title: siE1A_ATACseq

data_processing:
Reads were aligned to hg19 reference genome using bowtie2
Macs14 was used for calling peaks with the following parameters: --space=50 --keep-dup all --nomodel -p 1e-6
wiggle files were generated using Macs14 and converted to bigwig
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
ATAC-seq (Omni-ATAC protocol) was performed as described in Corces et al. 2017. HEK293 cells siRNA transfected for 4 days were lifted from plates using Accutase (Innovative Cell Technologies, Inc.) and 50,000 viable cells were gently pelleted at 500 RCF 4°C for 5min and resuspended in 50 uL cold ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. Cells were incubated on ice for 3min then washed with 1 ml of cold ATAC-RSB containing 0.1% Tween-20 to lyse plasma membranes. Nuclei were gently pelleted at 500 RCF for 10min at 4°C and resuspended in 50 uL of transposition mixture: 25 uL 2x TD buffer and 2.5 uL transposase (both supplied in the Nextera DNA Library Prep Kit), 16.5 uL PBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, 5 uL H2O. DNA was isolated using DNA Clean and Concentrator-5 Kit (Zymo cat# D4014) and eluted in 21uL of elution buffer.
20uL of eluted DNA was amplified for 5 cycles Amplify for 5 cycles using NEBNext 2x MasterMix with 25uM primer Ad1 + 25uM primer Ad2 or 25uM Ad1 + 25uM Ad3. Refer to Corces et al. 2017 for PCR protocol and primer sequences. 5uL of preamplified sample was used in qPCR to determine additional cycles needed.


title: Cortex1.CCKVLANXX.SM2_042518p4_A2

status: Public on Jun 01 2019

type: SRA

city: Cambridge

first: Aviv

last: Regev

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

country: USA

institute: Broad Institute

description:
scRNA-seq
full-length
cortex_mm10_count_matrix.mtx, cortex_mm10_gene.tsv, cortex_mm10_cell.tsv

library_source: transcriptomic

data_processing:
For scRNA-seq and snRNA-seq data, scumi v0.1.0 (https://bitbucket.org/jerry00/scumi-dev/src/master/) was used to produce cell by gene sparse matrices (UMI count matrices for 3'-end methods and read count matrices for Smart-seq2). More specifically, STAR v2.6.1a was used for alignment except for Smart-seq2 and CEL-Seq2 data where HISAT v2.0.5 was used. featureCounts from the Subread package, v1.6.2 was used to tag each alignment with a gene tag. For bulk RNA-Seq data, reads were mapped to the reference genomes using Bowtie v0.12.9, and further quantified by RSEM v1.3.0 to generate transcripts per million values.
Genome_build: scRNA-seq data: a merged hg19 and mm10 geome for human and mouse mixture datasets, hg38 (GRCh38) for human PBMCs, and mm10 for mouse cortex data; bulk RNA-Seq data, hg38 (GRCh38) for human data and mm10 for mouse data
Supplementary_files_format_and_content: scRNA-seq data: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary_files_format_and_content: scRNA-seq data: cell.tsv, cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: scRNA-seq data: gene.tsv, gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: Bulk RNA-Seq data: TPM_bulk.tsv, tab-delimited text files of transcripts per million measurements of genes in each sample
Supplementary_files_format_and_content: mixture_hg19_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: mixture_hg19_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: mixture_hg19_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_count_matrix.mtx :A gene by cell count matrix in the matrix market format
Supplementary_files_format_and_content: pbmc_hg38_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: cortex_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: HEK293_PBMC_TPM_bulk.tsv :A matrix of transcripts per million measurements
Supplementary_files_format_and_content: NIH3T3_cortex_TPM_bulk.tsv :A matrix of transcripts per million measurements

molecule: total RNA

organism: Mus musculus

source_name: Cortex

extract_protocol:
Total RNA from bulk samples was extracted using Quick-RNA Mini Prep (Zymo Research) following the vendor protocol with a DNase treatment step
For library construction methods, see SAMPLES, description: Library Construction field. For details see the Methods section in the manuscript

tag: Sex

value: Male

tag: age

value: one month

tag: strain

tag: library construction


title: Tuberculosis 951

type: genomic

city: Beijing

first: Yong-Biao

last: Zhang

state: Select a State or Province

address: Beichen west road 1#

country: China

institute: Beijing Institute of Genomics

description: Genomic DNAs extracted from whole blood were genotyped using Illumina human Omni-zhonghua chips

hyb_protocol: according to the manufacturer’s specifications

scan_protocol: chips were scanned using iScan instrument

data_processing: We used Genomestudio to call the genotypes of SNPs, and performed association study using plink.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Tuberculosis

growth_protocol: Extraction of genomic DNA from blood was performed using proteinase K and repeated phenol-chloroform extraction.

extract_protocol: genomic DNAs were extracted with DNA-extraction kits (Tiangen Biotech, Beijing, China)

treatment_protocol: the whole-blood was stored in -80 refrigerator

tag: tissue

value: Blood


title: Tuberculosis 950

label_protocol: according to the manufacturer’s specifications


title: Tuberculosis 952


title: Tuberculosis 949


title: Cortex1.CCKVLANXX.SM2_042518p4_A1


title: Tuberculosis 960


title: Tuberculosis 948


title: Tuberculosis 947


title: Tuberculosis 946


title: Tuberculosis 957


title: Cortex1.CCKVLANXX.SM2_042518p4_A12


title: Cortex1.CCKVLANXX.SM2_042518p4_A11


title: Tuberculosis 945


title: Cortex1.CCKVLANXX.SM2_042518p4_A10


title: Tuberculosis 944


title: Tuberculosis 943


title: Tuberculosis 941


title: Tuberculosis 942


title: Cortex1.CCKVLANXX.SM2_042518p3_H9


title: Tuberculosis 939


title: siCtrl_ATACseq

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: UCSD

library_source: genomic

growth_protocol: HEK293 (human embryonic kidney cell line) were maintained at 37°C in a 5% CO2 incubator in Dulbecco’s Modified Eagle Medium (DMEM) with 10% fetal bovine serum.

treatment_protocol: siRNA transfections were performed using Invitrogen RNAiMAX reverse transfection protocol. Cells were plated in antibiotic free 10% FBS DMEM containing indicated Ambion/ThermoFisher Silencer Select siRNA for a final concentration of 10nM that was pre-incubated in lipofectamine RNAiMAX reagent in Opti-MEM.

tag: cell line

tag: developmental stage

value: embryonic

value: kidney

tag: sirna transfection

value: Silencer Negative Control No. 2 siRNA, ThermoFisher Cat#AM4613


title: Tuberculosis 940


title: Tuberculosis 937


title: Tuberculosis 935


title: Tuberculosis 938


title: Cortex1.CCKVLANXX.SM2_042518p3_H6


title: Cortex1.CCKVLANXX.SM2_042518p3_H8


title: Cortex1.CCKVLANXX.SM2_042518p3_H7


title: Tuberculosis 934


title: Cortex1.CCKVLANXX.SM2_042518p3_H4


title: Tuberculosis 931


title: Cortex1.CCKVLANXX.SM2_042518p3_H5


title: Tuberculosis 932


title: Tuberculosis 933


title: CIP_20ug/ml_sub-inhibitory_biological replicate4_rep1

type: RNA

city: Powai, Mumbai

first: Sarika

last: Mehra

state: MH

address: IIT Bombay

department: Chemical Engineering

country: India

institute: IIT Bombay

description: Biological replicate4/4:Total RNA isolated from 20 mg/ml Ciprofloxacin treated cells and its corresponding control. During treatment the cultures were  shaken at 250 rpm at 30°C

hyb_protocol: Hybridazation and washing of array was carried out using TIGR protocol

scan_protocol: Scanned on an Perkin Elmer Scanner scannarryGX.

data_processing: Image analysis was performed using the Scanarray Express software (Perkin Elmer, Inc.). Raw median fluorescence intensity values were obtained from each hybridization data. After subtraction of background, integrated intensity is calculated for each spot by multiplying the background subtracted median intensity with the number of pixels. These integrated intensities are further normalized using the lowess normalization algorithm. Spots flagged manually were removed after normalization. After normalization, data from all hybridizations including biological replicates, technical replicates and dye swap experiments were pooled together. Since each array consists of duplicate spots for each gene, two expression ratios were obtained from each hybridization corresponding to a gene. Outliers were identified as spots whose log2 ratios fell outside the range defined as mean ±1.2 times the standard deviation. These spots were removed from further calculation. Fold change is defined as expression in ciprofloxacin treated cells to untreated control cells. Significance was determined based on Student's t-test. The fold change ≥ 1.5 in either direction was called significant if p-value ≤ 0.05 based on at least 6 replicate spots.

label: Alexa 555

organism: Streptomyces coelicolor

label_protocol: 10 µg of total RNA were primed with 9 µg of Random primers at 65°C for 15 min, then reversed transcribed by incubation at 25°C for 5 min, 37°Cfor 10 min and 50°Cfor 1 h 45 min in the presence of 400 U SuperScript III RTase (Invitrogen), and 100 µM each dATP, dCTP, dGTP, with 25 µM dUTP, 25 µM Cy3-labe

growth_protocol: For exponential phase cultures, the spores were pre-germinated in 2xYT media  and then inoculated into liquid R5  in baffled flasks with stainless steel (SS) springs. The cultures were shaken at a speed of 250 rpm at 30°C

extract_protocol: Total RNA extracted using Trizol reagent following manufacturer's instructions

treatment_protocol: Cells with OD ~1 were exposed to 20 µg/ml of ciprofloxacin for one hour with parallel controls.

tag: growth phase

value: Exponential

tag: genotype

value: wild type

label: Alexa 647

source_name: Ciprofloxacin treated (20ug/ml - sub-inhibitory)


title: CIP_20ug/ml_sub-inhibitory_biological replicate3_rep1

description: Biological replicate3/4:Total RNA isolated from 20 mg/ml Ciprofloxacin treated cells and its corresponding control. During treatment the cultures were  shaken at 250 rpm at 30°C


title: Tuberculosis 929


title: Tuberculosis 930


title: Tuberculosis 928


title: ND-3

city: Shenzhen

first: yao

last: zhenyu

state: Guang dong province

address: No. 1068 xueyuan road Nanshan District Shenzhen

department: Institute of biomedical and Health Engineering

institute: Shenzhen institutes of advanced technology, chinese academy of science

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Transcriptome Array 1.0 in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: epididymal adipose_normal diet

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

value: epididymal adipose

value: male

tag: diet

value: normal diet


title: ND-2


title: Cortex1.CCKVLANXX.SM2_042518p3_H2


title: ND-1


title: Tuberculosis 936


title: HFD-3

source_name: epididymal adipose_high fat diet

value: high fat diet


title: HFD-2


title: Tuberculosis 927


title: Tuberculosis 926


title: Tuberculosis 924


title: Cortex1.CCKVLANXX.SM2_042518p3_H1


title: Cortex1.CCKVLANXX.SM2_042518p3_H12


title: Tuberculosis 923


title: Cortex1.CCKVLANXX.SM2_042518p3_H3


title: S. coelicolor control vs inhibitory ciprofloxacin treated biological rep 1' dye swap

description:
S. coelicolor response to ciprofloxacin
Biological replicate 1'/3: Total RNA isolated from 80 mg/ml Ciprofloxacin treated cells and its corresponding control. During treatment the cultures were  sheken at 250 rpm at 30°C

hyb_protocol: Hybridization and washing of array was carried out using TIGR protocol

data_processing: Images were quantified using Perkin Elmer Scannarry Express Software

source_name: Ciprofloxacin treated (inhibitory)

growth_protocol: S. coelioclor cells Ciprofloxacin treated

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Cells with OD ~1 were exposed to 80 mg/ml of ciprofloxacin for one hour with parallel controls.

growth_protocol: For exponential phase cultures, the spores were pre-germinated in 2xYT media  and then inoculated into liquid R5 in baffled flasks with stainless steel (SS) springs. The cultures were shaken at a speed of 250 rpm at 30°C


title: Tuberculosis 922


title: CIP_20ug/ml_sub-inhibitory_biological replicate1_rep2

description: Biological replicate1/4:Total RNA isolated from 20 mg/ml Ciprofloxacin treated cells and its corresponding control. During treatment the cultures were  shaken at 250 rpm at 30°C


title: CIP_20ug/ml_sub-inhibitory_biological replicate1_rep1


title: Tuberculosis 920


title: CIP_20ug/ml_sub-inhibitory_biological replicate2_rep1

description: Biological replicate2/4:Total RNA isolated from 20 mg/ml Ciprofloxacin treated cells and its corresponding control. During treatment the cultures were  shaken at 250 rpm at 30°C


title: HFD-1


title: Cortex1.CCKVLANXX.SM2_042518p3_H11


title: S. coelicolor control vs inhibitory ciprofloxacin treated biological rep 2' (technical replicate)

description:
S. coelicolor response to ciprofloxacin
Biological replicate2/3:Total RNA isolated from 80mg/ml Ciprofloxacin treated cells and its corresponding control. During treatment the cultures were  sheken at 250 rpm at 30°C

growth_protocol: Cell cultured to exponetial phase in R5 media


title: S. coelicolor control vs inhibitory ciprofloxacin treated biological rep 3

description:
S. coelicolor response to ciprofloxacin
Biological replicate3/3:Total RNA isolated from 80 mg/ml Ciprofloxacin treated cells and its corresponding control. During treatment the cultures were  sheken at 250 rpm at 30°C


title: Tuberculosis 925


title: Tuberculosis 921


title: Cortex1.CCKVLANXX.SM2_042518p3_H10


title: S. coelicolor control vs inhibitory ciprofloxacin treated biological rep 2

description:
S. coelicolor response to ciprofloxacin
Biological replicate2/3:Total RNA isolated from 80 mg/ml Ciprofloxacin treated cells and its corresponding control. During treatment the cultures were  sheken at 250 rpm at 30°C


title: Tuberculosis 919


title: Tuberculosis 917


title: Cortex1.CCKVLANXX.SM2_042518p3_G9


title: Tuberculosis 916


title: Cortex1.CCKVLANXX.SM2_042518p3_G8


title: Tuberculosis 915


title: Tuberculosis 913


title: S. coelicolor control vs inhibitory ciprofloxacin treated biological rep 1

description:
S. coelicolor response to ciprofloxacin
Biological replicate1/3:Total RNA isolated from 80 mg/ml Ciprofloxacin treated cells and its corresponding control. During treatment the cultures were  sheken at 250 rpm at 30°C


title: Tuberculosis 914


title: Cortex1.CCKVLANXX.SM2_042518p3_G7


title: Drop-Seq_wing.disc_rep2_Lib1

city: Heidelberg

first: Erica

last: Valentini

address: Im Neuenheimer Feld 580

country: Germany

institute: DKFZ

description: Independent sets of cells were used from biological replicate 2 to prepare each of 2 libraries. This sample includes Rep 2 library 1.

