title: IL17raDermoCre neg2 whole lung

status: Public on Aug 31 2021

type: SRA

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

country: USA

institute: Tulane University

library_source: transcriptomic

data_processing:
FASTQ data were generated by Illumina Basespace.
FASTQ data quality assessment and trimming, read mapping, and expression analyses were done by Banana Slug Analytics Platform.

molecule: total RNA

organism: Mus musculus

source_name: Lung

growth_protocol: All mice were obtained from Jax farm and maintained in specific pathogen-free rooms at Tulane University. Experiment were preformed when mice were at age of six to ten weeks

extract_protocol:
Total RNA was extracted from lung tissue according to RNeasy Plus Mini Kit protocol from QIAGEN.
Library construction was performed according to TruSeq mRNA protocol from Illumina

treatment_protocol: I. immunization with OmpX and LTA1 twice 3 weeks apart

tag: strain

value: IL17raDermoCre mice

tag: time point of infection

value: K1 KP396 4hours post infection


title: IL17raDermoCre neg3 whole lung


title: vehicle_1

city: Cambridge

first: David

last: Bargiela

address: 4, 7 Downing Pl

country: United Kingdom

institute: University of Cambridge

data_processing:
RNA-sequencing: 2x75-nt sequence reads using Illumina NextSeq 550.
Basecalling and demultiplexing was performed using Illumina bcl2fastq.
Reads were aligned to the mm10 reference genome using STAR.
Read summarization to gene counts was performed using featureCounts.
Normalization of raw counts and differential gene expression were performed using DESeq2.
Genome_build: mm10.
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts for each sample.

source_name: CD8+ T cells

growth_protocol: Splenic CD8+ T cells from C57BL6/J mice were activated in complete RPMI (Gibco) with anti-CD3/anti-CD28 Dynabeads 100 units/ml recombinant human IL-2 and either water (vehicle) or 0.25mM AOA (Sigma). After 72 hours, cells were washed twice with PBS (Gibco) and then expanded in complete RPMI with 100 U/ml recombinant human IL-2 and either water (vehicle) or 0.25mM AOA (Sigma) for a further 4 days at a cell density lower than 2e6/ml.

extract_protocol:
On day 7 CD8+ T cells were washed twice with ice cold PBS (Gibco) and lysed with RLT buffer containing 1% β-mercaptoethanol (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD8+ T cells were treated with either water (vehicle) or 0.25mM AOA (Sigma) for a total of 7 days.

tag: treatment

value: vehicle (water)

tag: mouse donor


title: AOA_2

value: AOA 0.25mM


title: vehicle_3


title: AOA_1


title: AOA_3


title: IL17raDermoCre neg1 whole lung


title: vehicle_2


title: IL17raDermoCre pos3 whole lung


title: IL17raDermoCre pos1 whole lung


title: IL17raDermoCre pos2 whole lung


title: HeLa_pgPEN_CRISPR_screen_LTP_RepC

city: Seattle

first: Alice

last: Berger

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description: HeLa LTP (late time point) sample, replicate C, cells treated with Doxycycline to induce Cas9 expression

library_source: genomic

data_processing:
Library strategy: CRISPR DNA sequencing (custom Illumina reaction)
Image analysis and base calling were performed on board the Illumina HiSeq 2500 with RTA 1.18.66.3 software. Generation of Fastq files was performed with Illumina's bcl2fastq 2.20 Conversion Software, including the following non-default parameters:  --create-fastq-for-index-reads --with-failed-reads --minimum-trimmed-read-length 2 --mask-short-adapter-reads 2
Sample demultiplexing performed using idemp with parameters -n 1
Reads trimmed using FASTX-Toolkit v0.0.14 with parameters -f 1 -l 20 for read R1, -f 2 -l 21 for read I1, and -f 1 -l 6 for the index read
Reads aligned to the reference (paralog pgRNA library) using Bowtie v1.2.2 with parameters -q -v 1 --best --strata --all --sam -p 4
SAMtools v1.9 was used to (1) convert aligned files from SAM to BAM format using command view with parameters -bS and (2) sort the output BAM files using command sort parameters -O bam
Paired gRNA counts were obtained from BAM files using the custom script counter_efficient.R (see https://github.com/bergerbio/pgRNA_sequencing_analysis)
The log fold change for each pgRNA was calculated using the MAGeCK v0.5.9.2 test command with parameters --gene-lfc-method mean, with the plasmid counts used as --day0-label
Genome_build: Reference sequences used for alignment are contained in the pgPEN_counts.txt supplementary file
Supplementary_files_format_and_content: Processed data file (pgPEN_counts.txt) provided in tab-delimited text format, contains pgRNA IDs, sequences, and paralog pair targets as well as raw counts obtained from custom pgRNA-counting script that was run on processed BAM files. For custom script, see: https://github.com/bergerbio/pgRNA_sequencing_analysis

molecule: genomic DNA

organism: Homo sapiens

source_name: cervical carcinoma cell line

growth_protocol: PC9-Cas9 cells were a gift from Dr. Matthew Meyerson (Broad Institute) and cultured in RPMI-1640 (Gibco) supplemented with 10% Fetal Bovine Serum (FBS, Sigma). HeLa/iCas9 cells were previously generated (Cao et al., 2016) and cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Genesee Scientific) supplemented with 10% FBS. All cells were maintained at 37ºC in 5% CO2 and confirmed mycoplasma-free.

extract_protocol:
Genomic DNA was extracted using the QIAamp DNA Blood Maxi Kit (Qiagen catalog # 51192) with an additional overnight 4ºC incubation step before eluting the cleaned DNA from the column
The paired gRNA sequences were amplfiied using a three-step PCR protocol as described in the Methods. Each sample was assigned a unique barcoded primer, and samples were diluted and pooled at equimolar ratios prior to sequencing

treatment_protocol: Genomic DNA samples were pelleted by centrifugation at 1100 rpm for 4 minutes, resuspended in 1mL PBS, and frozen at -80ºC until extraction

tag: tissue

value: cervix

tag: cell line

value: HeLa/iCas9 cells

tag: tumor type

value: carcinoma

tag: timepoint

value: LTP (Day 22)

tag: expresses

value: iCas9, GFP

tag: drug treatment

value: Doxycycline (1 uM)


title: HeLa_pgPEN_CRISPR_screen_LTP_RepB

description: HeLa LTP (late time point) sample, replicate B, cells treated with Doxycycline to induce Cas9 expression


title: HeLa_pgPEN_CRISPR_screen_LTP_RepA

description: HeLa LTP (late time point) sample, replicate A, cells treated with Doxycycline to induce Cas9 expression


title: PC9_pgPEN_CRISPR_screen_LTP_RepC

description: PC9 LTP (late time point) sample, replicate C

source_name: lung adenocarcinoma cell line

value: lung

value: PC9-Cas9 cells

value: adenocarcinoma

value: LTP (Day 21)


title: PC9_pgPEN_CRISPR_screen_LTP_RepB

description: PC9 LTP (late time point) sample, replicate B


title: PC9_pgPEN_CRISPR_screen_ETP_RepC

description: PC9 ETP (early time point) sample, replicate C

value: ETP (Day 6)


title: PC9_pgPEN_CRISPR_screen_ETP_RepA

description: PC9 ETP (early time point) sample, replicate A


title: MCF10CA1a cells - OCT1 - PTS - rep2

city: Vancouver

first: Barbara

last: Stefanska

state: BC

address: 2205 East Mall

department: Land and Food Systems

country: Canada

institute: The University of British Columbia

description: OCT1_CvP (enriched in Ctrl) and OCT1_PvC (enriched in PTS)

