eppendorf pipette and Hank ́s buffered salt solution (HBSS) with 3% foetal calf serum (FCS) were prepared. Cells were then stained with anti-CD45.2-FITC (BD Pharmingen), biotinylated lineage antibodies (anti-B220, -CD3,Gr-1, and -Ter-119; all BD), anti-Mac1/CD11b-eFluor 450 (eBioscience), anti-CD117/c-kit-Alexa Fluor®780 (eBioscience) and anti-Sca-1-PeCy7 (eBioscience). Biotinylated monoclonal antibodies were labeled by incubation with Streptavidin-PerCP/PerCP-Cy5.5 (eBioscience) and cells sorted directly into lysis buffer (0.2%TritonX supplemented with RNAse Inhibitor (Promega))
RNA was cleaned-up from the crude lysate with Agencourt RNAclean XP SPRI beads (Beckman-Coulter). cDNA was synthesized and pre-amplified from 5 μ l of lysate as described in Picelli et al 2014 (Smart-seq2). 0.7 ng of pre-amplified cDNA was used as input for tagmentation by the Nextera XT Sample Preparation Kit (Illumina), where a second amplification round was performed for 12 cycles. For each sample, 5 ng of final library was pooled.

tag: strain

tag: Sex

value: not determined

tag: developmental stage

value: fetus

value: liver

tag: age

tag: genotype

value: Smarcd2 -/-

tag: cell markers


title: MEP_M34_KO_13

description: processed data file: MEP.counts.txt


title: MEP_M33_WT_12

description: processed data file: MEP.counts.txt

value: WT


title: Bulk_stimulated_DOK2_2

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA DOK2_2
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz

value: Jurkat

value: RNA-seq


title: Bulk_stimulated_CTRL00275

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA CTRL00275
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_DOK2_1

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA DOK2_1
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_CTRL00320

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA CTRL00320
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_CTRL00196

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA CTRL00196
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: MEP_M33_KO_11

description: processed data file: MEP.counts.txt


title: Bulk_stimulated_CTRL00096

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA CTRL00096
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: Bulk_stimulated_CTRL00087

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA CTRL00087
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: MEP_M33_Het_9

description: processed data file: MEP.counts.txt

value: Smarcd2 +/-


title: Bulk_stimulated_CTRL00080

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA CTRL00080
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: MEP_M33_Het_8

description: processed data file: MEP.counts.txt


title: Bulk_stimulated_CTRL00018

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA CTRL00018
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz


title: MEP_M33_Het_10

description: processed data file: MEP.counts.txt


title: MEP_M32_WT_5

description: processed data file: MEP.counts.txt


title: MEP_M32_WT_2

description: processed data file: MEP.counts.txt


title: KO-24h

city: Beijing

first: Xin

last: Lin

address: Haidian Qu Tsinghua yuan

institute: Tsinghua University

description: q5 in gene_exp. Diff

data_processing:
The filtered reads were aligned to the mouse most recent genome reference mm10 by using TopHat (version 2.1.0)
the BAM files of each individual alignment were used to analyze genes differential expression by using Cufflinks (version 2.2.1)
Supplementary_files_format_and_content: diff files

source_name: Macrophages

growth_protocol: Bone marrows cells were cultured for 6 days in DMEM supplemented with 10% FBS and 10% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor to generate

extract_protocol:
Cell supernatant were remove, wasded with PBS twice and TRIZOl were added to extract the total cell mRNA
Sequencing libraries were generated using NEBNext UltraTM Directional RNA Library Prep Kit for Illumina

treatment_protocol: C. albicans were heat-inactivaed and add to BMDMs for 24 hours for stimulation at MOI=10

tag: cell type

value: Bone marrow-derived macrophages

tag: genotype/variation

value: JNK1 knockout

value: Stimulated with yeast form Candida albicans for 24 hour


title: KO-0h

description: q4 in gene_exp. Diff

value: Untreated


title: CROP-seq_Jurkat_TCR_stimulated_run1

description:
Single-cell RNA-seq on Jurkat cells treated with anti-CD3/CD28 antibodies and infected with a population of gRNAs (CROP-seq) targeting components of TCR signaling and control gRNAs; Microfluidic run number 1
processed data file: CROP-seq_Jurkat_TCR.digital_expression.csv.gz