data_processing:
Drop-seq data (Drop-Seq_wing.disc*) were processed according to the published Makosco and Nemesh pipeline http://mccarrolllab.org/wp-content/uploads/2016/03/Drop-seqAlignmentCookbookv1.2Jan2016.pdf
The Drop-Seq experiment and 10x experiment sequence the cell barcode with read1. Drop-Seq: 1-20bp and 10x: 1-26bp
10X data (Tx7) were processed using the software cellranger provided by 10x Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Bulk data were processed using Kallisto (https://github.com/griffithlab/rnaseq_tutorial/wiki/Kallisto)
Genome_build: BDGP6 version 87 (GCA 000001215.4)
Supplementary_files_format_and_content: raw counts

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: wing imaginal disc cells

extract_protocol:
Larvae were dissected in Schneider’s medium in batches of 5 animals (to prevent hypoxia) and transferred into a tube containing Schneider’s medium on ice for a maximum time of 30 minutes. To isolate single cells TrypLE (10x) was added and the tissue incubated for 15 minutes in a water bath at 37°C , with gentle mixing every 5 minutes. Schneider’s medium was then added to the loosened tissue pellets, followed by gentle mechanical dissociation using a P1000 pipette. The cell suspension was then passed through a 10 μM cell strainer to remove undigested tissue and cell clumps.
Drop-Seq libraries were prepared according to Macosko et al., 2015 (PMID 26000488)  following the detailed online protocol (Drop-seq-Protocol-v1.0-May-2015)

value: wing imaginal disc

value: L3 wandering

value: female


title: Tuberculosis 912


title: Drop-Seq_wing.disc_rep2_Lib2

description: Independent sets of cells were used from biological replicate 2 to prepare each of 2 libraries. This sample includes Rep 2 library 2.


title: Cortex1.CCKVLANXX.SM2_042518p3_G6


title: Tuberculosis 911


title: Drop-Seq_wing.disc_rep1_Lib3

description: Independent sets of cells were used from biological replicate 1 to prepare each of 3 libraries. This sample includes Rep 1 library 3.


title: Tuberculosis 910


title: Tuberculosis 909


title: Drop-Seq_wing.disc_rep1_Lib2

description: Independent sets of cells were used from biological replicate 1 to prepare each of 3 libraries. This sample includes Rep 1 library 2.


title: Cortex1.CCKVLANXX.SM2_042518p3_G5


title: Tuberculosis 908


title: Tuberculosis 905


title: Tuberculosis 918


title: Drop-Seq_wing.disc_rep1_Lib1

description: Independent sets of cells were used from biological replicate 1 to prepare each of 3 libraries. This sample includes Rep 1 library 1.


title: Bulk_wing_disc

source_name: wing imaginal disc

extract_protocol:
Larvae were dissected in Schneider’s medium in batches of 5 animals (to prevent hypoxia) and transferred into a tube containing Schneider’s medium on ice for a maximum time of 30 minutes. To isolate single cells TrypLE (10x) was added and the tissue incubated for 15 minutes in a water bath at 37°C , with gentle mixing every 5 minutes. Schneider’s medium was then added to the loosened tissue pellets, followed by gentle mechanical dissociation using a P1000 pipette. The cell suspension was then passed through a 10 μM cell strainer to remove undigested tissue and cell clumps.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Sample Preparation Kit.


title: Tuberculosis 906


title: Tuberculosis 904


title: Cortex1.CCKVLANXX.SM2_042518p3_G3


title: Cortex1.CCKVLANXX.SM2_042518p3_G2


title: Tuberculosis 903


title: Cortex1.CCKVLANXX.SM2_042518p3_G1


title: Tuberculosis 900


title: Cortex1.CCKVLANXX.SM2_042518p3_G12


title: Tuberculosis 897


title: Tuberculosis 898


title: Tuberculosis 901


title: Tuberculosis 896


title: Cortex1.CCKVLANXX.SM2_042518p3_G11


title: Tuberculosis 907


title: Cortex1.CCKVLANXX.SM2_042518p3_G4


title: Cortex1.CCKVLANXX.SM2_042518p3_F9


title: Tuberculosis 902


title: Tuberculosis 895


title: Tuberculosis 894


title: Tuberculosis 892


title: Tuberculosis 893


title: Cortex1.CCKVLANXX.SM2_042518p3_F8


title: Tuberculosis 891


title: Tuberculosis 890


title: Cortex1.CCKVLANXX.SM2_042518p3_F7


title: Tuberculosis 899


title: Tuberculosis 889


title: Tuberculosis 888


title: Tuberculosis 887


title: Cortex1.CCKVLANXX.SM2_042518p3_F6


title: Tuberculosis 885


city: Fukuoka

first: Yoshikane

last: Kikushige

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

description: Gene expression of CD34+ ALL4 cells treated with gabapentin

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human Gene Expression 8x60K Microarrays (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Raw expression data was imported and normalized by using GeneSpring GX software (Agilent Technologies).

source_name: CD34+ ALL4 cells treated with 40mM gabapentin

label_protocol: Cyanine 3 (Cy3)-labeled cRNA was synthesized with Low Input Quick Amp Labeling kit, one-color (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Primary CD34+ ALL cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum for 9-12 hours with or without 40mM gabapentin. All samples were incubated for 9-12 hours at 37ºC in a humidified incubator with 5% CO2

extract_protocol: Total RNA was extracted by using Isogen2 (NIPPON GENE) according to the manufacturer's instructions.

value: bone marrow

tag: disease

value: acute lymphoblastic leukemia(B cell type)

tag: gender

tag: treatment

value: 40mM gabapentin


description: Gene expression of CD34+ ALL3 cells treated with gabapentin

source_name: CD34+ ALL3 cells treated with 40mM gabapentin

treatment_protocol: Primary CD34+ ALL cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum for 9-12 hours with or without 40mM gabapentin. All samples were incubated for 9-12 hours at 37ºC in a humidified incubator with 5% CO2


title: Tuberculosis 886

description: Genomic DNAs extracted from whole blood were genotyped using Illumina human Omni-zhonghua chips


description: Gene expression of CD34+ ALL1 cells treated with gabapentin

source_name: CD34+ ALL1 cells treated with 40mM gabapentin


title: Cortex1.CCKVLANXX.SM2_042518p3_F5

description:
scRNA-seq
full-length
cortex_mm10_count_matrix.mtx, cortex_mm10_gene.tsv, cortex_mm10_cell.tsv

value: Male

value: one month


title: Cortex1.CCKVLANXX.SM2_042518p3_G10


description: Gene expression of CD34+ ALL2 cells treated with gabapentin

source_name: CD34+ ALL2 cells treated with 40mM gabapentin


title: CD34+ ALL4 cells(control)

description: Gene expression of CD34+ ALL4 cells

source_name: CD34+ ALL4 cells culutred without gabapentin


title: CD34+ ALL3 cells(control)

description: Gene expression of CD34+ ALL3 cells

source_name: CD34+ ALL3 cells culutred without gabapentin


title: CD34+ ALL2 cells(control)

description: Gene expression of CD34+ ALL2 cells

source_name: CD34+ ALL2 cells culutred without gabapentin


title: Tuberculosis 884

value: Blood


title: Cortex1.CCKVLANXX.SM2_042518p3_F4


title: Tuberculosis 883


title: Tuberculosis 881


title: Tuberculosis 882


title: Cortex1.CCKVLANXX.SM2_042518p3_F3


description:
Gene expression of CD34+ AML4 cells treated with gabapentin
AML4 gabapentin

source_name: CD34+ AML4 cells treated with 40mM gabapentin

treatment_protocol: Primary CD34+ AML cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum for 9-12 hours with or without 40mM gabapentin. All samples were incubated for 9-12 hours at 37ºC in a humidified incubator with 5% CO2

value: acute myeloid leukemia

tag: individual

value: patient 4

value: gabapentin

tag: cell type

value: CD34+ AML cells


title: Tuberculosis 880


title: Cortex1.CCKVLANXX.SM2_042518p3_F2


title: Tuberculosis 879


title: CD34+ ALL1 cells(control)

description: Gene expression of CD34+ ALL1 cells

source_name: CD34+ ALL1 cells culutred without gabapentin


description:
Gene expression of CD34+ AML3 cells treated with gabapentin
AML3 gabapentin

source_name: CD34+ AML3 cells treated with 40mM gabapentin

value: patient 3


title: Tuberculosis 875

source_name: Tuberculosis


title: Tuberculosis 874


title: Cortex1.CCKVLANXX.SM2_042518p3_F12

source_name: Cortex


title: Tuberculosis 878


title: Tuberculosis 876


title: Cortex1.CCKVLANXX.SM2_042518p3_F1


title: CD34+ AML3 cells (control)

description:
Gene expression of CD34+ AML3 cells
AML3 control

source_name: CD34+ AML3 cells cultured without gabapentin

value: male

value: control


title: CD34+ AML4 cells (control)

description:
Gene expression of CD34+ AML4 cells
AML4 control

source_name: CD34+ AML4 cells cultured without gabapentin


title: Tuberculosis 873


title: Cortex1.CCKVLANXX.SM2_042518p3_F11


title: Tuberculosis 871


title: Tuberculosis 872


title: Cortex1.CCKVLANXX.SM2_042518p3_F10


title: Tuberculosis 870


title: Cortex1.CCKVLANXX.SM2_042518p3_E9


title: KO2 LEC RNAseq

city: Strasbourg

first: Christopher

middle: G.

last: Mueller

address: 2 Allée Gaspard Monge

department: IBMC

country: France

institute: CNRS

description:
MNCR19
Sample 5 KO2 LEC RNAseq (raw read counts)

data_processing:
Base calling : Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto mm10 assembly of mouse genome using Tophat v2.0.14 with bowtie v2.1.0.
Quantification : Gene expression was quantified using HTSeq v0.6.1 (intersection-nonempty mode) and Ensembl release 81 annotations.
Genome_build: mm10
Supplementary_files_format_and_content: Semicolon delimited text file (includes raw data for each sample)

source_name: stromal RANKL-conditional knock out_LEC_RNAseq

extract_protocol:
Lymphatic endothelial cells were isolated from lymph nodes by flow cytometry on the basis of CD45-, TER119-, CD31+, podoplanin38+ cells. Sorted cells were flash frozen on dry ice, and RNA was harvested using Quiagen RNA isolation kit. The library was sequenced on Illumina Hiseq 4000 sequencer as Single-Read 50 base reads following Illumina's instructions.
Full length cDNA were generated from 4 ng of total RNA using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio) according to manufacturer's instructions with 10 cycles of PCR for cDNA amplification by Seq-Amp polymerase. 600 pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (Illumina) followed by 12 cycles of library amplification.