data_processing:
ChIP-seq data were analyzed using Bioconductor tool in R
Adapter sequences were trimmed from sequencing reads using cutadapt and reads were aligned to the GRCh37/hg19 human reference genome using the Burrows-Wheeler Aligner
MACS2 peak calling software was used to identify enrichment patterns in vehicle-treated versus PTS-treated samples
the callpeak function was used to peaks in the control or treated samples, using the pooled ChIP-seq inputs as the background control and using 200bp as the estimated fragment size and an effective genome size of 2,700,000,000.
Differential peaks were called using the bdgdiff function. Fold enrichment over input tracks were generated from pileup tracks using the bdgcmp function, using the -m FE option. To visualize accurate representation of our results, read-extended bigwig files of our obtained genomic data were implemented in the genome browser.
ChIPSeeker Bioconductor package was used to associate the identified peaks to their target genes.
The ChIP quality control (CHIPQC) Bioconductor package calculated ChIP-seq specific quality metric for each sample and input in our experiment. CHIPQC further identifies both fragment length peak and a read length peak based on cross-coverage around the centers of binding sites. CHIPQC was used to both measure inequality of coverage across the genome via standardized Standard Deviation (SSD) and assess distribution of ChIP-seq signal over genomic regions.
Genome_build: GRCh37/hg19 human reference genome
Supplementary_files_format_and_content: Excel files: CvP presents peaks enriched in Control (vehicle-treated) cells versus PTS-treated cells; PvC presents peaks enriched in PTS-treated cells versus Control (vehicle-treated) cells.

source_name: MCF10CA1a breast cancer cells

growth_protocol: Human breast cancer MCF10CA1a cell lines were cultured in DMEM/F12 (1:1) medium (Gibco) supplemented with 5% horse serum (Gibco), 1U/ml penicillin and 1µg/ml streptomycin (Gibco).

extract_protocol:
Lysates were clarified from sonicated nuclei and DNMT3B- or OCT1-bound to DNA fractions were isolated with proper antibodies.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Cells, grown in a humidified atmosphere of 5% carbon dioxide at 37°C, were treated with pterostilbene (PTS, Cayman Chem., Ann Arbor, MI, USA) freshly resuspended in ethanol. 24 h prior to treatments, cells were plated at a density of 2-3 x 105 followed by exposure to PTS at 7µM concentration for 4 days. Cells were then passaged 1:50 and exposed for additional 4 days (9-day exposure).

tag: cell type

value: Human breast cancer cell line

tag: chip antibody

value: OCT1 (Millipore, MAB5434)

value: PTS-treated (pterostilbene, 7uM for 9 days)


title: MCF10CA1a cells - OCT1 - PTS - rep1


title: PC9_pgPEN_CRISPR_screen_ETP_RepB

description: PC9 ETP (early time point) sample, replicate B


title: MCF10CA1a cells - OCT1 - Ctrl - rep2

value: vehicle-treated (ethanol)


title: MCF10CA1a cells - DNMT3B - Ctrl - rep2

description: DNMT3B_CvP (enriched in Ctrl) and DNMT3B_PvC (enriched in PTS)

value: DNMT3B (Millipore, MABE305)


title: MCF10CA1a cells - Input DNA in OCT1 ChIP - PTS


title: MCF10CA1a cells - DNMT3B - PTS - rep1


title: primary CRC tissue from patient 5 [PT5]

city: shanghai

first: HONG

last: QIN

address: 130# Dongan road

country: China

institute: Fudan Univercity

data_processing:
HISAT2
stringtie
HTseq
DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: primary CRC tissue

extract_protocol:
tissue were stored in RNAlater™ Stabilization Solution.Total RNA samples were extracted with the TRIzol™ Reagent (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status/id

value: colorectal cancer (CRC) patient5

value: primary CRC tissue


title: MCF10CA1a cells - DNMT3B - Ctrl - rep3


title: MCF10CA1a cells - OCT1 - Ctrl - rep3


title: HeLa_pgPEN_CRISPR_screen_ETP

description: HeLa ETP (early time point) sample (cells not yet split into replicates)

value: cervix

value: HeLa/iCas9 cells

value: ETP (Day 5)


title: MCF10CA1a cells - Input DNA in OCT1 ChIP - Ctrl


title: MCF10CA1a cells - DNMT3B - Ctrl - rep1


title: MCF10CA1a cells - OCT1 - Ctrl - rep1


title: MCF10CA1a cells - Input DNA in DNMT3B ChIP- PTS


title: MCF10CA1a cells - Input DNA in DNMT3B ChIP - Ctrl


title: primary CRC tissue from patient 3 [PT3]

value: colorectal cancer (CRC) patient3


title: primary CRC tissue from patient 4 [PT4]

value: colorectal cancer (CRC) patient4


title: PC9_pgPEN_CRISPR_screen_LTP_RepA

description: PC9 LTP (late time point) sample, replicate A

value: lung


title: primary CRC tissue from patient 2 [PT2]

value: colorectal cancer (CRC) patient2


title: primary CRC tissue from patient 1 [PT1]

value: colorectal cancer (CRC) patient1


title: adenoma tissue from patient5 [PA5]

source_name: adenoma tissue

value: adenoma tissue


title: MCF10CA1a cells - DNMT3B - PTS - rep3


title: MCF10CA1a cells - DNMT3B - PTS - rep2


title: adenoma tissue from patient4 [PA4]


title: adenoma tissue from patient2 [PA2]


title: adenoma tissue from patient1 [PA1]


title: adjacent normal tissue from patient3 [PN3]

source_name: normal colon epithelium tissue

value: normal colon epithelium tissue


title: adjacent normal tissue from patient5 [PN5]


title: adjacent normal tissue from patient4 [PN4]


title: MCF10CA1a cells - OCT1 - PTS - rep3

value: Human breast cancer cell line


title: adjacent normal tissue from patient2 [PN2]


title: Thalidomide

city: Madras Institute of Technology, Chrompet

first: Suvro

last: Chatterjee

state: Tamil Nadu

address: Vascular Biology Laboratory

country: India

institute: AU-KBC Research Centre, Anna University

data_processing:
Illumina bcl2fastq Conversion Software v1.8.4 used for basecalling.
Alignment performed using STAR (2.4.2a) program to the Ensembl Release 81 Gallus gallus reference genome and genemodel
cuffllinks (version 2.2.1) used for gene and isoform expression estimation
cuffdiff program of cufflinks (version 2.2.1) used for differential expression  analysis
Genome_build: Hg19 Human Genome
Supplementary_files_format_and_content: Gene expression of the samples in excel format

source_name: HUVECs

growth_protocol: HUVECs were grown at 37° C and 5% CO2  in three 60mm culture dish for each treatment in EGM-Plus Growth Media obtained from Lonza®. At 90% confluence of cells the media was changed with treatment media containing vehicle control or 70ug/ml of drug.

extract_protocol:
Total RNA was isolated using Trizol® reagent, Invitrogen Life Technologies. The total RNA samples was checked for quality using Nanodrop and 1% agarose gel. RNA  samples, free of DNA and protein contamination was resuspended in nuclease free water. 1ug of RNA sample for each stage was submitted for Next Generation Sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The cells were further incubated for 8h at 37° C and 5% CO2. Media was removed and cells were washed with 1X PBS. Then cells were scraped in 500ul of RNA later®.

value: Thalidomide


title: Pomalidomide

value: Pomalidomide


title: adjacent normal tissue from patient1 [PN1]


title: adenoma tissue from patient3 [PA3]


title: Lenalidomide

value: Lenalidomide


title: Control

value: Control


title: wildtype, DMSO, replicate 2

type: RNA

city: Singapore

first: Ying

last: Liu

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description: Transcriptional profiling of the wildtype line treated with DMSO for 4 hours at around 28 hpi, replicate 2

hyb_protocol: Equal amounts of labelled sample and reference cDNA were hybridized on the microarray chip using the Agilent hybridization system. Hybridizations were performed for 20 hours at 65°C in a rotating hybridization oven at 10rpm.