data_processing:
Library strategy: CROP-seq
Single-cell sequencing: Data were processed using the Drop-seq Tools v1.12 software (Macosko et al, 2015). Briefly, each transcriptome Read 2 was tagged with the cell barcode (bases 1 to 12) and UMI (unique molecular identifier) barcode (bases 13 to 20) obtained from Read 1, trimmed for sequencing adapters and poly-A sequences, and aligned using STAR v2.4.0 15 to the human reference genome assembly (Ensembl GRCm38/GRCh38 release) containing artificial chromosomes that represent the CROPseq-Guide-Puro plasmid construct (250 bp common U6 promoter sequence, one gRNA sequence per artificial chromosome (20 bp), and the remaining 260 bp downstream plasmid backbone until the poly-A sequence). Cell barcodes were corrected for possible bead synthesis errors, allowing the removal of up to 4 bases using the DetectBeadSynthesisErrors tool from the Drop-seq Tools v1.12 software. Reads aligning to exons were tagged with the respective gene name, and counts of unique UMIs per gene within each cell were used to build a digital gene expression matrix for cells with counts for at least 500 genes. This matrix was converted to transcripts per million and log-transformed for further analysis. We excluded genes coding from ribosomal proteins from the analysis as we suspect their widespread detection is caused by solubilization of their mRNAs as noted previously (Macosko et al, 2015). For the assignment of gRNAs to cells, we quantified the overlap of reads to the specific gRNA sequence within the CROPseq-Guide-Puro plasmid chromosomes and assigned the most abundant gRNA to the respective cell.
Bulk RNA sequencing data: Reads were trimmed with Trimmomatic and aligned to the GRCh38 assembly of the human genome using Bowtie1 with the following parameters: -q -p 6 -a -m 100 -minins 0 maxins 5000 –fr –sam -chunkmbs 200. Duplicate reads were removed with Picard’s MarkDuplicates utility with standard parameters before transcript quantification with BitSeq 18 using the Markov chain Monte Carlo method and standard parameters. To obtain gene-level quantifications, we assigned the expression values of its highest expressed transcript to each gene.
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated values (CSV) files with genes as rows and samples/cells as columns. For the file with the single-cell expression values, we added 4 metadata header rows (stimulation condition, microfluidics run ("replicate"), cell barcode, assigned gRNA, targeted gene), which refer to the respective cells. The "replicate" field indicates the run referenced in the sample title.

value: CROP-seq

value: diverse, each knockout applied on single-cell basis (see processed data file)

value: diverse, each gRNA applied on single-cell basis (see processed data file)


title: CROP-seq_Jurkat_TCR_stimulated_run2

description:
Single-cell RNA-seq on Jurkat cells treated with anti-CD3/CD28 antibodies and infected with a population of gRNAs (CROP-seq) targeting components of TCR signaling and control gRNAs; Microfluidic run number 2
processed data file: CROP-seq_Jurkat_TCR.digital_expression.csv.gz


title: WT-48h

description: q3 in gene_exp. Diff

value: Wild type

value: Stimulated with yeast form Candida albicans for 48 hour


title: KO-48h

description: q6 in gene_exp. Diff


title: CROP-seq_Jurkat_TCR_unstimulated_run1

description:
Single-cell RNA-seq on Jurkat cells infected with a population of gRNAs (CROP-seq) targeting components of TCR signaling and control gRNAs; Microfluidic run number 1
processed data file: CROP-seq_Jurkat_TCR.digital_expression.csv.gz

value: naive


title: MEP_M32_Het_4

description: processed data file: MEP.counts.txt

value: not determined

value: fetus


title: MEP_M32_Het_7

description: processed data file: MEP.counts.txt

value: liver


title: WT-0h

description: q1 in gene_exp. diff


title: WT-24h

description: q2  in gene_exp.diff


title: pfsgrnaS4

city: Armilla

first: Elena

last: Gómez-Díaz

state: Granada

address: Avda. del Conocimiento, 17

department: Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN)