tag: strain background

value: 8 weeks

tag: genotype/variation

value: Ccl19 Cre Rankl flox/flox

value: lymph node

value: lymphatic endothelial cells (LEC)


title: Cortex1.CCKVLANXX.SM2_042518p3_E8

tag: Sex

tag: age


title: WT2 LEC RNAseq

description:
MNCR21
Sample 2 WT2 LEC RNAseq (raw read counts)

value: Rankl flox/flox


title: KO1 LEC RNAseq

description:
MNCR17
Sample 4 KO1 LEC RNAseq (raw read counts)


title: Tuberculosis 877


title: Tuberculosis 869


title: CD34+ AML2 cells (control)

description:
Gene expression of CD34+ AML2 cells
AML2 control

source_name: CD34+ AML2 cells cultured without gabapentin

value: bone marrow

value: patient 2


title: Tuberculosis 868


title: WT3 LEC RNAseq

description:
MNCR22
Sample 3 WT3 LEC RNAseq (raw read counts)


title: Tuberculosis 866


title: CD34+ AML1 cells (control)

description:
Gene expression of CD34+ AML1 cells
AML1 control

source_name: CD34+ AML1 cells cultured without gabapentin

value: patient 1

value: female


title: Cortex1.CCKVLANXX.SM2_042518p3_E7

value: Male

value: one month

tag: strain

tag: library construction


title: Tuberculosis 865

tag: tissue

value: Blood


title: WT1 LEC RNAseq

description:
MNCR18
Sample 1 WT1 LEC RNAseq (raw read counts)


title: Cortex1.CCKVLANXX.SM2_042518p3_E6


title: Tuberculosis 864


title: Tuberculosis 863


title: Tuberculosis 862


title: Tuberculosis 861


title: Cortex1.CCKVLANXX.SM2_042518p3_E5


title: Tuberculosis 859


title: Tuberculosis 867


description:
Gene expression of CD34+ AML2 cells treated with gabapentin
AML2 gabapentin

source_name: CD34+ AML2 cells treated with 40mM gabapentin

value: acute myeloid leukemia

value: gabapentin


title: Tuberculosis 858


description:
Gene expression of CD34+ AML1 cells treated with gabapentin
AML1 gabapentin

source_name: CD34+ AML1 cells treated with 40mM gabapentin

value: CD34+ AML cells


title: Cortex1.CCKVLANXX.SM2_042518p3_E3


title: CHiC E12.5 InvIntra

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

institute: Berlin Institute of Health

data_processing:
Preprocessing and mapping of paired-end raw sequencing reads, as well as filtering of mapped di-tags was performed with the Hi-CUP pipeline v.0.5.8 (Wingett et al., 2015) (Nofill: 1, no size selection, Format: Sanger). The pipeline uses the alignment tool bowtie2 v.2.2.6 (Langmead and Salzberg, 2012) for mapping short reads to the reference genome (mm9). Aligned and filtered reads were combined for all replicates and further reduced to a minimum mapping quality of MAPQ=30. Filtered di-tags were further processed with the Juicer tool kit (Durand et al., 2016) (v1.7.5) to bin di-tags (10 kb bins) and to normalize the interaction matrix by the Knight-Ruiz (KR) matrix balancing method (Durand et al., 2016; Knight and Ruiz, 2013; Lieberman-Aiden et al., 2009). The DNA-capturing step enriches the genomic region chr1:71,000,001-81,000,000 on mm9 leading to three different regimes in the cHi-C map: (i) enriched versus enriched, (ii) enriched versus non-enriched, and (iii) non-enriched versus non- enriched. For binning and normalization only di-tags in regime (i) were considered.
All maps were mapped to a customized reference genome that incorporates the respective inversion. Additionally the capture-Hi-C map that is based on the WT experiment was also mapped to each customized reference genome and interaction matrices were generated. Half of this map was subsequently substracted from all heterozygous contact matrices to generate a homozygous map that is just showing the inversion. For this the WT map and the respective heterozygous map were scaled to the same amount of reads. For the substraction of interaction maps all maps were converted to reads per million (RPM) to account for different sequencing depths.
Genome_build: mm9
Supplementary_files_format_and_content: Pairwise interactions files

source_name: Embryonic Limb Bud

growth_protocol: Forelimb and hindlilmb buds were micro-dissected from E12.5 mouse embryos

extract_protocol:
Limbs were re-suspended in Trypsin and incubated for 10 minutes at 37°C. Tissues were disrupted by pipetting and single cells were retrieved using cell strainer and fixed for 10 minutes at room temperature in 10ml (2%PFA, 10%FCS, 1XPBS). Final 140mM glycine was added to stop crosslinking. Cells were then lysed for 10’ at 4°C in lysis buffer (50mM TRIS pH7.5, 150mM NaCl, 5mM EDTA, 0.5%NP-40, 1.15% TX-100 and 1X Proteinase Inhibitor). For capture Hi-C a 3C-library was generated by  overnight digestion with 110 units DpnII (10 U/µl, NEB R0543S) (40 units for 4 h at 37°C, shaker at 900 RPM; further 30 units DpnII with incubation overnight; 30 units DpnII for another 4h the next day). After heat-inactivation of DpnII, the sample was transferred to a 50 ml falcon tube, diluted in 5.1 ml of water and mixed with 700 µl 10x T4-DNA-ligase buffer and 5 µl T4-DNA-ligase (30 U/µl, Thermo Fisher Scientific EL0013). Ligation was performed overnight at 16°C and another 30 min at RT.
The 3C-libary was then purified by Proteinase K treatment and crosslink-reversal overnight at 65°C, followed by 45min RNase digestion and phenol-chloroform extraction. The 3C-library was then sheared using a Covaris sonicator (duty cycle: 10%, intensity: 5, cycles per burst: 200, time: 6 cycles of 60 s each, set mode: frequency sweeping, temperature: 4 to 7 °C). Adaptors were added to the sheared DNA and amplified according to Agilent instructions for Illumina sequencing. The library was hybridized to the custom-designed sure-select beads and indexed for sequencing (50 to 125 bp paired-end) following Agilent instructions.
library strategy: Capture Hi-C-seq

value: InvIntra

value: Embryonic Limb Bud

value: mutant

tag: embryonic stage

tag: background

value: G4 ESC


title: CHiC E12.5 InvC

value: InvC


title: CHiC E12.5 InvC∆Bor

value: InvC<delta>Bor


title: Tuberculosis 856

description: Genomic DNAs extracted from whole blood were genotyped using Illumina human Omni-zhonghua chips


title: Tuberculosis 855


title: Cortex1.CCKVLANXX.SM2_042518p3_E2


title: Tuberculosis 854


title: CHiC E12.5 BorKnockIn

value: BorKnockIn


title: CHiC E12.5 ∆BorC1-4


title: Tuberculosis 852


title: Tuberculosis 857


title: Cortex1.CCKVLANXX.SM2_042518p3_E12


title: Tuberculosis 851


title: Cortex1.CCKVLANXX.SM2_042518p3_E1


title: Tuberculosis 850


title: Cortex1.CCKVLANXX.SM2_042518p3_E11


title: CHiC E12.5 ∆CTCF

value: deltaCTCF


title: Tuberculosis 853


title: Tuberculosis 849


title: Tuberculosis 848


title: Tuberculosis 860


title: Cortex1.CCKVLANXX.SM2_042518p3_E4


title: CHiC E12.5 ∆BorC1


title: Tuberculosis 847


title: CHiC E12.5 ∆BorC1-2


title: Tuberculosis 846


title: Tuberculosis 845


title: Cortex1.CCKVLANXX.SM2_042518p3_D9


title: A-NKO-10

city: Baltimore

first: Drew

last: Pardoll

state: Maryland

address: 1650 Orlean St.

department: Oncology

institute: Johns Hopkins Medical Institute

description:
peptide induced tolerance model: 5x10^6 thy1.1+ OTII cells from Nrn1+/-OTII mice cotransferred with.5x10^5 wt Treg into TCRα -/- mice followed by 3 treatment of soluble peptide. Cells recovered on day13 post transfer
group B

data_processing:
Sorted cells stored in RNAprotect were sent to Admera Health to process library construction and data analysis.The NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® was used for library construction. Sequencing was performed on Illumina Hiseq   2x150 (paired end) for a total of 40M PE reads each (20M SR reads in each direction).
The pre-processing operations included a quality check (FastQC), removal of adapter content (used during sequencing), quality thresholding (remove any bad quality reads)
The Quality control checks on raw sequences was done using FastQC v0.11.5 (Babraham Institute).
The adapter trimming and quality control was carried out using Trim Galore v0.4.2 (Babraham Institute). The Alignment of RNA-Seq reads to genomes using the ultra-high-throughput short read aligner Bowtie, and the identification of splice junctions between exons was performed by a fast splice junction mapper Tophat v2.1.1 (cole-trapnell-lab and Center for Computational Biology (JHU)). The Transcript assemblies, abundance estimation and differential expression and regulation in RNA-Seq samples was carried out by Cufflinks v2.2.1 (cole-trapnell-lab).
Gene and transcript expression between the comparing RNASeq samples were quantified and reported as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) units
Genome_build: GRCM38
Supplementary_files_format_and_content: Excel file with FPKM

source_name: sorted CD4+Thy1.1+Vb5+ Nko OTII

growth_protocol: Nrn1-/- and Nrn1+/- Thy1.1+ OTII cells were cotransferred with wt Treg cell into TCRa-/- hosts and subjected to soluble OVA peptide i.v. treatment for anergy induction on day 1, 4, and 7 post transfer. Nrn1-/- and Nrn1+/- Thy1.1+ OTII cells were recoverred by cell sorting 13 days after cell transferand subjected to RNA-Sequencing analysis

extract_protocol:
Cells stored in RNA protect
Samples were sent to Admera Health for RNA extraction (RNeasy Mini Kit (QIAGEN)) and to process library construction and data analysis. Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used.

treatment_protocol: Sorting with FACSAria Fusion

value: Nrn-/-

value: OTII

tag: cell markers

value: 100ug of OVA peptide i.v. on day1, 4, 7 post cell transfer


title: Tuberculosis 844


title: Cortex1.CCKVLANXX.SM2_042518p3_D7

description:
scRNA-seq
full-length
cortex_mm10_count_matrix.mtx, cortex_mm10_gene.tsv, cortex_mm10_cell.tsv

value: Male


title: Tuberculosis 842


title: Tuberculosis 843


title: Cortex1.CCKVLANXX.SM2_042518p3_D8

value: one month


title: A-NKO-6

tag: genotype


title: Tuberculosis 839

value: Blood


title: Tuberculosis 840


title: Tuberculosis 841


title: A-NKO-7


title: Tuberculosis 838


title: A-Het-4

description:
peptide induced tolerance model: 5x10^6 thy1.1+ OTII cells from Nrn1+/-OTII mice cotransferred with.5x10^5 wt Treg into TCRα -/- mice followed by 3 treatment of soluble peptide. Cells recovered on day13 post transfer
group A

source_name: sorted CD4+Thy1.1+Vb5+ Nhet OTII


title: Cortex1.CCKVLANXX.SM2_042518p3_D6


title: Cortex1.CCKVLANXX.SM2_042518p3_D5


title: Tuberculosis 837


title: A-Het-3


title: Tuberculosis 836


title: Cortex1.CCKVLANXX.SM2_042518p3_D4


title: Tuberculosis 835


title: Tuberculosis 834


title: eTreg-NKO-35

description: group B

growth_protocol: Nrn1-/- and Nrn1+/- CD4+CD25+Cd62LlowCD44highFoxp3gfp+ were sorted from Nrn1-/- and Nrn1+/- mice on Foxp3DTRgfp background and subjected to RNASeq analysis

extract_protocol:
Cells stored in RNA protect before subject to RNA extraction
Samples were sent to Admera Health for RNA extraction (RNeasy Mini Kit (QIAGEN)) and to process library construction and data analysis. Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used.

tag: background strain

value: eTreg


title: Cortex1.CCKVLANXX.SM2_042518p3_E10


title: Tuberculosis 833


title: Tuberculosis 832


title: eTreg-NKO-33

description: group B


title: Tuberculosis 831


title: Tuberculosis 830


title: A-Het-5


title: Tuberculosis 829


title: Tuberculosis 827


title: Cortex1.CCKVLANXX.SM2_042518p3_D1


title: Tuberculosis 828


title: Cortex1.CCKVLANXX.SM2_042518p3_D12


title: eTreg-Het-36

description: group A


title: Tuberculosis 826


title: Tuberculosis 825


title: eTreg-Het-34

description: group A


title: Tuberculosis 824


title: Tuberculosis 823


title: eTreg-Het-32

description: group A


title: Cortex1.CCKVLANXX.SM2_042518p3_D11


title: Cortex1.CCKVLANXX.SM2_042518p3_D3


title: Cortex1.CCKVLANXX.SM2_042518p3_D10


title: Tuberculosis 822


title: Cortex1.CCKVLANXX.SM2_042518p3_C9


title: Tuberculosis 821


title: Tuberculosis 820


title: Cortex1.CCKVLANXX.SM2_042518p3_C8


title: Tuberculosis 819


title: Cortex1.CCKVLANXX.SM2_042518p3_C7


title: eTreg-NKO-31

description: group B


title: Cortex1.CCKVLANXX.SM2_042518p3_D2


title: Tuberculosis 817


title: Tuberculosis 815


title: Tuberculosis 814


title: Tuberculosis 816


title: Cortex1.CCKVLANXX.SM2_042518p3_C5


title: Cortex1.CCKVLANXX.SM2_042518p3_C4


title: Tuberculosis 809


title: Tuberculosis 812


title: Tuberculosis 811


title: Tuberculosis 813


title: Tuberculosis 808


title: NUID-0000-0163-0821

city: Charlestown

first: Kamil

last: Slowikowski

state: Massachusetts

address: Mailstop CNY 149-8, 149 13th Street

institute: Massachusetts General Brigham

hyb_protocol: Following fragmentation, cRNA was hybridized on Affymetrix Human Gene 1.0 ST Array

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000  Scanner 3000

data_processing: Expression data are normalized using RMA algorithm, then scaled so that the 2% trimmed mean is 150.

source_name: synovium

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol.

growth_protocol: Fibroblasts (RA-32, RA-449, OA-6, OA-502) were plated on day 1 at 50,000 cells per well in 24-well plates in 10% FBS containing media. Cells were serum-starved on day 2 by changing to 1% FBS-containing media.

extract_protocol: Trizol extraction of total RNA was performed using the Qiagen RNeasy Mini Kit.

treatment_protocol: Cells were either left unstimulated or stimulated with TNF (1 ng/mL) or TNF (1 ng/mL) + IL-17A (1 ng/mL) for approximately 20 hours on day 3.