scan_protocol: Microarray scanning was done using PowerScanner (Tecan, Austria) at 10uM resolution and with autogain PMT adjustments for both channels. Data was acquired using GenePix Pro v6.0 software (Axon Instruments, USA) as described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391.

data_processing: Features with flag>0 and with median foreground intensity greater than 1.5 fold median background intensity for either channel passed quality control and were accepted. Local  background correction using normexp, followed by lowess normalization across all features were carried out to generate the normalized Log2 gene expression ratios.

organism: Plasmodium falciparum

source_name: P. falciparum T996 RNA, wildtype

label_protocol: Synthesis of aminoallyl-coupled cDNA by reverse transcription and labeling of samples with cy fluorophore were carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

growth_protocol: P. falciparum parasites were cultured in RPMI-HEPES medium , supplemented with 0.25% Albumax , 0.2% sodium bicarbonate, 100 µM hypoxanthine  and 10 µg/ml Gentamycin with 2% hematocrit.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions and as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

treatment_protocol: Selective drugs were removed from medium two intraerythrocytic life cycles before harvesting parasites for RNA extraction. Parasites at 24 hpi were incubated in 20 μg/ml actD or equal volume of DMSO for four hours.

tag: genotype

value: wildtype

value: DMSO

tag: culture

value: In vitro culture

tag: Stage

value: asexual blood stage

value: laboratory strain T996

tag: estimated developmental age

value: 28 hpi

tag: microarray autogain intensity

source_name: P. falciparum 3D7 RNA reference pool

tag: composition

value: mixture of equal amounts of RNA harvested every 8 hours over the 48-hour parasite's intraerythrocytic life cycle


title: wildtype, actD, replicate 2

description: Transcriptional profiling of the wildtype line treated with actD for 4 hours at around 28 hpi, replicate 2

tag: treatment

value: actD

tag: strain


title: wildtype, initial, replicate 2

description: Transcriptional profiling of the wildtype line at around 24 hpi replicate 2

value: initial

value: 24 hpi


title: wildtype, initial, replicate 1

description: Transcriptional profiling of the wildtype line at around 24 hpi replicate 1


title: wildtype, DMSO, replicate 1

description: Transcriptional profiling of the wildtype line treated with DMSO for 4 hours at around 28 hpi, replicate 1


title: PfNot1.1 knockout, initial, replicate 1

description: Transcriptional profiling of the PfNot1.1 knockout line at around 24 hpi replicate 1

source_name: P. falciparum T996 RNA, PfNot1.1 knockout

value: PfNot1.1 knockout


title: wildtype, actD, replicate 1

description: Transcriptional profiling of the wildtype line treated with actD for 4 hours at around 28 hpi, replicate 1


title: PfNot1.1 knockout, DMSO, replicate 2

description: Transcriptional profiling of the PfNot1.1 knockout line treated with DMSO for 4 hours at around 28 hpi, replicate 2


title: PfNot1.1 knockout, actD, replicate 2

description: Transcriptional profiling of the PfNot1.1 knockout line treated with actD for 4 hours at around 28 hpi, replicate 2


title: PfNot1.1 knockout, actD, replicate 1

description: Transcriptional profiling of the PfNot1.1 knockout line treated with actD for 4 hours at around 28 hpi, replicate 1


title: PfNot1.1 knockout, initial, replicate 2

description: Transcriptional profiling of the PfNot1.1 knockout line at around 24 hpi replicate 2


title: PfNot1.1 knockout, DMSO, replicate 1

description: Transcriptional profiling of the PfNot1.1 knockout line treated with DMSO for 4 hours at around 28 hpi, replicate 1


title: wildtype line for PfNot1.1 knockout, RNAPII, TP6, replicate 3

type: genomic

description:
107039_Cycle1_2018-05-01_RNAPII_WT_TP6_rep3
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 6 at around 44 hpi, replicate 3

hyb_protocol: Equal amounts of labelled ChIP DNA and Input DNA were hybridized on the microarray chip using the Agilent hybridization system. Hybridizations were performed for 20 hours at 65°C in a rotating hybridization oven at 10rpm.

source_name: P. falciparum T996 ChIP DNA, wildtype line for PfNot1.1 knockout

label_protocol: Synthesis of aminoallyl-coupled DNA and labeling of samples with cy fluorophore were carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

growth_protocol: RPMI-HEPES medium

extract_protocol: P. falciparum parasite were fixed with 1% formaldehyde at room temperature followed by quenching with 0.125 M glycine. The cells were washed twice with ice-cold PBS and lysed in 5 pellet volume of Buffer A (1 mM EDTA, pH8.0; 0.25% NP40; 1x protease inhibitor; 2 mM PMSF). The resulting nuclei pellet was lysed with SDS Lysis Buffer (1% SDS; 50 mM Tris, pH8.1; 10 mM EDTA; 1x protease inhibitor; 2 mM PMSF), sonicated into 200-1,000 bp DNA fragments and diluted with ChIP Dilution Buffer (0.01% SDS; 1.1% Triton X-100; 16.7 mM Tris, pH8.1; 1.2 mM EDTA; 167 mM NaCl; 1x protease inhibitor; 2 mM PMSF), as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

treatment_protocol: Parasites were crosslinked with 0.1% v/v formaldehyde

tag: culture, stage, strain, harvest timepoint, estimated developmental age

value: In vitro culture, asexual blood stage, laboratory strain T996, TP6, 44 hpi

source_name: P. falciparum T996 Input DNA, wildtype line for PfNot1.1 knockout


title: wildtype line for PfNot1.1 knockout, RNAPII, TP4, replicate 2

description:
107024_Cycle1_2018-04-29_RNAPII_WT_TP4_rep2
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 4 at around 28 hpi, replicate 2

value: In vitro culture, asexual blood stage, laboratory strain T996, TP4, 28 hpi


title: wildtype line for PfNot1.1 knockout, RNAPII, TP5, replicate 3

description:
107036_Cycle1_2018-05-01_RNAPII_WT_TP5_rep3
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 5 at around 36 hpi, replicate 3

value: In vitro culture, asexual blood stage, laboratory strain T996, TP5, 36 hpi


title: wildtype line for PfNot1.1 knockout, RNAPII, TP1, replicate 3

description:
107031_Cycle1_2018-05-01_RNAPII_WT_TP1_rep3
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 1 at around 4 hpi, replicate 3

value: In vitro culture, asexual blood stage, laboratory strain T996, TP1, 4 hpi


title: wildtype line for PfNot1.1 knockout, RNAPII, TP3, replicate 3

description:
107033_Cycle1_2018-05-01_RNAPII_WT_TP3_rep3
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 3 at around 20 hpi, replicate 3

value: In vitro culture, asexual blood stage, laboratory strain T996, TP3, 20 hpi


title: wildtype line for PfNot1.1 knockout, RNAPII, TP4, replicate 3

description:
107035_Cycle1_2018-05-01_RNAPII_WT_TP4_rep3
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 4 at around 28 hpi, replicate 3


title: wildtype line for PfNot1.1 knockout, RNAPII, TP6, replicate 2

description:
107027_Cycle1_2018-04-29_RNAPII_WT_TP6_rep2
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 6 at around 44 hpi, replicate 2


title: wildtype line for PfNot1.1 knockout, RNAPII, TP5, replicate 2

description:
107026_Cycle1_2018-04-29_RNAPII_WT_TP5_rep2
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 5 at around 36 hpi, replicate 2