institute: Spanish National Research Council (CSIC)

data_processing:
Reads were trimmed using FASTX-Toolkit based on quality scores on both ends.
ChIP-seq reads were aligned to the Pf3D7 (v25.0) genome assembly using Bowtie version 1.0.0 with the following configuration: -t -m 1
Peak calling of histone modification marks was performed using MACS version 1.4 with the following configuration: -f SAM -g 2.29e+7 -p 1e-5 -s 50 -w --single-profile.
RNA-seq reads were aligned to the PF3D7 (v25.0) genome assembly using TopHat version 2.0.10 with the following configuration: -p 8 --bowtie1  --segment-length 20 --library-type=fr-firststrand --min-intron-length 5 --max-intron-length 1000 -G
Transcript counts per gene were obtained using HTSeq with the following configuration: htseq-count -f bam --stranded=yes -m intersection-nonempty -i ID (Sense), and htseq-count -f bam --stranded=reverse -m intersection-nonempty -i ID (Antisense)
Differential expression on exons was performed using DEXSeq using HTSeq counts considering both paired and unpaired mapped reads
Genome_build: Pf3D7 v25.0 (PlasmoDB)
Supplementary_files_format_and_content: Wig files were generated using MACS 1.4
Supplementary_files_format_and_content: Gene expression normalized count files were generated using HTSeq, DESeq2 and DEXSeq

organism: Plasmodium falciparum

source_name: Pf salivary glands sporozoites

extract_protocol:
Illumina libraries were prepared and sequenced at the HudsonAlpha Institute for Biotechnology, using an Illumina HiSeq2000 sequencer. Standard directional RNA-seq library construction, 50 bp paired end reads with ribosomal reduction (RiboMinus™ Eukaryote Kit, Ambion®).
Total RNA was extracted from fresh mosquito tissues (~50 midguts and ~ 50 salivary glands) using the mirVana™ RNA Isolation Kit (Ambion®) according to the manufacturer’s protocol.  Nuclei extraction was performed on formaldehid fixed tissues (~50 midguts and ~ 50 salivary glands) followed by chromatin immunoprecipitation according to previously published protocols.

treatment_protocol: A. gambiae mosquitoes were maintained under standard insectary conditions (27 ± 2°C, 70 ± 5% relative humidity, 12:12 LD). Two independent experimental infections, biological replicates, were carried out by membrane blood feeding in the laboratory on gametocyte-infected blood from malaria patients in Burkina Faso. Dissection of the midguts and the salivary glands was performed on adult females aged 3-4 days. Tissues were maintained in ice-cold Schneider’s insect culture medium (Sigma-Aldrich) to avoid degradation, and fresh tissues were immediately processed for chromatin and RNA analyses.

value: Anopheles coluzzii infected salivary glands

value: natural isolate


title: pfbloodrnaS1

source_name: Pf blood asexual stages

value: Anopheles gambiae infected blood


title: pfbloodrnaS4

value: Anopheles coluzzii infected blood


title: pfbloodrnaS3


title: pfsgrnaS3

value: Anopheles gambiae infected salivary glands


title: MEP_M32_Het_3

description: processed data file: MEP.counts.txt

value: Smarcd2 +/-


title: Bulk_stimulated_CTRL00022

description:
RNA-seq on a bulk population of Jurkat cells treated with anti-CD3/CD28 antibodies and transduced with gRNA CTRL00022
processed data file: CROP-seq_Jurkat_TCR.count_matrix.csv.gz

value: Jurkat

value: RNA-seq


title: MEP_M32_Het_1

description: processed data file: MEP.counts.txt


title: CROP-seq_Jurkat_TCR_unstimulated_run2

description:
Single-cell RNA-seq on Jurkat cells infected with a population of gRNAs (CROP-seq) targeting components of TCR signaling and control gRNAs; Microfluidic run number 2
processed data file: CROP-seq_Jurkat_TCR.digital_expression.csv.gz