tag: disease

value: RA

tag: donor

value: low

tag: passage

tag: stimulation


title: Tuberculosis 807


title: Cortex1.CCKVLANXX.SM2_042518p3_C3


title: Tuberculosis 818


title: NUID-0000-0163-0822

value: OA

value: high

value: TNF


title: Tuberculosis 810


title: Tuberculosis 806


title: NUID-0000-0163-0819


title: Cortex1.CCKVLANXX.SM2_042518p3_C2


title: Cortex1.CCKVLANXX.SM2_042518p3_C1


title: Tuberculosis 805


title: Cortex1.CCKVLANXX.SM2_042518p3_C6


title: Tuberculosis 804


title: Tuberculosis 803


title: NUID-0000-0163-0820


title: NUID-0000-0163-0816

value: Baseline


title: Tuberculosis 802


title: NUID-0000-0163-0817


title: Tuberculosis 801


title: NUID-0000-0163-0815


title: NUID-0000-0163-0814


title: NUID-0000-0163-0818


title: Cortex1.CCKVLANXX.SM2_042518p3_C10


title: NUID-0000-0163-0813


title: NUID-0000-0163-0812


title: Tuberculosis 799


title: Tuberculosis 798


title: Cortex1.CCKVLANXX.SM2_042518p3_B9


title: Tuberculosis 796


title: Tuberculosis 797


title: Cortex1.CCKVLANXX.SM2_042518p3_B8


title: Tuberculosis 795


title: Tuberculosis 793


title: Cortex1.CCKVLANXX.SM2_042518p3_B7


title: Tuberculosis 794


title: Tuberculosis 792


title: Cortex1.CCKVLANXX.SM2_042518p3_B6


title: Cortex1.CCKVLANXX.SM2_042518p3_C11


title: Tuberculosis 791


title: Cortex1.CCKVLANXX.SM2_042518p3_C12


title: Tuberculosis 800


title: NUID-0000-0163-0810


title: NUID-0000-0163-0808


title: NUID-0000-0163-0811


title: Tuberculosis 790


title: Cortex1.CCKVLANXX.SM2_042518p3_B5


title: Tuberculosis 788


title: Tuberculosis 789


title: Cortex1.CCKVLANXX.SM2_042518p3_B4


title: NUID-0000-0163-0807


title: Tuberculosis 785


title: Tuberculosis 786


title: Tuberculosis 787


title: NUID-0000-0163-0806


title: Tuberculosis 784


title: NUID-0000-0163-0809


title: Cortex1.CCKVLANXX.SM2_042518p3_B3


title: NUID-0000-0163-0805


title: Tuberculosis 783


title: Cortex1.CCKVLANXX.SM2_042518p3_B1


title: Tuberculosis 782


title: Tuberculosis 779


title: Cortex1.CCKVLANXX.SM2_042518p3_B11


title: Cortex1.CCKVLANXX.SM2_042518p3_B2


title: Tuberculosis 781


title: Tuberculosis 780


title: Tuberculosis 777


title: Tuberculosis 778


title: NUID-0000-0163-0803


title: NUID-0000-0163-0802


title: NUID-0000-0163-0804


title: NUID-0000-0163-0800


title: Cortex1.CCKVLANXX.SM2_042518p3_B10


title: NUID-0000-0163-0799


title: Tuberculosis 772


title: NUID-0000-0163-0801


title: Cortex1.CCKVLANXX.SM2_042518p3_B12


title: Tuberculosis 771


title: Cortex1.CCKVLANXX.SM2_042518p3_A9


title: Tuberculosis 770


title: Cortex1.CCKVLANXX.SM2_042518p3_A8


title: Tuberculosis 769


title: Cortex1.CCKVLANXX.SM2_042518p3_A7


title: Tuberculosis 768


title: Cortex1.CCKVLANXX.SM2_042518p3_A6


title: Tuberculosis 767


title: Cortex1.CCKVLANXX.SM2_042518p3_A5


title: Tuberculosis 776


title: NUID-0000-0163-0798


title: Tuberculosis 766


title: Tuberculosis 775


title: NUID-0000-0163-0797


title: NUID-0000-0163-0796


title: Tuberculosis 765


title: Tuberculosis 774


title: Tuberculosis 763


title: Tuberculosis 773


title: Tuberculosis 764


title: Cortex1.CCKVLANXX.SM2_042518p3_A4


title: Tuberculosis 762


title: NUID-0000-0163-0795


title: Tuberculosis 759


title: Cortex1.CCKVLANXX.SM2_042518p3_A3


title: Tuberculosis 760


title: NUID-0000-0163-0792


title: Cortex1.CCKVLANXX.SM2_042518p3_A2


title: Tuberculosis 758


title: Cortex1.CCKVLANXX.SM2_042518p3_A1


title: NUID-0000-0163-0793


title: Tuberculosis 757


title: Tuberculosis 756


title: NUID-0000-0163-0790


title: Tuberculosis 755


title: Cortex1.CCKVLANXX.SM2_042518p3_A11


title: Tuberculosis 754


title: Cortex1.CCKVLANXX.SM2_042518p3_A12


title: Tuberculosis 753


title: Cortex1.CCKVLANXX.SM2_042518p3_A10


title: Tuberculosis 751


title: Tuberculosis 752


title: NUID-0000-0163-0791


title: Tuberculosis 750


title: Cortex1.CCKVLANXX.SM2_042518p2_H9


title: NUID-0000-0163-0794


title: NUID-0000-0163-0789


title: NUID-0000-0163-0788


title: Tuberculosis 761


title: NUID-0000-0163-0787


title: Tuberculosis 748


title: Tuberculosis 747


title: Tuberculosis 746


title: Tuberculosis 745


title: NUID-0000-0163-0786


title: NUID-0000-0163-0785


title: Tuberculosis 744


title: Cortex1.CCKVLANXX.SM2_042518p2_H6


title: NUID-0000-0163-0784


title: Tuberculosis 742


title: Tuberculosis 740


title: Cortex1.CCKVLANXX.SM2_042518p2_H4


title: Tuberculosis 743


title: Cortex1.CCKVLANXX.SM2_042518p2_H5


title: NUID-0000-0163-0783


title: Tuberculosis 739


title: Tuberculosis 738


title: Tuberculosis 737


title: NUID-0000-0163-0782


title: Tuberculosis 749


title: Cortex1.CCKVLANXX.SM2_042518p2_H3


title: Cortex1.CCKVLANXX.SM2_042518p2_H8


title: Cortex1.CCKVLANXX.SM2_042518p2_H2


title: Cortex1.CCKVLANXX.SM2_042518p2_H7


title: Tuberculosis 735


title: NUID-0000-0163-0781


title: NUID-0000-0163-0780


title: Cortex1.CCKVLANXX.SM2_042518p2_H1


title: Tuberculosis 734


title: Tuberculosis 733


title: Tuberculosis 732


title: Tuberculosis 741


title: Cortex1.CCKVLANXX.SM2_042518p2_H12


title: Tuberculosis 731


title: Tuberculosis 730


title: NUID-0000-0163-0778


title: NUID-0000-0163-0779


title: NUID-0000-0163-0777


title: Tuberculosis 729


title: Tuberculosis 736


title: NUID-0000-0163-0776


title: Cortex1.CCKVLANXX.SM2_042518p2_H10


title: Tuberculosis 728


title: Tuberculosis 726


title: Tuberculosis 727


title: Cortex1.CCKVLANXX.SM2_042518p2_G9


title: Tuberculosis 725


title: Tuberculosis 724


title: Tuberculosis 723


title: Tuberculosis 722


title: Cortex1.CCKVLANXX.SM2_042518p2_G8


title: Cortex1.CCKVLANXX.SM2_042518p2_G7


title: NUID-0000-0163-0775


title: Tuberculosis 721


title: Tuberculosis 719


title: Tuberculosis 720


title: Cortex1.CCKVLANXX.SM2_042518p2_G6


title: Cortex1.CCKVLANXX.SM2_042518p2_G5


title: Tuberculosis 717


title: Tuberculosis 716


title: Cortex1.CCKVLANXX.SM2_042518p2_G4


title: Tuberculosis 715


title: Tuberculosis 713


title: Cortex1.CCKVLANXX.SM2_042518p2_G2


title: MDA-MB-175-VII 16 h 1 nM E2 281

city: Eindhoven

first: Marcia

middle: Alves de

last: Inda

address: High Tech Campus 11

department: PDx

country: Netherlands

institute: Philips Research

hyb_protocol: Done by service lab (ServiceXS) per default Affymetrix HT HG-U133Plus2.0 Array Plate protocol.

data_processing: fRMA (McCall, Biostatistics. 2010 Apr;11(2):242-53).

growth_protocol: Cells were maintained at 37°C and 5% CO2 in DMEM/F12 1:1 (DF) supplemented with 10% (FCS) with exception of MDA-MB-134-VI (20% FCS) and MDA-MB-361 and BT-483 (20% FCS and 0.01 mg/ml insulin).

extract_protocol: Nucleospin RNA isolation kit (Macherey-Nagel).

treatment_protocol: Two days before experiments, cells were seeded in 60 mm plates in DF with charcoal stripped phenol red-free serum supplemented with non-essential amino-acids and pen/strep, at a density such that 75%-90% confluence was obtained by the time of harvesting. Medium was refreshed 24 hours before exposure to 1 nM E2, 10 nM E2 or with 0.1% DMSO (control) for 16h.

tag: cell line

tag: er status

value: pos

tag: exposure

value: 16 h 1 nM E2


title: Cortex1.CCKVLANXX.SM2_042518p2_G3

tag: Sex


title: MDA-MB-175-VII 16 h 10 nM E2 285

scan_protocol: Done by service lab (ServiceXS) per default Affymetrix HT HG-U133Plus2.0 Array Plate protocol.


title: Tuberculosis 711


title: Tuberculosis 712


title: Tuberculosis 710


title: MCF-7 16 h 10 nM E2 223

label_protocol: Done by service lab (ServiceXS) per default Affymetrix HT HG-U133Plus2.0 Array Plate protocol.