title: wildtype line for PfNot1.1 knockout, RNAPII, TP2, replicate 2

description:
107022_Cycle1_2018-04-29_RNAPII_WT_TP2_rep2
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 2 at around 12 hpi, replicate 2

value: In vitro culture, asexual blood stage, laboratory strain T996, TP2, 12 hpi


title: wildtype line for PfNot1.1 knockout, RNAPII, TP2, replicate 3

description:
107032_Cycle1_2018-05-01_RNAPII_WT_TP2_rep3
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 2 at around 12 hpi, replicate 3


title: wildtype line for PfNot1.1 knockout, RNAPII, TP2, replicate 1

description:
106023_Cycle1_2018-03-25_RNAPII_WT_TP2_rep1
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 2 at around 12 hpi, replicate 1


title: wildtype line for PfNot1.1 knockout, RNAPII, TP6, replicate 1

description:
106024_Cycle1_2018-03-25_RNAPII_WT_TP6_rep1
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 6 at around 44 hpi, replicate 1


title: PfNot1.1 knockout, RNAPII, TP5, replicate 2

description:
107026_Cycle2_2018-04-29_RNAPII_KO_TP5_rep2
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 5 at around 36 hpi, replicate 2

source_name: P. falciparum T996 ChIP DNA, PfNot1.1 knockout

source_name: P. falciparum T996 Input DNA, PfNot1.1 knockout


title: wildtype line for PfNot1.1 knockout, RNAPII, TP5, replicate 1

description:
106035_Cycle1_2018-03-20_RNAPII_WT_TP5_rep1
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 5 at around 36 hpi, replicate 1


title: PfNot1.1 knockout, RNAPII, TP6, replicate 2

description:
107027_Cycle2_2018-04-29_RNAPII_KO_TP6_rep2
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 6 at around 44 hpi, replicate 2


title: wildtype line for PfNot1.1 knockout, RNAPII, TP1, replicate 1

description:
106031_Cycle1_2018-03-20_RNAPII_WT_TP1_rep1
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 1 at around 4 hpi, replicate 1


title: wildtype line for PfNot1.1 knockout, RNAPII, TP3, replicate 2

description:
107023_Cycle1_2018-04-29_RNAPII_WT_TP3_rep2
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 3 at around 20 hpi, replicate 2


title: PfNot1.1 knockout, RNAPII, TP6, replicate 3

description:
107039_Cycle2_2018-05-01_RNAPII_KO_TP6_rep3
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 6 at around 44 hpi, replicate 3


title: PfNot1.1 knockout, RNAPII, TP3, replicate 2

description:
107023_Cycle2_2018-04-29_RNAPII_KO_TP3_rep2
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 3 at around 20 hpi, replicate 2


title: PfNot1.1 knockout, RNAPII, TP4, replicate 1

description:
106034_Cycle2_2018-03-20_RNAPII_KO_TP4_rep1
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 4 at around 28 hpi, replicate 1


title: PfNot1.1 knockout, RNAPII, TP2, replicate 2

description:
107022_Cycle2_2018-04-29_RNAPII_KO_TP2_rep2
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 2 at around 12 hpi, replicate 2


title: PfNot1.1 knockout, RNAPII, TP1, replicate 2

description:
107021_Cycle2_2018-04-29_RNAPII_KO_TP1_rep2
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 1 at around 4 hpi, replicate 2


title: PfNot1.1 knockout, RNAPII, TP1, replicate 3

description:
107031_Cycle2_2018-05-01_RNAPII_KO_TP1_rep3
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 1 at around 4 hpi, replicate 3


title: wildtype line for PfNot1.1 knockout, RNAPII, TP4, replicate 1

description:
106023_Cycle2_2018-03-25_RNAPII_WT_TP4_rep1
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 4 at around 28 hpi, replicate 1


title: PfNot1.1 knockout, RNAPII, TP3, replicate 3

description:
107033_Cycle2_2018-05-01_RNAPII_KO_TP3_rep3
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 3 at around 20 hpi, replicate 3


title: wildtype line for PfNot1.1 knockout, RNAPII, TP3, replicate 1

description:
106033_Cycle1_2018-03-20_RNAPII_WT_TP3_rep1
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 3 at around 20 hpi, replicate 1


title: PfNot1.1 knockout, RNAPII, TP4, replicate 2

description:
107024_Cycle2_2018-04-29_RNAPII_KO_TP4_rep2
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 4 at around 28 hpi, replicate 2


title: PfNot1.1 knockout, RNAPII, TP5, replicate 3

description:
107036_Cycle2_2018-05-01_RNAPII_KO_TP5_rep3
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 5 at around 36 hpi, replicate 3


title: wildtype line for PfNot1.1 knockout, RNAPII, TP1, replicate 2

description:
107021_Cycle1_2018-04-29_RNAPII_WT_TP1_rep2
RNAPII recruitment of the wildtype line for the PfNot1.1 knockout line at Timepoint 1 at around 4 hpi, replicate 2


title: PfNot1.1 knockout, RNAPII, TP6, replicate 1

description:
106024_Cycle2_2018-03-25_RNAPII_KO_TP6_rep1
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 6 at around 44 hpi, replicate 1


title: PfNot1.1 knockout, RNAPII, TP2, replicate 3

description:
107032_Cycle2_2018-05-01_RNAPII_KO_TP2_rep3
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 2 at around 12 hpi, replicate 3


title: PfNot1.1 knockout, RNAPII, TP4, replicate 3

description:
107035_Cycle2_2018-05-01_RNAPII_KO_TP4_rep3
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 4 at around 28 hpi, replicate 3


title: PfNot1.1 knockout, RNAPII, TP5, replicate 1

description:
106035_Cycle2_2018-03-20_RNAPII_KO_TP5_rep1
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 5 at around 36 hpi, replicate 1


title: PfNot1.1 knockout, RNAPII, TP2, replicate 1

description:
106032_Cycle2_2018-03-20_RNAPII_KO_TP2_rep1
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 2 at around 12 hpi, replicate 1


title: PfNot1.1 knockout, RNAPII, TP1, replicate 1

description:
106031_Cycle2_2018-03-20_RNAPII_KO_TP1_rep1
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 1 at around 4 hpi, replicate 1


title: PfNot1.1 knockout, RNAPII, TP3, replicate 1

description:
106033_Cycle2_2018-03-20_RNAPII_KO_TP3_rep1
RNAPII recruitment of the PfNot1.1 knockout line at Timepoint 3 at around 20 hpi, replicate 1


title: wildtype line for PfNot1.2 knockdown, TP5, replicate 3

description:
105125_Cycle1_2018-03-03_WT_TP5_rep3
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 5 at around 36 hpi, replicate 3

source_name: P. falciparum T996 RNA, wildtype line for PfNot1.2 knockdown

treatment_protocol: Selective drugs were removed from medium two intraerythrocytic life cycles before harvesting parasites for RNA extraction.