value: CROP-seq


title: MEP_M32_KO_6

description: processed data file: MEP.counts.txt

value: Smarcd2 -/-


title: pfmgrnaS4

source_name: Pf midgut oocysts

value: Anopheles coluzzii infected midguts


title: pfmgrnaS2

value: Anopheles gambiae infected midguts


title: pfmgrnaS1


title: pfsgrnaS1


title: pfbloodrnaS2


title: GMP_M34_KO_13

description: processed data file: GMP.counts.txt

source_name: GMP hematopoetic stem cell


title: GMP_M33_WT_12

description: processed data file: GMP.counts.txt

value: WT


title: pfsgrnaS2


title: psgh3k27ac

description: Chromatin IP against H3K27ac

extract_protocol:
Sequencing libraries were prepared following the protocol described by Bowman et al. BMC Genomics 2013, 14:466  doi:10.1186/1471-2164-14-4662013. ChIP libraries were sequenced at the HudsonAlpha Institute for Biotechnology using an Illumina HiSeq2000 sequencer.
Total RNA was extracted from fresh mosquito tissues (~50 midguts and ~ 50 salivary glands) using the mirVana™ RNA Isolation Kit (Ambion®) according to the manufacturer’s protocol.  Nuclei extraction was performed on formaldehid fixed tissues (~50 midguts and ~ 50 salivary glands) followed by chromatin immunoprecipitation according to previously published protocols.

tag: chip antibody

value: H3K27ac (Abcam ab4729)


title: GMP_M33_Het_9

description: processed data file: GMP.counts.txt

value: not determined


title: pfsgh3k4me3

description: Chromatin IP against H3K4me3

value: H3K4me3 (Abcam ab8580)


title: psginput

description: Input Control


title: GMP_M33_Het_8

description: processed data file: GMP.counts.txt

value: fetus

value: liver


title: GMP_M33_Het_10

description: processed data file: GMP.counts.txt


title: pfsgh3k9ac

description: Chromatin IP against H3K9ac

value: natural isolate

value: H3K9ac (Millipore #07-352)


title: GMP_M34_KO_15

description: processed data file: GMP.counts.txt


title: pmgh3k27ac

description: Chromatin IP against H3K27ac


title: pfmgh3k9ac

description: Chromatin IP against H3K9ac


title: pfmgh3k9me3

description: Chromatin IP against H3K9me3

value: H3K9me3 (Abcam ab8898)


title: pmginput

description: Input Control


title: pfmgh3k4me3

description: Chromatin IP against H3K4me3


title: GMP_M32_WT_5

description: processed data file: GMP.counts.txt


title: GMP_M32_KO_6

description: processed data file: GMP.counts.txt


title: GMP_M32_WT_2

description: processed data file: GMP.counts.txt


title: GMP_M32_Het_7

description: processed data file: GMP.counts.txt


title: CMP_M34_KO_15

description: processed data file: CMP.counts.txt

source_name: CMP hematopoetic stem cell


title: GMP_M32_Het_1

description: processed data file: GMP.counts.txt


title: GMP_M32_Het_4

description: processed data file: GMP.counts.txt


title: CMP_M33_KO_11

description: processed data file: CMP.counts.txt


title: GMP_M32_Het_3

description: processed data file: GMP.counts.txt


title: CMP_M33_Het_8

description: processed data file: CMP.counts.txt


title: CMP_M33_WT_12

description: processed data file: CMP.counts.txt


title: CMP_M34_KO_13

description: processed data file: CMP.counts.txt


title: CMP_M33_Het_10

description: processed data file: CMP.counts.txt


title: pfsgh3k9me3

description: Chromatin IP against H3K9me3

value: Anopheles gambiae infected salivary glands


title: CMP_M32_WT_5

description: processed data file: CMP.counts.txt


title: CMP_M32_WT_2

description: processed data file: CMP.counts.txt


title: CMP_M32_Het_4

description: processed data file: CMP.counts.txt

value: Smarcd2 +/-


title: CMP_M32_KO_6

description: processed data file: CMP.counts.txt


title: CMP_M32_Het_7

description: processed data file: CMP.counts.txt