value: MCF-7 ATCC


title: Cortex1.CCKVLANXX.SM2_042518p2_G1

tag: age


title: Tuberculosis 709


title: Tuberculosis 708


title: Tuberculosis 718


title: Tuberculosis 707


title: Cortex1.CCKVLANXX.SM2_042518p2_G12

tag: strain


title: MCF-7 16 h 1 nM E2 220


title: MDA-MB-175-VII 16 h DMSO 277

source_name: MDA-MB-175-VII 16 h DMSO 277

value: 16 h DMSO


title: Tuberculosis 706


title: Cortex1.CCKVLANXX.SM2_042518p2_G11

tag: library construction


title: Tuberculosis 714

tag: tissue


title: Tuberculosis 704


title: Cortex1.CCKVLANXX.SM2_042518p2_H11


title: MDA-MB-157 16 h 1 nM E2 202

value: neg


title: MDA-MB-134-VI 16 h 10 nM E2 187


title: MDA-MB-157 16 h 10 nM E2 205


title: Tuberculosis 705


title: MDA-MB-134-VI 16 h 1 nM E2 184


title: MDA-MB-157 16 h DMSO 199

source_name: MDA-MB-157 16 h DMSO 199


title: Tuberculosis 702


title: MDA-MB-134-VI 16 h DMSO 181

source_name: MDA-MB-134-VI 16 h DMSO 181


title: MCF-7 16 h DMSO 217

source_name: MCF-7 16 h DMSO 217


title: Cortex1.CCKVLANXX.SM2_042518p2_F9


title: Tuberculosis 703

source_name: Tuberculosis


title: Cortex1.CCKVLANXX.SM2_042518p2_F8

source_name: Cortex


title: Tuberculosis 700


title: Tuberculosis 701


title: Tuberculosis 697


title: Tuberculosis 699


title: Tuberculosis 698


title: Cortex1.CCKVLANXX.SM2_042518p2_F6


title: Cortex1.CCKVLANXX.SM2_042518p2_F7


title: Tuberculosis 696


title: Tuberculosis 695


title: Tuberculosis 694


title: Tuberculosis 693


title: Cortex1.CCKVLANXX.SM2_042518p2_F5


title: Tuberculosis 692


title: Tuberculosis 691


title: BT-483 16 h 1 nM E2 166


title: Tuberculosis 690


title: Tuberculosis 689


title: MDA-MB-415 16 h 10 nM E2 151


title: Cortex1.CCKVLANXX.SM2_042518p2_F3


title: Tuberculosis 688


title: Cortex1.CCKVLANXX.SM2_042518p2_F2


title: Tuberculosis 687


title: Cortex1.CCKVLANXX.SM2_042518p2_F4


title: Tuberculosis 686


title: Tuberculosis 685


title: BT-483 16 h DMSO 163


title: Tuberculosis 683


title: MDA-MB-415 16 h 1 nM E2 148


title: T47D 16 h 10 nM E2 115


title: T47D 16 h 1 nM E2 112


title: BT-483 16 h 10 nM E2 169


title: Tuberculosis 681


title: Cortex1.CCKVLANXX.SM2_042518p2_F11


title: T47D 16 h DMSO 109

source_name: T47D 16 h DMSO 109


title: Tuberculosis 680


title: BT-20 16 h 1 nM E2 94


title: MDA-MB-415 16 h DMSO 145

source_name: MDA-MB-415 16 h DMSO 145


title: Cortex1.CCKVLANXX.SM2_042518p2_F12


title: Cortex1.CCKVLANXX.SM2_042518p2_F10


title: Tuberculosis 679


title: Tuberculosis 678


title: Cortex1.CCKVLANXX.SM2_042518p2_F1


title: Tuberculosis 677


title: Cortex1.CCKVLANXX.SM2_042518p2_E9


title: Tuberculosis 684


title: BT-20 16 h DMSO 91

source_name: BT-20 16 h DMSO 91


title: Tuberculosis 676


title: Tuberculosis 675


title: Cortex1.CCKVLANXX.SM2_042518p2_E8


title: Cortex1.CCKVLANXX.SM2_042518p2_E7


title: Tuberculosis 674


title: Tuberculosis 672


title: Cortex1.CCKVLANXX.SM2_042518p2_E6


title: HCC1428 16 h 10 nM E2 79


title: BT-20 16 h 10 nM E2 97


title: Tuberculosis 670


title: Tuberculosis 671


title: HCC1428 16 h 1 nM E2 76


title: Tuberculosis 669


title: BT-474 16 h 10 nM E2 61


title: HCC1428 16 h DMSO 73

source_name: HCC1428 16 h DMSO 73


title: Cortex1.CCKVLANXX.SM2_042518p2_E5


title: Cortex1.CCKVLANXX.SM2_042518p2_E4


title: Tuberculosis 666


title: Tuberculosis 668


title: Tuberculosis 664


title: Cortex1.CCKVLANXX.SM2_042518p2_E3


title: Cortex1.CCKVLANXX.SM2_042518p2_E2


title: Tuberculosis 663


title: Tuberculosis 667


title: Tuberculosis 665


title: Tuberculosis 662


title: Tuberculosis 673


title: BT-474 16 h 1 nM E2 58


title: Cortex1.CCKVLANXX.SM2_042518p2_E12


title: Cortex1.CCKVLANXX.SM2_042518p2_E1


title: Tuberculosis 658


title: Tuberculosis 660


title: Tuberculosis 661


title: CAMA-1 16 h 10 nM E2 43


title: Cortex1.CCKVLANXX.SM2_042518p2_E11


title: CAMA-1 16 h 1 nM E2 40

source_name: CAMA-1 16 h 1 nM E2 40


title: Tuberculosis 682


title: Tuberculosis 656


title: Tuberculosis 655


title: Cortex1.CCKVLANXX.SM2_042518p2_E10


title: CAMA-1 16 h DMSO 37

source_name: CAMA-1 16 h DMSO 37


title: Tuberculosis 653


title: Tuberculosis 652


title: MDA-MB-361 16 h 10 nM E2 7


title: Tuberculosis 650


title: BT-474 16 h DMSO 55


title: Tuberculosis 659


title: Tuberculosis 649


title: Tuberculosis 657


title: Cortex1.CCKVLANXX.SM2_042518p2_D7


title: MDA-MB-361 16 h 1 nM E2 4


title: Tuberculosis 647


title: MDA-MB-361 16 h DMSO 1

source_name: MDA-MB-361 16 h DMSO 1


title: Cortex1.CCKVLANXX.SM2_042518p2_D6


title: Tuberculosis 646


title: hSKP-HPC_'NASH'_elafibranor 30 µM 2

city: Brussels

first: Joost

last: Boeckmans

address: Laarbeeklaan 103

department: In Vitro Toxicology & Dermato-Cosmetology (IVTD)

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

hyb_protocol: 1) 11 µg fragmented aRNA was hybridized to Affymetrix Human Genome U133 plus 2.0 chips with hybridization cocktail solution.  2) Chips were incubated in an Genechip Hybridization Oven-645 (Affymetrix) (60 RPM / 45 °C /16h)  3) Chips were washed on a Genechip Fluidics Station-450 (Affymetrix)  4) Chips were stained with the Affymetrix HWS kit

scan_protocol: The chips were scanned with an Affymetrix Gene-Chip Scanner-3000-7G.

data_processing: Robust Multichip Average (RMA) Express was used for normalization and summarization.

source_name: foreskin

label_protocol: RNA (100 ng) was amplified using the GeneChip 3' IVT PLUS Reagent Kit (Affymetrix). The amplified RNA was purified using magnetic beads and treated with fragmentation reagent.

growth_protocol: hSKP were isolated, cultivated and differentiated towards hepatic cells according to Rodrigues et al. (2014) (DOI: 10.1089/scd.2013.0157).

extract_protocol: Total RNA was extracted using the GenElute Mammalian Total RNA Purification Miniprep Kit (Sigma-Aldrich).

treatment_protocol: See SAMPLES section.

tag: treatment

value: Elafibranor 30 microM


title: hSKP-HPC_'NASH'_elafibranor 30 µM 3


title: hSKP-HPC_'NASH'_elafibranor 30 µM 1


title: Tuberculosis 654


title: Tuberculosis 645


title: Cortex1.CCKVLANXX.SM2_042518p2_D5


title: Cortex1.CCKVLANXX.SM2_042518p2_D9


title: Tuberculosis 644


title: Tuberculosis 651


title: Cortex1.CCKVLANXX.SM2_042518p2_D8


title: Cortex1.CCKVLANXX.SM2_042518p2_D4


title: Tuberculosis 640


title: Tuberculosis 642


title: Tuberculosis 641


title: Cortex1.CCKVLANXX.SM2_042518p2_D3


title: Cortex1.CCKVLANXX.SM2_042518p2_D2


title: Tuberculosis 648


title: hSKP-HPC_'NASH'_elafibranor 10 µM 3

value: Elafibranor 10 microM


title: Tuberculosis 639


title: Tuberculosis 638


title: Cortex1.CCKVLANXX.SM2_042518p2_D1

value: Male


title: hSKP-HPC_'NASH'_elafibranor 10 µM 1


title: hSKP-HPC_'NASH'_elafibranor 10 µM 2


title: Tuberculosis 637


title: Tuberculosis 643


title: Tuberculosis 636


title: Cortex1.CCKVLANXX.SM2_042518p2_D12

value: one month


title: Tuberculosis 630

value: Blood


title: Tuberculosis 632


title: Cortex1.CCKVLANXX.SM2_042518p2_D10


title: Tuberculosis 633


title: Cortex1.CCKVLANXX.SM2_042518p2_D11


title: Tuberculosis 634


title: Tuberculosis 629


title: Cortex1.CCKVLANXX.SM2_042518p2_C9


title: Tuberculosis 631


title: Tuberculosis 635


title: sgRNA_METTL3_wildtype_RNA_seq_rep2

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

data_processing:
Adaptor AAAAAAAAAA and low quality bases were removed by Cutadapt. The reads with trimmed length shorter than 15 nt were discarded.
The trimmed reads were aligned to human transcriptome (GRCh38.81), by bowtie using parameters: -a --best -m1 --strata. To compile the unique human transcripts, for each gene, the longest isoform was used, based on CDS length. In the case of equal CDS length, the isoform with longer UTRs was selected.
Peak calling was performed according the work of Schwartz et al., 2014 (PMC4142486).
Genome_build: GRCh38.81
Supplementary_files_format_and_content: m6A_peak_sgControl_forFTO.txt: Tab-delimited peak file. The columns are: transcript name, peak start, peak stop, peak summit, normalized m6A coverage, m6A coverage, input coverage.
Supplementary_files_format_and_content: m6A_peak_sgControl_forMETTL3.txt: Tab-delimited peak file. The columns are: transcript name, peak start, peak stop, peak summit, normalized m6A coverage, m6A coverage, input coverage.
Supplementary_files_format_and_content: m6A_peak_sgRNA_FTO_mutation.txt: Tab-delimited peak file. The columns are: transcript name, peak start, peak stop, peak summit, normalized m6A coverage, m6A coverage, input coverage.
Supplementary_files_format_and_content: m6A_peak_sgRNA_FTO_wildtype.txt: Tab-delimited peak file. The columns are: transcript name, peak start, peak stop, peak summit, normalized m6A coverage, m6A coverage, input coverage.
Supplementary_files_format_and_content: m6A_peak_sgRNA_METTL3_mutation.txt: Tab-delimited peak file. The columns are: transcript name, peak start, peak stop, peak summit, normalized m6A coverage, m6A coverage, input coverage.
Supplementary_files_format_and_content: m6A_peak_sgRNA_METTL3_wildtype.txt: Tab-delimited peak file. The columns are: transcript name, peak start, peak stop, peak summit, normalized m6A coverage, m6A coverage, input coverage.
Supplementary_files_format_and_content: 7_coverage_sgControl_RNA_seq.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 8_coverage_sgRNA_METTL3_wildtype_RNA_seq_rep3.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 9_coverage_sgsgRNA_FTO_wildtype_RNA_seq_rep1.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 10_coverage_sgRNA_FTO_mutation_RNA_seq_rep1.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 11_coverage_sgRNA_METTL3_wildtype_RNA_seq_rep1.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 12_coverage_sgRNA_METTL3_mutation_RNA_seq_rep1.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 13_coverage_sgRNA_FTO_wildtype_RNA_seq_rep2.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 14_coverage_sgRNA_FTO_mutation_RNA_seq_rep2.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 15_coverage_sgRNA_METTL3_wildtype_RNA_seq_rep2.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 16_coverage_sgRNA_METTL3_mutation_RNA_seq_rep2.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.

source_name: HeLa

growth_protocol: HeLa cells were maintained in Dulbecco's Modification of Eagle's Medium (Corning 10-013-CV) with 10% Fetal Bovine Serum (FBS, Sigma 12306C).

extract_protocol:
Total RNA was isolated using Trizol reagent followed by fragmentation using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl pH 7.0, 10 mM ZnCl2). 180 μg fragmented RNA was incubated with 6 μg anti-m6A antibody in 1× m6A IP buffer (10 mM Tris-HCl pH 7.4, 150 mM NaCl, and 0.1% Igepal CA-630) supplemented with 6 µL RNase OUT (40 U/µL) and 2 mM RVC for 2 h at 4°C. The m6A-IP mixture was then incubated with Protein A/G beads and rotated for additional 3 h at 4°C. Following four washes in 1× IP buffer, m6A-containing RNA fragments were eluted by incubation with 200 μl elution buffer (6.7 mM N6-methyladenosine 5’-monophosphate sodium salt in 1× IP buffer) for 1 h at 4°C. Eluted RNA was used for libraries constrution.
m6A-containing RNAs (m6A-seq) or fragmented total RNAs (RNA-seq) were dephosphorylated for 1 hr at 37°C in 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). The gel with selected regions 40-60 nt was excised and disrupted by using centrifugation through the holes at the bottom of the tube. RNA fragments were dissolved by soaking overnight in 400 μl gel elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U/ml SUPERase_In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were re-suspended in nuclease-free water. Poly-(A) tailing reaction was carried out for 45 min at 37°C (1 × poly-(A) polymerase buffer, 1 mM ATP, 0.75 U/μl SUPERase_ In and 3 U E. coli poly-(A) polymerase).

treatment_protocol: Cells were washed three times by using PBS. RNA was isolated after adding the Trizol reagent.

value: HeLa


title: Cortex1.CCKVLANXX.SM2_042518p2_C8


title: Cortex1.CCKVLANXX.SM2_042518p2_G10


title: Tuberculosis 625


title: Cortex1.CCKVLANXX.SM2_042518p2_C7


title: Tuberculosis 626


title: sgRNA_METTL3_mutation_RNA_seq_rep2


title: Tuberculosis 627


title: sgRNA_FTO_wildtype_RNA_seq_rep2


title: Cortex1.CCKVLANXX.SM2_042518p2_C6


title: sgRNA_FTO_mutation_RNA_seq_rep2


title: Tuberculosis 623


title: Tuberculosis 624


title: Cortex1.CCKVLANXX.SM2_042518p2_C5


title: Tuberculosis 621


title: Tuberculosis 620


title: sgRNA_METTL3_mutation_RNA_seq_rep1


title: sgRNA_METTL3_wildtype_RNA_seq_rep1


title: Tuberculosis 628


title: Tuberculosis 618


title: Cortex1.CCKVLANXX.SM2_042518p2_C4


title: Tuberculosis 617


title: Cortex1.CCKVLANXX.SM2_042518p2_C3


title: sgRNA_FTO_wildtype_RNA_seq_rep1


title: Tuberculosis 619


title: sgRNA_FTO_mutation_RNA_seq_rep1


title: Tuberculosis 615


title: Cortex1.CCKVLANXX.SM2_042518p2_C1


title: sgRNA_METTL3_wildtype_RNA_seq_rep3


title: Tuberculosis 614


title: Tuberculosis 612


title: sgControl_RNA_seq


title: Tuberculosis 611


title: Tuberculosis 610


title: Tuberculosis 609


title: sgRNA_FTO_mutation_m6A_seq

data_processing:
Library strategy: m6A-seq
Adaptor AAAAAAAAAA and low quality bases were removed by Cutadapt. The reads with trimmed length shorter than 15 nt were discarded.
The trimmed reads were aligned to human transcriptome (GRCh38.81), by bowtie using parameters: -a --best -m1 --strata. To compile the unique human transcripts, for each gene, the longest isoform was used, based on CDS length. In the case of equal CDS length, the isoform with longer UTRs was selected.
Peak calling was performed according the work of Schwartz et al., 2014 (PMC4142486).
Genome_build: GRCh38.81
Supplementary_files_format_and_content: m6A_peak_sgControl_forFTO.txt: Tab-delimited peak file. The columns are: transcript name, peak start, peak stop, peak summit, normalized m6A coverage, m6A coverage, input coverage.
Supplementary_files_format_and_content: m6A_peak_sgControl_forMETTL3.txt: Tab-delimited peak file. The columns are: transcript name, peak start, peak stop, peak summit, normalized m6A coverage, m6A coverage, input coverage.
Supplementary_files_format_and_content: m6A_peak_sgRNA_FTO_mutation.txt: Tab-delimited peak file. The columns are: transcript name, peak start, peak stop, peak summit, normalized m6A coverage, m6A coverage, input coverage.
Supplementary_files_format_and_content: m6A_peak_sgRNA_FTO_wildtype.txt: Tab-delimited peak file. The columns are: transcript name, peak start, peak stop, peak summit, normalized m6A coverage, m6A coverage, input coverage.
Supplementary_files_format_and_content: m6A_peak_sgRNA_METTL3_mutation.txt: Tab-delimited peak file. The columns are: transcript name, peak start, peak stop, peak summit, normalized m6A coverage, m6A coverage, input coverage.
Supplementary_files_format_and_content: m6A_peak_sgRNA_METTL3_wildtype.txt: Tab-delimited peak file. The columns are: transcript name, peak start, peak stop, peak summit, normalized m6A coverage, m6A coverage, input coverage.
Supplementary_files_format_and_content: 7_coverage_sgControl_RNA_seq.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 8_coverage_sgRNA_METTL3_wildtype_RNA_seq_rep3.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 9_coverage_sgsgRNA_FTO_wildtype_RNA_seq_rep1.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 10_coverage_sgRNA_FTO_mutation_RNA_seq_rep1.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 11_coverage_sgRNA_METTL3_wildtype_RNA_seq_rep1.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 12_coverage_sgRNA_METTL3_mutation_RNA_seq_rep1.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 13_coverage_sgRNA_FTO_wildtype_RNA_seq_rep2.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 14_coverage_sgRNA_FTO_mutation_RNA_seq_rep2.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 15_coverage_sgRNA_METTL3_wildtype_RNA_seq_rep2.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.
Supplementary_files_format_and_content: 16_coverage_sgRNA_METTL3_mutation_RNA_seq_rep2.txt.gz: Tab-delimited text file includes coverage at individual sites of transcript.