tag: culture, stage, strain, composition

value: In vitro culture, asexual blood stage, laboratory strain T996, mixture of equal amounts of RNA harvested every 8 hours over the 48-hour parasite's intraerythrocytic life cycle


title: wildtype line for PfNot1.2 knockdown, TP6, replicate 3

description:
106044_Cycle1_2018-03-23_WT_TP6_rep3
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 6 at around 44 hpi, replicate 3


title: wildtype line for PfNot1.2 knockdown, TP3, replicate 3

description:
105123_Cycle1_2018-03-03_WT_TP3_rep3
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 3 at around 20 hpi, replicate 3


title: wildtype line for PfNot1.2 knockdown, TP6, replicate 1

description:
105110_Cycle1_2018-03-03_WT_TP6_rep1
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 6 at around 44 hpi, replicate 1


title: PfNot1.2 knockdown, TP4, replicate 3

description:
105124_Cycle2_2018-03-03_KD_TP4_rep3
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 4 at around 28 hpi, replicate 3

source_name: P. falciparum T996 RNA, PfNot1.2 knockdown


title: wildtype line for PfNot1.2 knockdown, TP3, replicate 2

description:
105051_Cycle1_2018-03-04_WT_TP3_rep2
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 3 at around 20 hpi, replicate 2


title: PfNot1.2 knockdown, TP4, replicate 2

description:
105114_Cycle2_2018-03-03_KD_TP4_rep2
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 4 at around 28 hpi, replicate 2


title: wildtype line for PfNot1.2 knockdown, TP2, replicate 2

description:
105039_Cycle1_2018-03-04_WT_TP2_rep2
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 2 at around 12 hpi, replicate 2


title: PfNot1.2 knockdown, TP3, replicate 3

description:
105123_Cycle2_2018-03-03_KD_TP3_rep3
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 3 at around 20 hpi, replicate 3


title: wildtype line for PfNot1.2 knockdown, TP6, replicate 2

description:
105116_Cycle1_2018-03-03_WT_TP6_rep2
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 6 at around 44 hpi, replicate 2


title: PfNot1.2 knockdown, TP5, replicate 3

description:
105125_Cycle2_2018-03-03_KD_TP5_rep3
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 5 at around 36 hpi, replicate 3


title: PfNot1.2 knockdown, TP2, replicate 3

description:
105122_Cycle2_2018-03-03_KD_TP2_rep3
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 2 at around 12 hpi, replicate 3


title: wildtype line for PfNot1.2 knockdown, TP1, replicate 3

description:
105121_Cycle1_2018-03-03_WT_TP1_rep3
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 1 at around 4 hpi, replicate 3


title: wildtype line for PfNot1.2 knockdown, TP2, replicate 1

description:
104072_Cycle1_2018-02-09_WT_TP2_rep1
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 2 at around 12 hpi, replicate 1


title: wildtype line for PfNot1.2 knockdown, TP1, replicate 2

description:
105038_Cycle1_2018-03-04_WT_TP1_rep2
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 1 at around 4 hpi, replicate 2


title: wildtype line for PfNot1.2 knockdown, TP2, replicate 3

description:
105122_Cycle1_2018-03-03_WT_TP2_rep3
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 2 at around 12 hpi, replicate 3


title: PfNot1.2 knockdown, TP6, replicate 3

description:
105126_Cycle2_2018-03-03_KD_TP6_rep3
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 6 at around 44 hpi, replicate 3


title: wildtype line for PfNot1.2 knockdown, TP5, replicate 1

description:
104083_Cycle1_2018-02-12_WT_TP5_rep1
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 5 at around 36 hpi, replicate 1


title: wildtype line for PfNot1.2 knockdown, TP5, replicate 2

description:
105115_Cycle1_2018-03-03_WT_TP5_rep2
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 5 at around 36 hpi, replicate 2


title: wildtype line for PfNot1.2 knockdown, TP4, replicate 3

description:
105124_Cycle1_2018-03-03_WT_TP4_rep3
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 4 at around 28 hpi, replicate 3


title: PfNot1.2 knockdown, TP1, replicate 2

description:
105038_Cycle2_2018-03-04_KD_TP1_rep2
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 1 at around 4 hpi, replicate 2


title: PfNot1.2 knockdown, TP6, replicate 2

description:
105116_Cycle2_2018-03-03_KD_TP6_rep2
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 6 at around 44 hpi, replicate 2


title: PfNot1.2 knockdown, TP3, replicate 2

description:
105051_Cycle2_2018-03-04_KD_TP3_rep2
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 3 at around 20 hpi, replicate 2


title: wildtype line for PfNot1.2 knockdown, TP1, replicate 1

description:
104071_Cycle1_2018-02-09_WT_TP1_rep1
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 1 at around 4 hpi, replicate 1


title: PfNot1.2 knockdown, TP5, replicate 2

description:
105115_Cycle2_2018-03-03_KD_TP5_rep2
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 5 at around 36 hpi, replicate 2


title: PfNot1.2 knockdown, TP1, replicate 3

description:
105121_Cycle2_2018-03-03_KD_TP1_rep3
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 1 at around 4 hpi, replicate 3


title: PfNot1.2 knockdown, TP2, replicate 2

description:
105039_Cycle2_2018-03-04_KD_TP2_rep2
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 2 at around 12 hpi, replicate 2


title: wildtype line for PfNot1.2 knockdown, TP4, replicate 2

description:
105114_Cycle1_2018-03-03_WT_TP4_rep2
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 4 at around 28 hpi, replicate 2


title: wildtype line for PfNot1.2 knockdown, TP3, replicate 1

description:
104069_Cycle1_2018-02-12_WT_TP3_rep1
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 3 at around 20 hpi, replicate 1


title: PfNot1.2 knockdown, TP6, replicate 1

description:
105110_Cycle2_2018-03-03_KD_TP6_rep1
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 6 at around 44 hpi, replicate 1


title: PfNot1.2 knockdown, TP3, replicate 1

description:
104069_Cycle2_2018-02-12_KD_TP3_rep1
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 3 at around 20 hpi, replicate 1


title: PfNot1.2 knockdown, TP2, replicate 1

description:
104072_Cycle2_2018-02-09_KD_TP2_rep1
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 2 at around 12 hpi, replicate 1


title: wildtype line for PfNot1.1 knockout, TP1, replicate 3

description:
100007_Cycle1_2017-10-23_WT_TP1_rep3
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 1 at around 4 hpi, replicate 3

source_name: P. falciparum T996 RNA, wildtype line for PfNot1.1 knockout


title: wildtype line for PfNot1.1 knockout, TP3, replicate 3

description:
100029_Cycle1_2017-10-23_WT_TP3_rep3
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 3 at around 20 hpi, replicate 3


title: wildtype line for PfNot1.1 knockout, TP4, replicate 3

description:
100030_Cycle1_2017-10-23_WT_TP4_rep3
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 4 at around 28 hpi, replicate 3


title: wildtype line for PfNot1.1 knockout, TP4, replicate 1

description:
100024_Cycle1_2017-10-10_WT_TP4_rep1
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 4 at around 28 hpi, replicate 1


title: wildtype line for PfNot1.1 knockout, TP6, replicate 2

description:
100049_Cycle1_2017-10-22_WT_TP6_rep2
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 6 at around 44 hpi, replicate 2


title: wildtype line for PfNot1.1 knockout, TP3, replicate 1

description:
100023_Cycle1_2017-10-10_WT_TP3_rep1
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 3 at around 20 hpi, replicate 1


title: wildtype line for PfNot1.1 knockout, TP2, replicate 2

description:
100042_Cycle1_2017-10-22_WT_TP2_rep2
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 2 at around 12 hpi, replicate 2


title: wildtype line for PfNot1.1 knockout, TP4, replicate 2

description:
101046_Cycle1_2017-11-08_WT_TP4_rep2
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 4 at around 28 hpi, replicate 2


title: wildtype line for PfNot1.1 knockout, TP5, replicate 3

description:
100031_Cycle1_2017-10-23_WT_TP5_rep3
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 5 at around 36 hpi, replicate 3


title: wildtype line for PfNot1.1 knockout, TP6, replicate 3

description:
100032_Cycle1_2017-10-23_WT_TP6_rep3
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 6 at around 44 hpi, replicate 3


title: wildtype line for PfNot1.2 knockdown, TP4, replicate 1

description:
104070_Cycle1_2018-02-12_WT_TP4_rep1
Transcriptional profiling of the wildtype line for the PfNot1.2 knockdown line at Timepoint 4 at around 28 hpi, replicate 1


title: wildtype line for PfNot1.1 knockout, TP2, replicate 3

description:
100028_Cycle1_2017-10-23_WT_TP2_rep3
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 2 at around 12 hpi, replicate 3


title: wildtype line for PfNot1.1 knockout, TP5, replicate 1

description:
100026_Cycle1_2017-10-10_WT_TP5_rep1
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 5 at around 36 hpi, replicate 1


title: PfNot1.2 knockdown, TP1, replicate 1

description:
104071_Cycle2_2018-02-09_KD_TP1_rep1
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 1 at around 4 hpi, replicate 1


title: wildtype line for PfNot1.1 knockout, TP3, replicate 2

description:
101048_Cycle2_2017-11-08_WT_TP3_rep2
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 3 at around 20 hpi, replicate 2


title: PfNot1.2 knockdown, TP5, replicate 1

description:
104083_Cycle2_2018-02-12_KD_TP5_rep1
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 5 at around 36 hpi, replicate 1


title: wildtype line for PfNot1.1 knockout, TP2, replicate 1

description:
100022_Cycle1_2017-10-10_WT_TP2_rep1
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 2 at around 12 hpi, replicate 1


title: wildtype line for PfNot1.1 knockout, TP6, replicate 1

description:
100027_Cycle1_2017-10-10_WT_TP6_rep1
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 6 at around 44 hpi, replicate 1


title: wildtype line for PfNot1.1 knockout, TP1, replicate 1

description:
100020_Cycle1_2017-10-10_WT_TP1_rep1
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 1 at around 4 hpi, replicate 1


title: PfNot1.1 knockout, TP6, replicate 3

description:
100032_Cycle2_2017-10-23_KO_TP6_rep3
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 6 at around 44 hpi, replicate 3


title: PfNot1.2 knockdown, TP4, replicate 1

description:
104070_Cycle2_2018-02-12_KD_TP4_rep1
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 4 at around 28 hpi, replicate 1


title: wildtype line for PfNot1.1 knockout, TP5, replicate 2

description:
101047_Cycle1_2017-11-08_WT_TP5_rep2
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 5 at around 36 hpi, replicate 2


title: wildtype line for PfNot1.1 knockout, TP1, replicate 2

description:
100041_Cycle1_2017-10-22_WT_TP1_rep2
Transcriptional profiling of the wildtype line for the PfNot1.1 knockout line at Timepoint 1 at around 4 hpi, replicate 2


title: PfNot1.1 knockout, TP5, replicate 3

description:
100031_Cycle2_2017-10-23_KO_TP5_rep3
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 5 at around 36 hpi, replicate 3


title: PfNot1.1 knockout, TP4, replicate 3

description:
100030_Cycle2_2017-10-23_KO_TP4_rep3
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 4 at around 28 hpi, replicate 3


title: PfNot1.1 knockout, TP2, replicate 3

description:
100028_Cycle2_2017-10-23_KO_TP2_rep3
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 2 at around 12 hpi, replicate 3


title: PfNot1.1 knockout, TP3, replicate 3

description:
100029_Cycle2_2017-10-23_KO_TP3_rep3
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 3 at around 20 hpi, replicate 3


title: F2 Embry.63 T CM mi 387 Mu

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

country: Germany

institute: FBN

description:
microRNA expression data from skeletal muscle of 63 dpc of F2 population based breed Pi and DL.
Muscle samples of foetuses (F2) derived from the F1 sows were collected and evaluated at gestational day 63. Muscle (longissimus dorsi) samples were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip miRNA arrays. GeneChips were washed and processed to detect biotin-containing transcripts by Streptavidin-PE (Phycoerythrin) conjugate.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Expression Console and quantify by med polish

label: biotin

organism: Sus scrofa

source_name: Musculus longissimus dorsi tissue from 63 dpc pig

label_protocol: Biotinylated cRNA were prepared from miRNA according to FlashTag Biotin RNA Labeling Kit for Affymetrix GeneChip miRNA arrays (Genisphere, Hatfield, PA, USA) according to the manufacturer’s recommendations Affymetrix GeneChip miRNA Array protocols (Affymetrix, Santa Clara, CA, USA)

extract_protocol: Total RNA was isolated using Qiagen miReasy Mini kit TRI Reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol for small-RNA. Then small RNA was cleaned up using the Rneasy MinElute Clean up kit  (Qiagen, Hilden, Germany).

tag: breed

value: F2 based German Landrace (DL) x Pietrain (Pi)

tag: tissue

value: Musculus longissimus dorsi

tag: age

value: 63 days post conception (dpc)


title: F2 Embry.63 T CM mi 388 Mu


title: PfNot1.1 knockout, TP4, replicate 1

description:
100024_Cycle2_2017-10-10_KO_TP4_rep1
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 4 at around 28 hpi, replicate 1


title: F2 Embry.63 T CM mi 383 Mu


title: F2 Embry.63 T CM mi 385 Mu


title: F2 Embry.63 T CM mi 382 Mu


title: F2 Embry.63 T CM mi 386 Mu


title: F2 Embry.63 T CM mi 389 Mu


title: PfNot1.1 knockout, TP6, replicate 2

description:
101048_Cycle1_2017-11-08_KO_TP6_rep2
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 6 at around 44 hpi, replicate 2


title: PfNot1.1 knockout, TP4, replicate 2

description:
101046_Cycle2_2017-11-08_KO_TP4_rep2
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 4 at around 28 hpi, replicate 2


title: F2 Embry.63 T CM mi 380 Mu


title: PfNot1.1 knockout, TP5, replicate 2

description:
101047_Cycle2_2017-11-08_KO_TP5_rep2
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 5 at around 36 hpi, replicate 2


title: PfNot1.1 knockout, TP1, replicate 3

description:
100007_Cycle2_2017-10-23_KO_TP1_rep3
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 1 at around 4 hpi, replicate 3


title: PfNot1.1 knockout, TP1, replicate 2

description:
101045_Cycle1_2017-11-08_KO_TP1_rep2
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 1 at around 4 hpi, replicate 2


title: PfNot1.1 knockout, TP2, replicate 2

description:
101045_Cycle2_2017-11-08_KO_TP2_rep2
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 2 at around 12 hpi, replicate 2


title: PfNot1.1 knockout, TP3, replicate 2

description:
100043_Cycle2_2017-10-22_KO_TP3_rep2
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 3 at around 20 hpi, replicate 2


title: PfNot1.1 knockout, TP5, replicate 1

description:
100026_Cycle2_2017-10-10_KO_TP5_rep1
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 5 at around 36 hpi, replicate 1


title: F2 Embry.63 T CM mi 369 Mu


title: F2 Embry.63 T CM mi 378 Mu


title: F2 Embry.63 T CM mi 381 Mu


title: F2 Embry.63 T CM mi 379 Mu


title: F2 Embry.63 T CM mi 362 Mu


title: F2 Embry.63 T CM mi 364 Mu


title: F2 Embry.63 T CM mi 365 Mu


title: F2 Embry.63 T CM mi 361 Mu


title: F2 Embry.63 T CM mi 368 Mu


title: PfNot1.1 knockout, TP2, replicate 1

description:
100022_Cycle2_2017-10-10_KO_TP2_rep1
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 2 at around 12 hpi, replicate 1


title: F2 Embry.63 T CM mi 371 Mu


title: F2 Embry.63 T CM mi 372 Mu


title: F2 Embry.63 T CM mi 374 Mu


title: F2 Embry.63 T CM mi 373 Mu


title: F2 Embry.63 T CM mi 375 Mu


title: PfNot1.1 knockout, TP6, replicate 1

description:
100027_Cycle2_2017-10-10_KO_TP6_rep1
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 6 at around 44 hpi, replicate 1