tag: antibody

value: Anti-m6A (Abcam, ab151230)


title: Tuberculosis 622


title: Cortex1.CCKVLANXX.SM2_042518p2_C11


title: Tuberculosis 608


title: Cortex1.CCKVLANXX.SM2_042518p2_C12


title: Cortex1.CCKVLANXX.SM2_042518p2_C10


title: Tuberculosis 606


title: Tuberculosis 607


title: Tuberculosis 613


title: Tuberculosis 605


title: Cortex1.CCKVLANXX.SM2_042518p2_B9


title: Tuberculosis 604


title: sgRNA_METTL3_mutation_m6A_seq


title: sgControl_forFTO_m6A_seq


title: Cortex1.CCKVLANXX.SM2_042518p2_C2


title: Cortex1.CCKVLANXX.SM2_042518p2_B8


title: Cortex1.CCKVLANXX.SM2_042518p2_B7


title: sgRNA_METTL3_wildtype_m6A_seq


title: Tuberculosis 602


title: Tuberculosis 601


title: Tuberculosis 616


title: Cortex1.CCKVLANXX.SM2_042518p2_B6


title: Tuberculosis 600


title: sgControl_forMETTL3_m6A_seq


title: Tuberculosis 599


title: Tuberculosis 598


title: Tuberculosis 603


title: Cortex1.CCKVLANXX.SM2_042518p2_B5


title: Tuberculosis 597


title: Tuberculosis 595


title: PBMC2.CC86JANXX.SM2_011818p5_H9

description:
scRNA-seq
full-length
pbmc_hg38_count_matrix.mtx, pbmc_hg38_gene.tsv, pbmc_hg38_cell.tsv

source_name: Peripheral blood mononuclear cell

value: Female


title: PBMC2.CC86JANXX.SM2_011818p5_H8


title: Cortex1.CCKVLANXX.SM2_042518p2_B4


title: PBMC2.CC86JANXX.SM2_011818p5_H7


title: Tuberculosis 594


title: Tuberculosis 593


title: Tuberculosis 592


title: PBMC2.CC86JANXX.SM2_011818p5_H6


title: Tuberculosis 591


title: Tuberculosis 590


title: PBMC2.CC86JANXX.SM2_011818p5_H5


title: Cortex1.CCKVLANXX.SM2_042518p2_B2


title: Tuberculosis 589


title: Tuberculosis 588


title: PBMC2.CC86JANXX.SM2_011818p5_H4


title: Tuberculosis 587


title: Cortex1.CCKVLANXX.SM2_042518p2_B12


title: Tuberculosis 586


title: Tuberculosis 596


title: Tuberculosis 585


title: Cortex1.CCKVLANXX.SM2_042518p2_B11


title: PBMC2.CC86JANXX.SM2_011818p5_H2


title: Tuberculosis 584


title: PBMC2.CC86JANXX.SM2_011818p5_H3


title: Cortex1.CCKVLANXX.SM2_042518p2_B10


title: Cortex1.CCKVLANXX.SM2_042518p2_A9


title: PBMC2.CC86JANXX.SM2_011818p5_H1


title: Cortex1.CCKVLANXX.SM2_042518p2_B3


title: PBMC2.CC86JANXX.SM2_011818p5_H12


title: Cortex1.CCKVLANXX.SM2_042518p2_A8


title: Tuberculosis 579


title: Tuberculosis 578


title: Cortex1.CCKVLANXX.SM2_042518p2_B1


title: PBMC2.CC86JANXX.SM2_011818p5_H11


title: Tuberculosis 577


title: Cortex1.CCKVLANXX.SM2_042518p2_A7


title: PBMC2.CC86JANXX.SM2_011818p5_H10


title: Tuberculosis 576


title: Cortex1.CCKVLANXX.SM2_042518p2_A6


title: Tuberculosis 575


title: Tuberculosis 574


title: Tuberculosis 573


title: Tuberculosis 572


title: PBMC2.CC86JANXX.SM2_011818p5_G9


title: PBMC2.CC86JANXX.SM2_011818p5_G8


title: Tuberculosis 583


title: Cortex1.CCKVLANXX.SM2_042518p2_A5


title: Tuberculosis 571


title: Tuberculosis 570


title: Cortex1.CCKVLANXX.SM2_042518p2_A3


title: Tuberculosis 580


title: Tuberculosis 581


title: Tuberculosis 582


title: PBMC2.CC86JANXX.SM2_011818p5_G7


title: Cortex1.CCKVLANXX.SM2_042518p2_A4


title: Tuberculosis 569


title: PBMC2.CC86JANXX.SM2_011818p5_G6


title: Tuberculosis 568


title: Tuberculosis 567


title: Tuberculosis 566


title: Tuberculosis 565


title: PBMC2.CC86JANXX.SM2_011818p5_G5


title: PBMC2.CC86JANXX.SM2_011818p5_G4


title: Cortex1.CCKVLANXX.SM2_042518p2_A12


title: PBMC2.CC86JANXX.SM2_011818p5_G3


title: Cortex1.CCKVLANXX.SM2_042518p2_A2


title: Cortex1.CCKVLANXX.SM2_042518p2_A1


title: Cortex1.CCKVLANXX.SM2_042518p2_A11


title: PBMC2.CC86JANXX.SM2_011818p5_G2


title: Cortex1.CCKVLANXX.SM2_042518p2_A10


title: Tuberculosis 561


title: Tuberculosis 562


title: Tuberculosis 563


title: PBMC2.CC86JANXX.SM2_011818p5_G1


title: Tuberculosis 564


title: Tuberculosis 558


title: Tuberculosis 560


title: Tuberculosis 559


title: Cortex1.CCKVLANXX.SM2_042518p1_H9


title: PBMC2.CC86JANXX.SM2_011818p5_G12


title: Tuberculosis 556


title: Tuberculosis 555


title: Cortex1.CCKVLANXX.SM2_042518p1_H8


title: PBMC2.CC86JANXX.SM2_011818p5_G11


title: Tuberculosis 557


title: Tuberculosis 554


title: Tuberculosis 553


title: Cortex1.CCKVLANXX.SM2_042518p1_H7


title: PBMC2.CC86JANXX.SM2_011818p5_G10


title: Tuberculosis 552


title: Tuberculosis 551


title: Cortex1.CCKVLANXX.SM2_042518p1_H6


title: Tuberculosis 550


title: Cortex1.CCKVLANXX.SM2_042518p1_H5


title: PBMC2.CC86JANXX.SM2_011818p5_F8


title: Tuberculosis 548


title: Tuberculosis 547


title: Tuberculosis 546


title: PBMC2.CC86JANXX.SM2_011818p5_F7


title: Cortex1.CCKVLANXX.SM2_042518p1_H2


title: PBMC2.CC86JANXX.SM2_011818p5_F6


title: Cortex1.CCKVLANXX.SM2_042518p1_H3


title: Cortex1.CCKVLANXX.SM2_042518p1_H4


title: Tuberculosis 544


title: Tuberculosis 545


title: Tuberculosis 540


title: Tuberculosis 542


title: PBMC2.CC86JANXX.SM2_011818p5_F4


title: PBMC2.CC86JANXX.SM2_011818p5_F5


title: Cortex1.CCKVLANXX.SM2_042518p1_H1


title: Tuberculosis 541


title: Cortex1.CCKVLANXX.SM2_042518p1_H12


title: Tuberculosis 543


title: sgRNA_FTO_wildtype_m6A_seq


title: Tuberculosis 539


title: PBMC2.CC86JANXX.SM2_011818p5_F3


title: PBMC2.CC86JANXX.SM2_011818p5_F2


title: Tuberculosis 538


title: Tuberculosis 537


title: PBMC2.CC86JANXX.SM2_011818p5_F9


title: Cortex1.CCKVLANXX.SM2_042518p1_H11


title: Cortex1.CCKVLANXX.SM2_042518p1_H10


title: Tuberculosis 549


title: PBMC2.CC86JANXX.SM2_011818p5_F1


title: Tuberculosis 535


title: Tuberculosis 534


title: Tuberculosis 536


title: Cortex1.CCKVLANXX.SM2_042518p1_G9


title: PBMC2.CC86JANXX.SM2_011818p5_F12


title: Tuberculosis 531


title: Cortex1.CCKVLANXX.SM2_042518p1_G8


title: Tuberculosis 530


title: Tuberculosis 529


title: PBMC2.CC86JANXX.SM2_011818p5_F11


title: Cortex1.CCKVLANXX.SM2_042518p1_G6


title: Tuberculosis 526


title: Cortex1.CCKVLANXX.SM2_042518p1_G7


title: Tuberculosis 528


title: Tuberculosis 525


title: PBMC2.CC86JANXX.SM2_011818p5_E9


title: Tuberculosis 524


title: Cortex1.CCKVLANXX.SM2_042518p1_G5


title: PBMC2.CC86JANXX.SM2_011818p5_E8


title: Tuberculosis 523


title: PBMC2.CC86JANXX.SM2_011818p5_E7


title: Cortex1.CCKVLANXX.SM2_042518p1_G4


title: Cortex1.CCKVLANXX.SM2_042518p1_G3


title: Tuberculosis 521


title: Tuberculosis 519


title: PBMC2.CC86JANXX.SM2_011818p5_E6


title: Cortex1.CCKVLANXX.SM2_042518p1_G2


title: Tuberculosis 533


title: Tuberculosis 520


title: Tuberculosis 532


title: Tuberculosis 518


title: PBMC2.CC86JANXX.SM2_011818p5_E5


title: PBMC2.CC86JANXX.SM2_011818p5_F10


title: Tuberculosis 517


title: Tuberculosis 515


title: Cortex1.CCKVLANXX.SM2_042518p1_G12


title: Cortex1.CCKVLANXX.SM2_042518p1_G1


title: Tuberculosis 516


title: PBMC2.CC86JANXX.SM2_011818p5_E3


title: Cortex1.CCKVLANXX.SM2_042518p1_G11


title: PBMC2.CC86JANXX.SM2_011818p5_E2


title: Tuberculosis 527


title: Tuberculosis 522


title: Cortex1.CCKVLANXX.SM2_042518p1_G10


title: Tuberculosis 513


title: Tuberculosis 512


title: Tuberculosis 511


title: Tuberculosis 514


title: Tuberculosis 510


title: PBMC2.CC86JANXX.SM2_011818p5_E1


title: Tuberculosis 509


title: Cortex1.CCKVLANXX.SM2_042518p1_F9


title: PBMC2.CC86JANXX.SM2_011818p5_E12


title: Tuberculosis 507


title: PBMC2.CC86JANXX.SM2_011818p5_E11


title: Cortex1.CCKVLANXX.SM2_042518p1_F8


title: Cortex1.CCKVLANXX.SM2_042518p1_F7


title: PBMC2.CC86JANXX.SM2_011818p5_E4


title: Tuberculosis 504


title: PBMC2.CC86JANXX.SM2_011818p5_E10


title: Cortex1.CCKVLANXX.SM2_042518p1_F6


title: Tuberculosis 502


title: Tuberculosis 506


title: Cortex1.CCKVLANXX.SM2_042518p1_F5


title: Tuberculosis 501


title: Tuberculosis 500


title: Tuberculosis 497


title: Tuberculosis 499


title: Tuberculosis 498


title: Cortex1.CCKVLANXX.SM2_042518p1_F4


title: Tuberculosis 495


title: PBMC2.CC86JANXX.SM2_011818p5_D7


title: PBMC2.CC86JANXX.SM2_011818p5_D6


title: Tuberculosis 494


title: Tuberculosis 496


title: Tuberculosis 508


title: Cortex1.CCKVLANXX.SM2_042518p1_F2


title: PBMC2.CC86JANXX.SM2_011818p5_D8


title: PBMC2.CC86JANXX.SM2_011818p5_D5


title: Tuberculosis 505


title: Tuberculosis 493


title: PBMC2.CC86JANXX.SM2_011818p5_D4


title: Tuberculosis 492


title: Tuberculosis 491


title: Tuberculosis 503


title: PBMC2.CC86JANXX.SM2_011818p5_D9


title: Cortex1.CCKVLANXX.SM2_042518p1_F12


title: Tuberculosis 488


title: Tuberculosis 489


title: Cortex1.CCKVLANXX.SM2_042518p1_F3


title: PBMC2.CC86JANXX.SM2_011818p5_D2


title: Cortex1.CCKVLANXX.SM2_042518p1_F10


title: Tuberculosis 486


title: Tuberculosis 484


title: PBMC2.CC86JANXX.SM2_011818p5_D12


title: Tuberculosis 483


title: Cortex1.CCKVLANXX.SM2_042518p1_E8


title: PBMC2.CC86JANXX.SM2_011818p5_D11


title: Cortex1.CCKVLANXX.SM2_042518p1_E7


title: Cortex1.CCKVLANXX.SM2_042518p1_E9


title: Tuberculosis 481


title: Tuberculosis 482


title: Tuberculosis 480


title: Cortex1.CCKVLANXX.SM2_042518p1_E6


title: Tuberculosis 490


title: Tuberculosis 479


title: PBMC2.CC86JANXX.SM2_011818p5_D1


title: Tuberculosis 477


title: Cortex1.CCKVLANXX.SM2_042518p1_E5


title: PBMC2.CC86JANXX.SM2_011818p5_D3


title: PBMC2.CC86JANXX.SM2_011818p5_D10


title: PBMC2.CC86JANXX.SM2_011818p5_C9


title: Tuberculosis 478


title: Cortex1.CCKVLANXX.SM2_042518p1_F11


title: PBMC2.CC86JANXX.SM2_011818p5_C8


title: Tuberculosis 476


title: Cortex1.CCKVLANXX.SM2_042518p1_F1


title: Tuberculosis 487


title: Tuberculosis 485


title: Cortex1.CCKVLANXX.SM2_042518p1_E4


title: PBMC2.CC86JANXX.SM2_011818p5_C7


title: Tuberculosis 475


title: Cortex1.CCKVLANXX.SM2_042518p1_E3


title: Tuberculosis 473


title: Tuberculosis 472


title: PBMC2.CC86JANXX.SM2_011818p5_C6


title: Cortex1.CCKVLANXX.SM2_042518p1_E2


title: Tuberculosis 471


title: Cortex1.CCKVLANXX.SM2_042518p1_E1


title: PBMC2.CC86JANXX.SM2_011818p5_C5


title: Tuberculosis 469


title: Tuberculosis 470


title: PBMC2.CC86JANXX.SM2_011818p5_C4


title: Tuberculosis 468


title: Tuberculosis 467


title: Tuberculosis 466


title: Tuberculosis 464


title: Tuberculosis 465


title: PBMC2.CC86JANXX.SM2_011818p5_C2


title: Cortex1.CCKVLANXX.SM2_042518p1_E12


title: Cortex1.CCKVLANXX.SM2_042518p1_E11


title: Tuberculosis 462


title: PBMC2.CC86JANXX.SM2_011818p5_C3


title: PBMC2.CC86JANXX.SM2_011818p5_C1


title: Tuberculosis 461


title: Cortex1.CCKVLANXX.SM2_042518p1_E10


title: Tuberculosis 460


title: PBMC2.CC86JANXX.SM2_011818p5_C12


title: Cortex1.CCKVLANXX.SM2_042518p1_D9


title: Cortex1.CCKVLANXX.SM2_042518p1_D8


title: Tuberculosis 459


title: PBMC2.CC86JANXX.SM2_011818p5_C11


title: Tuberculosis 458


title: Tuberculosis 457


title: Tuberculosis 474


title: Cortex1.CCKVLANXX.SM2_042518p1_D7


title: PBMC2.CC86JANXX.SM2_011818p5_C10


title: Cortex1.CCKVLANXX.SM2_042518p1_D6


title: Cortex1.CCKVLANXX.SM2_042518p1_D5


title: PBMC2.CC86JANXX.SM2_011818p5_B9


title: Tuberculosis 455


title: Tuberculosis 453


title: PBMC2.CC86JANXX.SM2_011818p5_B8


title: Tuberculosis 463


title: Tuberculosis 451


title: PBMC2.CC86JANXX.SM2_011818p5_B7


title: Tuberculosis 450


title: Tuberculosis 449


title: Cortex1.CCKVLANXX.SM2_042518p1_D3


title: Tuberculosis 448


title: Cortex1.CCKVLANXX.SM2_042518p1_D4


title: Tuberculosis 446


title: Cortex1.CCKVLANXX.SM2_042518p1_D2


title: Tuberculosis 447


title: PBMC2.CC86JANXX.SM2_011818p5_B6


title: PBMC2.CC86JANXX.SM2_011818p5_B5


title: Tuberculosis 445


title: Cortex1.CCKVLANXX.SM2_042518p1_D1


title: Tuberculosis 452


title: Tuberculosis 444


title: PBMC2.CC86JANXX.SM2_011818p5_B4


title: Cortex1.CCKVLANXX.SM2_042518p1_D12


title: Tuberculosis 456


title: Tuberculosis 443


title: Tuberculosis 454


title: Tuberculosis 442


title: PBMC2.CC86JANXX.SM2_011818p5_B3


title: Cortex1.CCKVLANXX.SM2_042518p1_D11


title: Tuberculosis 440


title: Cortex1.CCKVLANXX.SM2_042518p1_D10


title: Tuberculosis 441


title: Tuberculosis 438


title: Tuberculosis 439


title: PBMC2.CC86JANXX.SM2_011818p5_B1


title: Cortex1.CCKVLANXX.SM2_042518p1_C9


title: PBMC2.CC86JANXX.SM2_011818p5_B2


title: Tuberculosis 436


title: PBMC2.CC86JANXX.SM2_011818p5_B12


title: Tuberculosis 435


title: Cortex1.CCKVLANXX.SM2_042518p1_C8


title: PBMC2.CC86JANXX.SM2_011818p5_B11


title: Tuberculosis 434


title: Tuberculosis 432


title: PBMC2.CC86JANXX.SM2_011818p5_B10


title: Tuberculosis 437


title: Cortex1.CCKVLANXX.SM2_042518p1_C6


title: Tuberculosis 431


title: Tuberculosis 430


title: PBMC2.CC86JANXX.SM2_011818p5_A9


title: Tuberculosis 429


title: PBMC2.CC86JANXX.SM2_011818p5_A8


title: Tuberculosis 428


title: Cortex1.CCKVLANXX.SM2_042518p1_C5


title: Cortex1.CCKVLANXX.SM2_042518p1_C4


title: PBMC2.CC86JANXX.SM2_011818p5_A7


title: Tuberculosis 427


title: Tuberculosis 426


title: Tuberculosis 425


title: Cortex1.CCKVLANXX.SM2_042518p1_C3


title: PBMC2.CC86JANXX.SM2_011818p5_A6


title: Cortex1.CCKVLANXX.SM2_042518p1_C2


title: Tuberculosis 424


title: Tuberculosis 422


title: Tuberculosis 423


title: Tuberculosis 433


title: Cortex1.CCKVLANXX.SM2_042518p1_C7


title: Tuberculosis 420


title: Cortex1.CCKVLANXX.SM2_042518p1_C12


title: Tuberculosis 421


title: Tuberculosis 418


title: Tuberculosis 417


title: PBMC2.CC86JANXX.SM2_011818p5_A3


title: PBMC2.CC86JANXX.SM2_011818p5_A4


title: Tuberculosis 416


title: Tuberculosis 415


title: Cortex1.CCKVLANXX.SM2_042518p1_C10


title: Tuberculosis 414


title: PBMC2.CC86JANXX.SM2_011818p5_A1


title: PBMC2.CC86JANXX.SM2_011818p5_A2


title: Tuberculosis 413


title: Tuberculosis 412


title: Cortex1.CCKVLANXX.SM2_042518p1_C1


title: PBMC2.CC86JANXX.SM2_011818p5_A12


title: Tuberculosis 411


title: Cortex1.CCKVLANXX.SM2_042518p1_B8


title: Tuberculosis 410


title: PBMC2.CC86JANXX.SM2_011818p5_A11


title: PBMC2.CC86JANXX.SM2_011818p5_A5


title: Cortex1.CCKVLANXX.SM2_042518p1_B7


title: Tuberculosis 409


title: PBMC2.CC86JANXX.SM2_011818p5_A10


title: Cortex1.CCKVLANXX.SM2_042518p1_B6


title: Cortex1.CCKVLANXX.SM2_042518p1_C11


title: Tuberculosis 407


title: Tuberculosis 406


title: Tuberculosis 405


title: Tuberculosis 419


title: Cortex1.CCKVLANXX.SM2_042518p1_B5


title: Tuberculosis 408


title: PBMC2.CC86JANXX.SM2_011818p4_H8


title: Cortex1.CCKVLANXX.SM2_042518p1_B4


title: Tuberculosis 403


title: Tuberculosis 404


title: Cortex1.CCKVLANXX.SM2_042518p1_B9


title: Tuberculosis 402


title: PBMC2.CC86JANXX.SM2_011818p4_H7


title: Tuberculosis 401


title: Cortex1.CCKVLANXX.SM2_042518p1_B2


title: Tuberculosis 400


title: PBMC2.CC86JANXX.SM2_011818p4_H6


title: Tuberculosis 399


title: Tuberculosis 398


title: Cortex1.CCKVLANXX.SM2_042518p1_B3


title: Tuberculosis 397


title: PBMC2.CC86JANXX.SM2_011818p4_H4


title: Cortex1.CCKVLANXX.SM2_042518p1_B1


title: Tuberculosis 396


title: PBMC2.CC86JANXX.SM2_011818p4_H5


title: Cortex1.CCKVLANXX.SM2_042518p1_B12


title: PBMC2.CC86JANXX.SM2_011818p4_H9


title: Tuberculosis 395


title: PBMC2.CC86JANXX.SM2_011818p4_H3


title: Tuberculosis 394


title: Tuberculosis 393


title: Tuberculosis 392


title: Cortex1.CCKVLANXX.SM2_042518p1_B11


title: PBMC2.CC86JANXX.SM2_011818p4_H2


title: Tuberculosis 391


title: PBMC2.CC86JANXX.SM2_011818p4_H1


title: Cortex1.CCKVLANXX.SM2_042518p1_B10


title: PBMC2.CC86JANXX.SM2_011818p4_H12


title: Tuberculosis 388


title: Cortex1.CCKVLANXX.SM2_042518p1_A8


title: Tuberculosis 386


title: PBMC2.CC86JANXX.SM2_011818p4_H11


title: Tuberculosis 389


title: Cortex1.CCKVLANXX.SM2_042518p1_A9


title: Cortex1.CCKVLANXX.SM2_042518p1_A7


title: Tuberculosis 384


title: Tuberculosis 382


title: Tuberculosis 383


title: PBMC2.CC86JANXX.SM2_011818p4_G9


title: Cortex1.CCKVLANXX.SM2_042518p1_A6


title: Cortex1.CCKVLANXX.SM2_042518p1_A5


title: Tuberculosis 380


title: PBMC2.CC86JANXX.SM2_011818p4_G8


title: Tuberculosis 379


title: PBMC2.CC86JANXX.SM2_011818p4_H10


title: Cortex1.CCKVLANXX.SM2_042518p1_A3


title: Tuberculosis 378


title: Tuberculosis 390


title: Cortex1.CCKVLANXX.SM2_042518p1_A4


title: Tuberculosis 376


title: Cortex1.CCKVLANXX.SM2_042518p1_A2


title: PBMC2.CC86JANXX.SM2_011818p4_G6


title: Tuberculosis 374


title: PBMC2.CC86JANXX.SM2_011818p4_G5


title: Tuberculosis 375


title: Tuberculosis 385


title: PBMC2.CC86JANXX.SM2_011818p4_G7


title: Tuberculosis 381


title: Tuberculosis 373


title: Tuberculosis 387


title: Tuberculosis 372


title: PBMC2.CC86JANXX.SM2_011818p4_G4


title: Cortex1.CCKVLANXX.SM2_042518p1_A12


title: Tuberculosis 377


title: Tuberculosis 371


title: Tuberculosis 370


title: PBMC2.CC86JANXX.SM2_011818p4_G3


title: Cortex1.CCKVLANXX.SM2_042518p1_A11


title: PBMC2.CC86JANXX.SM2_011818p4_G2


title: Cortex1.CCKVLANXX.SM2_042518p1_A10


title: Tuberculosis 367


title: PBMC2.CC86JANXX.SM2_011818p4_G1


title: Tuberculosis 366


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_H9

description:
scRNA-seq
3'-end
cortex_mm10_count_matrix.mtx, cortex_mm10_gene.tsv, cortex_mm10_cell.tsv