title: F2 Embry.63 T CM mi 351 Mu


title: F2 Embry.63 T CM mi 350 Mu


title: F2 Embry.63 T CM mi 358 Mu


title: F2 Embry.63 T CM mi 353 Mu


title: F2 Embry.63 T CM mi 357 Mu


title: F2 Embry.63 T CM mi 359 Mu


title: F2 Embry.63 T CM mi 356 Mu


title: F2 Embry.63 T CM mi 354 Mu


title: F2 Embry.63 T CM mi 339 Mu


title: F2 Embry.63 T CM mi 335 Mu


title: F2 Embry.63 T CM mi 337 Mu


title: F2 Embry.63 T CM mi 336 Mu


title: F2 Embry.63 T CM mi 346 Mu


title: F2 Embry.63 T CM mi 347 Mu


title: F2 Embry.63 T CM mi 348 Mu


title: F2 Embry.63 T CM mi 341 Mu


title: F2 Embry.63 T CM mi 343 Mu


title: F2 Embry.63 T CM mi 349 Mu


title: F2 Embry.63 T CM mi 344 Mu


title: F2 Embry.63 T CM mi 342 Mu


title: F2 Embry.63 T CM mi 345 Mu


title: PfNot1.1 knockout, TP3, replicate 1

description:
100023_Cycle2_2017-10-10_KO_TP3_rep1
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 3 at around 20 hpi, replicate 1


title: F2 Embry.63 T CM mi 331 Mu


title: F2 Embry.63 T CM mi 325 Mu


title: F2 Embry.63 T CM mi 326 Mu


title: F2 Embry.63 T CM mi 323 Mu


title: F2 Embry.63 T CM mi 367 Mu


title: F2 Embry.63 T CM mi 366 Mu


title: F2 Embry.63 T CM mi 321 Mu


title: F2 Embry.63 T CM mi 322 Mu


title: F2 Embry.63 T CM mi 330 Mu


title: F2 Embry.63 T CM mi 328 Mu


title: F2 Embry.63 T CM mi 334 Mu


title: F2 Embry.63 T CM mi 333 Mu


title: PfNot1.1 knockout, TP1, replicate 1

description:
100020_Cycle2_2017-10-10_KO_TP1_rep1
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 1 at around 4 hpi, replicate 1


title: F2 Embry.63 T CM mi 319 Mu


title: F2 Embry.63 T CM mi 332 Mu


title: F2 Embry.63 T CM mi 316 Mu


title: F2 Embry.63 T CM mi 317 Mu


title: F2 Embry.63 T CM mi 302 Mu


title: F2 Embry.63 T CM mi 304 Mu


title: F2 Embry.63 T CM mi 315 Mu


title: F2 Embry.63 T CM mi 314 Mu


title: F2 Embry.63 T CM mi 310 Mu


title: F2 Embry.63 T CM mi 309 Mu


title: F2 Embry.63 T CM mi 301 Mu


title: F2 Embry.63 T CM mi 296 Mu


title: F2 Embry.63 T CM mi 298 Mu


title: F2 Embry.63 T CM mi 294 Mu


title: F2 Embry.63 T CM mi 292 Mu


title: F2 Embry.63 T CM mi 295 Mu


title: F2 Embry.63 T CM mi 299 Mu


title: F2 Embry.63 T CM mi 306 Mu


title: F2 Embry.63 T CM mi 308 Mu


title: F2 Embry.63 T CM mi 318 Mu


title: F2 Embry.63 T CM mi 289 Mu


title: F2 Embry.63 T CM mi 287 Mu


title: F2 Embry.63 T CM mi 290 Mu


title: F2 Embry.63 T CM mi 286 Mu


title: F2 Embry.63 T CM mi 305 Mu


title: F2 Embry.63 T CM mi 300 Mu


title: F2 Embry.63 T CM mi 288 Mu


title: F2 Embry.63 T CM mi 293 Mu


title: F2 Embry.63 T CM mi 285 Mu


title: F2 Embry.63 T CM mi 291 Mu


title: F2 Embry.63 T CM mi 282 Mu


title: F2 Embry.63 T CM mi 284 Mu


title: HeLa_pgPEN_CRISPR_screen_plasmid

description: sample of plasmid pool sequenced with HeLa screen

molecule: other

organism: synthetic construct

source_name: plasmid

tag: cell line

tag: tumor type

tag: timepoint

tag: expresses

tag: sample type

value: plasmid library

tag: drug treatment


title: RNA-Seq DS 3

city: Winnipeg

first: Mark

last: Belmonte

state: Manitoba

address: 50 Sifton Rd

department: Biological Sciences

institute: University of Manitoba

description: DS 3

data_processing:
WGBS: TRIMMING. Quality trimming and adaptor removal were performed using Trimmomatic (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
WGBS: ALIGNMENT. Successfully paired reads were aligned to the DH12075 genome using BSMap2
WBGS: BASE CALLING. cytosine methylation levels were called using the methratio script (Xi and Li 2009). Individual cytosines had to be covered by at least 4 reads to be considered for analysis.
sRNAseq: TRIMMING. Quality trimming and adaptor removal were completed with Trimmomatic
sRNAseq: ALIGNMENT.  sRNAseq: ALIGNMENT. Surviving reads were aligned to the DH12075 genome using Bowtie on default settings. Aligned reads were then filtered for rRNA, tRNA, snRNA, and snoRNA species by aligning them to known records in NCBI under all Viridiplantae
sRNAseq: sRNA PREDICTION. siRNA prediction was done using Short Stack on default settings (Axtell, 2013). SRCs overlapping 90% with a predicted SRC in another bioreplicate were passed through analysis to coincide with miRNA criteria covered in Axtell and Meyers (2018). SRCs overlapping with REs were classified as rasiRNAs, and SRCs exceeding a phase score of 25 were classified as phasiRNAs.
Genome_build: Brassica napus cv. BioProject ID: PRJNA218846.
Supplementary_files_format_and_content: WGBS: tab-delimited text file indicating the C/T conversion ratio by which methylation ratio can be determined for each locus in the CG, CHG, and CHH contexts

organism: Brassica napus

source_name: Dry seed (35 DPF)

growth_protocol: Methylome analyses were performed in B. napus cv. DH12075. Plants were grown in growth chambers under long day conditions at 22°C. Flowers were hand-pollinated and collected at 0 DPF (OV), 7 DPF (GLOB), 10 DPF (HEART), 28 DPF (MG), and 35 DPF (DS).

extract_protocol:
DNA was isolated from seeds using the Qiagen Plant DNeasy Mini Kit. RNA was isolated from seeds using the Qiagen miRNeasy mini kit.
WGBS: Library preparation for bisulfite sequencing was performed at Genome Quebec. DNA was sheared via sonication on the Covaris platform prior adaptor ligation and bisulfite conversion using the EZ-96 DNA Methylation-Lightning Kit (Zymo®). Libraries were then amplified using the DNA UltraII Kit (NEB®). sRNAseq: Total RNA collected from seeds was used for library prep with the NEBNext® Small RNA Library Prep Set for Illumina® (Multiplex compatible).