value: sci-RNA-seq


title: Tuberculosis 365


title: Tuberculosis 364


title: PBMC2.CC86JANXX.SM2_011818p4_G12


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_H8


title: Tuberculosis 363


title: PBMC2.CC86JANXX.SM2_011818p4_G11


title: Tuberculosis 362


title: Cortex1.CCKVLANXX.SM2_042518p1_A1


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_H7


title: Tuberculosis 360


title: Tuberculosis 359


title: PBMC2.CC86JANXX.SM2_011818p4_G10


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_H6


title: Tuberculosis 357


title: PBMC2.CC86JANXX.SM2_011818p4_F9


title: Tuberculosis 355


title: Tuberculosis 361


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_H4


title: Tuberculosis 358


title: Tuberculosis 368


title: Tuberculosis 369


title: Tuberculosis 356


title: Tuberculosis 354


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_H3


title: PBMC2.CC86JANXX.SM2_011818p4_F6


title: Tuberculosis 352


title: PBMC2.CC86JANXX.SM2_011818p4_F8


title: Tuberculosis 353


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_H2


title: Tuberculosis 351


title: PBMC2.CC86JANXX.SM2_011818p4_F5


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_H1


title: Tuberculosis 350


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_H12


title: Tuberculosis 347


title: Tuberculosis 348


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_H5


title: PBMC2.CC86JANXX.SM2_011818p4_F3


title: Tuberculosis 345


title: Tuberculosis 349


title: Tuberculosis 346


title: PBMC2.CC86JANXX.SM2_011818p4_F2


title: Tuberculosis 344


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_G9


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_H10


title: Tuberculosis 341


title: Tuberculosis 342


title: PBMC2.CC86JANXX.SM2_011818p4_F1


title: PBMC2.CC86JANXX.SM2_011818p4_F7


title: Tuberculosis 338


title: Tuberculosis 339


title: PBMC2.CC86JANXX.SM2_011818p4_F11


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_G7


title: PBMC2.CC86JANXX.SM2_011818p4_F12


title: Tuberculosis 340


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_G8


title: PBMC2.CC86JANXX.SM2_011818p4_F4


title: Tuberculosis 336


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_H11


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_G6


title: Tuberculosis 335


title: PBMC2.CC86JANXX.SM2_011818p4_F10


title: PBMC2.CC86JANXX.SM2_011818p4_E9


title: Tuberculosis 334


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_G5


title: Tuberculosis 333


title: Tuberculosis 332


title: Tuberculosis 343


title: Tuberculosis 331


title: Tuberculosis 330


title: PBMC2.CC86JANXX.SM2_011818p4_E7


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_G3


title: PBMC2.CC86JANXX.SM2_011818p4_E6


title: Tuberculosis 328


title: Tuberculosis 337


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_G2


title: Tuberculosis 329


title: Tuberculosis 326


title: Tuberculosis 325


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_G1


title: PBMC2.CC86JANXX.SM2_011818p4_E5


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_G12


title: PBMC2.CC86JANXX.SM2_011818p4_E4


title: PBMC2.CC86JANXX.SM2_011818p4_E8


title: Tuberculosis 321


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_G4


title: PBMC2.CC86JANXX.SM2_011818p4_E3


title: Tuberculosis 323


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_G11


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_G10


title: Tuberculosis 318


title: Tuberculosis 320


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_F9


title: Tuberculosis 319


title: PBMC2.CC86JANXX.SM2_011818p4_E1


title: Tuberculosis 317


title: PBMC2.CC86JANXX.SM2_011818p4_E12


title: Tuberculosis 316


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_F8


title: PBMC2.CC86JANXX.SM2_011818p4_E11


title: Tuberculosis 314


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_F7


title: Tuberculosis 327


title: Tuberculosis 313


title: Tuberculosis 312


title: PBMC2.CC86JANXX.SM2_011818p4_E10


title: Tuberculosis 311


title: Tuberculosis 324


title: PBMC2.CC86JANXX.SM2_011818p4_D9


title: Tuberculosis 322


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_F6


title: PBMC2.CC86JANXX.SM2_011818p4_E2


title: Tuberculosis 310


title: Tuberculosis 307


title: Tuberculosis 308


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_F5


title: Tuberculosis 309


title: PBMC2.CC86JANXX.SM2_011818p4_D7


title: Tuberculosis 306


title: PBMC2.CC86JANXX.SM2_011818p4_D8


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_F4


title: PBMC2.CC86JANXX.SM2_011818p4_D6


title: Tuberculosis 305


title: Tuberculosis 303


title: Tuberculosis 304


title: Tuberculosis 315


title: Tuberculosis 302


title: PBMC2.CC86JANXX.SM2_011818p4_D5


title: Tuberculosis 301


title: PBMC2.CC86JANXX.SM2_011818p4_D4


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_F1


title: Tuberculosis 299


title: Tuberculosis 300


title: PBMC2.CC86JANXX.SM2_011818p4_D3


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_F12


title: Tuberculosis 297


title: Tuberculosis 298


title: PBMC2.CC86JANXX.SM2_011818p4_D2


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_F11


title: Tuberculosis 296


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_F10


title: Tuberculosis 295


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_F3


title: Tuberculosis 293


title: Tuberculosis 292


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_E9


title: PBMC2.CC86JANXX.SM2_011818p4_D1


title: Tuberculosis 294


title: PBMC2.CC86JANXX.SM2_011818p4_D11


title: Tuberculosis 290


title: PBMC2.CC86JANXX.SM2_011818p4_D12


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_F2


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_E7


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_E8


title: Tuberculosis 288


title: PBMC2.CC86JANXX.SM2_011818p4_D10


title: Tuberculosis 287


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_E6


title: Tuberculosis 289


title: PBMC2.CC86JANXX.SM2_011818p4_C9


title: Tuberculosis 286


title: Tuberculosis 285


title: Tuberculosis 284


title: Tuberculosis 283


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_E4


title: PBMC2.CC86JANXX.SM2_011818p4_C7


title: PBMC2.CC86JANXX.SM2_011818p4_C8


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_E3


title: Tuberculosis 280


title: Tuberculosis 281


title: Tuberculosis 282


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_E2


title: PBMC2.CC86JANXX.SM2_011818p4_C6


title: Tuberculosis 291


title: Tuberculosis 278


title: Tuberculosis 277


title: PBMC2.CC86JANXX.SM2_011818p4_C5


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_E1


title: Tuberculosis 276


title: PBMC2.CC86JANXX.SM2_011818p4_C4


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_E12


title: Tuberculosis 275


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_E11


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_E5


title: PBMC2.CC86JANXX.SM2_011818p4_C3


title: Tuberculosis 273


title: Tuberculosis 274


title: PBMC2.CC86JANXX.SM2_011818p4_C2


title: Tuberculosis 272


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_E10


title: Tuberculosis 270


title: Tuberculosis 271


title: Tuberculosis 269


title: PBMC2.CC86JANXX.SM2_011818p4_C1


title: PBMC2.CC86JANXX.SM2_011818p4_C12


title: Tuberculosis 268


title: Tuberculosis 266


title: PBMC2.CC86JANXX.SM2_011818p4_C11


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_D9


title: Tuberculosis 267


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_D8


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_D7


title: Tuberculosis 265


title: Tuberculosis 264


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_D5


title: Tuberculosis 262


title: Tuberculosis 263


title: Tuberculosis 261


title: PBMC2.CC86JANXX.SM2_011818p4_B9


title: Tuberculosis 260


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_D4


title: PBMC2.CC86JANXX.SM2_011818p4_B7


title: Tuberculosis 258


title: PBMC2.CC86JANXX.SM2_011818p4_B8


title: Tuberculosis 257


title: Tuberculosis 256


title: Tuberculosis 255


title: PBMC2.CC86JANXX.SM2_011818p4_B5


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_D3


title: Tuberculosis 254


title: Tuberculosis 253


title: PBMC2.CC86JANXX.SM2_011818p4_B4


title: PBMC2.CC86JANXX.SM2_011818p4_C10


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_D1


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_D6


title: PBMC2.CC86JANXX.SM2_011818p4_B3


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_D12


title: Tuberculosis 250


title: Tuberculosis 252


title: Tuberculosis 251


title: Tuberculosis 279


title: Tuberculosis 259


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_D11


title: Tuberculosis 247


title: PBMC2.CC86JANXX.SM2_011818p4_B2


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_D10


title: Tuberculosis 249


title: PBMC2.CC86JANXX.SM2_011818p4_B6


title: PBMC2.CC86JANXX.SM2_011818p4_B1


title: Tuberculosis 245


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_C9


title: Tuberculosis 246


title: Tuberculosis 244


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_D2


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_C8


title: Tuberculosis 243


title: Tuberculosis 242


title: PBMC2.CC86JANXX.SM2_011818p4_B11


title: Tuberculosis 241


title: PBMC2.CC86JANXX.SM2_011818p4_B10


title: Tuberculosis 240


title: Tuberculosis 239


title: Tuberculosis 238


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_C6


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_C7


title: PBMC2.CC86JANXX.SM2_011818p4_A9


title: Tuberculosis 237


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_C5


title: Tuberculosis 236


title: Tuberculosis 248


title: Tuberculosis 235


title: PBMC2.CC86JANXX.SM2_011818p4_A8


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_C4


title: PBMC2.CC86JANXX.SM2_011818p4_B12


title: PBMC2.CC86JANXX.SM2_011818p4_A7


title: Tuberculosis 234


title: Tuberculosis 232


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_C3


title: PBMC2.CC86JANXX.SM2_011818p4_A6


title: PBMC2.CC86JANXX.SM2_011818p4_A5


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_C2


title: Tuberculosis 231


title: Tuberculosis 230


title: Tuberculosis 233


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_C1


title: Tuberculosis 228


title: PBMC2.CC86JANXX.SM2_011818p4_A4


title: Tuberculosis 227


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_C12


title: PBMC2.CC86JANXX.SM2_011818p4_A3


title: Tuberculosis 225


title: Tuberculosis 224


title: Tuberculosis 226


title: PBMC2.CC86JANXX.SM2_011818p4_A2


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_C10


title: PBMC2.CC86JANXX.SM2_011818p4_A1


title: Tuberculosis 222


title: Tuberculosis 221


title: Tuberculosis 223


title: PBMC2.CC86JANXX.SM2_011818p4_A11


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_B9


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_B7


title: Tuberculosis 219


title: Tuberculosis 218


title: Tuberculosis 220


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_B6


title: Tuberculosis 217


title: PBMC2.CC86JANXX.SM2_011818p4_A10


title: Tuberculosis 215


title: Tuberculosis 216


title: PBMC2.CC86JANXX.SM2_011818p3_H9


title: Tuberculosis 214


title: PBMC2.CC86JANXX.SM2_011818p4_A12


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_C11


title: PBMC2.CC86JANXX.SM2_011818p3_H8


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_B5


title: Tuberculosis 213


title: Tuberculosis 211


title: Tuberculosis 212


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_B4


title: PBMC2.CC86JANXX.SM2_011818p3_H7


title: Tuberculosis 210


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_B3


title: Tuberculosis 229


title: Tuberculosis 209


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_B8


title: Tuberculosis 208


title: PBMC2.CC86JANXX.SM2_011818p3_H6


title: Tuberculosis 207


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_B2


title: PBMC2.CC86JANXX.SM2_011818p3_H5


title: PBMC2.CC86JANXX.SM2_011818p3_H4


title: Tuberculosis 203


title: Tuberculosis 202


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_B1


title: PBMC2.CC86JANXX.SM2_011818p3_H3


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_B11


title: Tuberculosis 200


title: Tuberculosis 204


title: Tuberculosis 201


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_B10


title: Tuberculosis 198


title: PBMC2.CC86JANXX.SM2_011818p3_H1


title: Tuberculosis 197


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_B12


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_A9


title: PBMC2.CC86JANXX.SM2_011818p3_H12


title: Tuberculosis 199


title: Tuberculosis 196


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_A8


title: PBMC2.CC86JANXX.SM2_011818p3_H11


title: Tuberculosis 194


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_A7


title: Tuberculosis 206


title: Tuberculosis 205


title: PBMC2.CC86JANXX.SM2_011818p3_H10


title: Tuberculosis 195


title: Tuberculosis 193


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_A6


title: Tuberculosis 191


title: Tuberculosis 190


title: PBMC2.CC86JANXX.SM2_011818p3_G9


title: Tuberculosis 189


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_A5


title: PBMC2.CC86JANXX.SM2_011818p3_H2


title: PBMC2.CC86JANXX.SM2_011818p3_G8


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_A4


title: Tuberculosis 188


title: PBMC2.CC86JANXX.SM2_011818p3_G7


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_A3


title: Tuberculosis 185


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_A2


title: Tuberculosis 183


title: Tuberculosis 192


title: Tuberculosis 181


title: Tuberculosis 182


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_A1


title: PBMC2.CC86JANXX.SM2_011818p3_G4


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_A12


title: Tuberculosis 179


title: PBMC2.CC86JANXX.SM2_011818p3_G5


title: PBMC2.CC86JANXX.SM2_011818p3_G3


title: Tuberculosis 177


title: Tuberculosis 178


title: Tuberculosis 180


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_A11


title: Tuberculosis 187


title: Tuberculosis 175


title: Tuberculosis 176


title: Cortex1.CCKVLANXX.042518-SciSeq-p2_A10


title: PBMC2.CC86JANXX.SM2_011818p3_G1


title: Tuberculosis 186


title: Cortex1.CCJ15ANXX.SM2_042518p4_H9


title: Tuberculosis 173


title: Tuberculosis 174


title: Tuberculosis 184


title: Tuberculosis 172


title: Cortex1.CCJ15ANXX.SM2_042518p4_H8


title: PBMC2.CC86JANXX.SM2_011818p3_G12


title: Tuberculosis 171


title: Tuberculosis 170


title: Tuberculosis 169


title: Cortex1.CCJ15ANXX.SM2_042518p4_H7


title: PBMC2.CC86JANXX.SM2_011818p3_G10


title: Tuberculosis 168


title: Cortex1.CCJ15ANXX.SM2_042518p4_H6


title: PBMC2.CC86JANXX.SM2_011818p3_G2


title: PBMC2.CC86JANXX.SM2_011818p3_F9


title: Tuberculosis 165


title: Tuberculosis 166


title: PBMC2.CC86JANXX.SM2_011818p3_F8


title: Tuberculosis 164


title: Cortex1.CCJ15ANXX.SM2_042518p4_H4


title: Cortex1.CCJ15ANXX.SM2_042518p4_H5


title: Tuberculosis 163


title: PBMC2.CC86JANXX.SM2_011818p3_F7


title: Tuberculosis 161


title: Tuberculosis 162


title: Tuberculosis 160


title: PBMC2.CC86JANXX.SM2_011818p3_F6