treatment_protocol: Seeds were manually harvested from siliques and ground in liquid nitrogen for nucleic acid extractions

tag: seed stage

value: DS

tag: cultivar


title: F2 Embry.63 T CM mi 276 Mu


title: F2 Embry.63 T CM mi 277 Mu


title: PC9_pgPEN_CRISPR_screen_plasmid

description: sample of plasmid pool sequenced with PC9 screen


title: F2 Embry.63 T CM mi 278 Mu


title: RNA-Seq MG 2

description: MG 2

source_name: Mature green seed (28DPF)

value: MG


title: RNA-Seq HEART 1

description: HEART 1

source_name: Heart seed (10DPF)

value: HEART


title: RNA-Seq GLOB 3

description: GLOB 3

source_name: Globular seed (7DPF)

value: GLOB


title: RNA-Seq HEART 3

description: HEART 3


title: RNA-Seq HEART 2

description: HEART 2


title: RNA-Seq GLOB 2

description: GLOB 2


title: RNA-Seq MG 3

description: MG 3


title: RNA-Seq OV 3

description: OV 3

source_name: Ovule (0DPF)

value: OV


title: RNA-Seq GLOB 1

description: GLOB 1


title: RNA-Seq OV 2

description: OV 2


title: RNA-Seq OV 1

description: OV 1


title: RNA-Seq DS 2

description: DS 2


title: DS_1

data_processing:
Quality trimming and adaptor removal from sequencing reads was performed using Trimmomatic (Bolger et al., 2014). Read quality was evaluated using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
High quality reads were then aligned to the DH12075 genome (Parkin et al., unpublished) using tophat2
Uniquely mapping reads were then passed through to cuffnorm and cuffdiff (Trapnell et al., 2013) to determine transcript accumulation levels and differential gene expression.
Genome_build: Brassica napus DH12075 (CanSeq)
Supplementary_files_format_and_content: Normalized counts (FPKM matrix)

molecule: polyA RNA

source_name: Whole seed

growth_protocol: Plants were grown in growth chambers under long day conditions at 22°C. Flowers were hand-pollinated and collected at 0 DPF (OV), 7DPF (GLOB), 10DPF (HEART), 28DPF (MG), and 35 DPF (DS). Seeds were manually harvested from siliques.

extract_protocol:
RNA isolation was performed using PureLink™ Plant RNA reagent (Ambion®).
Library preparation and quality control was prepared as in Becker et al. (2017), modified from a high throughput RNA-seq library preparation protocol (Kumar et al., 2012).

treatment_protocol: Samples were flash frozen and ground in liquid nitrogen.

value: Whole seed

tag: stage (days post fertilization)


title: F2 Embry.63 T CM mi 279 Mu


title: F2 Embry.63 T CM mi 280 Mu


title: DS_2


title: MG_3


title: RNA-Seq DS 1

description: DS 1


title: MG 1


title: MG_2


title: RNA-Seq MG 1

description: MG 1


title: F2 Embry.63 T CM mi 275 Mu


title: F2 Embry.63 T CM mi 273 Mu


title: HEART_3


title: HEART_2


title: GLOB_2


title: HEART_1


title: GLOB_3


title: OV_3

source_name: Whole ovule

value: Whole ovule


title: OV_1


title: OV_2


title: PD1-032-AR_RNA

city: Washington

first: Krithika

last: Bhuvaneshwar

state: DC

address: 2115 Wisconsin Ave NW

institute: Georgetown University

description:
20180514_ThymusCa_countMatrix_anno.csv
multi_sample_vcf_file_tar.gz
ClinicalData.xlsx
Sample excluded from analysis due to poor quality

data_processing:
Variants were obtained using the well known open source GATK variant calling pipeline. All the VCF files were merged to make a multi sample vcf
The raw FASTQ files were filtered for high quality reads and aligned to Human Reference Genome Version GRCh38.84. RNA-seq gene counts were obtained using RSEM which performed alignment and quantification. The gene counts were collated to make a multi sample gene count file
Genome_build: GRCh38
Supplementary_files_format_and_content: Multi sample matrix file with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Multi-sample variant call file (VCF) file containing mutation information

source_name: Thymus tissue

extract_protocol:
Tumor DNA and RNA samples were extracted from formalin-fixed-paraffin-embedded (FFPE) tissue blocks of patients with thymic carcinoma using the DNA/RNA AllPrep Kit (Qiagen, Valencia, CA), as described previously (Petrini et al., 2014). Briefly, FFPE blocks were cut and subjected to hematoxylin and eosin (H&E) staining, and the tumor component was macrodissected from unstained slides that matched to the H&E staining slides. Control DNA for whole exome sequencing was extracted from paired patients’ peripheral blood samples using Genfind v2 kit (Beckman Coulter, Brea, CA).
The library construction for RNA-seq was performed by Tempus using KAPA HiFi Library Amplification kit (Beaubier et al., 2019). RNA libraries were prepared for sequencing using standard Illumina protocols. The whole exome library construction was performed using The Tempus xE hybrid capture Next-Generation sequencing panel (~20,000 gene) consisting of IDT xGen LockDown probes. The WES panel was sequenced to a depth of at least 150x for tumor and 50x for germline using 126 bp paired end reads on the Illumina HiSeq 4000.

value: thymus

tag: patient diagnosis

value: thymic carcinoma


title: GLOB_1


title: PD1-027-SD_exome_tumor

data_processing:
Library strategy: DNA-seq
Variants were obtained using the well known open source GATK variant calling pipeline. All the VCF files were merged to make a multi sample vcf
The raw FASTQ files were filtered for high quality reads and aligned to Human Reference Genome Version GRCh38.84. RNA-seq gene counts were obtained using RSEM which performed alignment and quantification. The gene counts were collated to make a multi sample gene count file
Genome_build: GRCh38
Supplementary_files_format_and_content: Multi sample matrix file with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Multi-sample variant call file (VCF) file containing mutation information


title: PD1-019-WC_RNA


title: WT_4

city: St Louis

first: Matthew

middle: J

last: Walter

state: MISSOURI

address: 660 South Euclid Avenue

department: Oncology

institute: Washington University School of Medicine

description: FACS sorted

data_processing:
Illumina HiSeq-3000 using single reads extending 50 bases
Reads were then were aligned to the mouse genome (mm9/NCBI build 37) using Hisat2 version 2.0.6 with annotations provided by Ensembl version 67.
Gene counts were determined by  processing the resulting reads using HTseq5 version 0.5.4p1.
Genome_build: mm9
Supplementary_files_format_and_content: "merged-final.tsv" file includes raw counts of reads spanning genes for all samples.

source_name: bulk bone marrow cells enriched for c-Kit+

extract_protocol:
RNA was isolated using NucleoSpin RNA XS kit (MACHEREY-NAGEL) per manufacturer’s instructions. Per sample, RNA equivalent of 5000-15000 BLPs from 2-3 mice were pooled. Total RNA integrity and concentration were assessed using a 2100 Bioanalyzer and an RNA 6000 Pico kit (Agilent). Double stranded-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer’s protocol. cDNA was fragmented using a Covaris E220 sonicator using duty cycle 10, intensity 5, cycles/burst 200, time 180 seconds.
Illumina HiSeq-3000 using single reads extending 50 bases

treatment_protocol: Bone marrow cells were harvested from H2afy+/+ and H2afy-/-mice of 5-12 weeks age. Cells were enriched for c-Kit+ cells using CD117 MicroBeads on the autoMACS Pro Separator (Miltenyi Biotec). Subsequently, cells were stained according to the staining scheme described above, and BLPs were sorted by FACS (Moflo, Beckman Coulter) directly into the lysis buffer of NucleoSpin RNA XS kit (MACHEREY-NAGEL).

tag: genotype

tag: cell type

value: B-cell biased-lymphoid progenitors

value: bone marrow


title: PD1-005-ET_exome_tumor

description:
20180514_ThymusCa_countMatrix_anno.csv
multi_sample_vcf_file_tar.gz
ClinicalData.xlsx


title: PD1-011-MD_RNA


title: PD1-032-AR_exome_tumor


title: PD1-020-JS_RNA


title: PD1-011-MD_exome_normal


title: PD1-004-SS_RNA


title: PD1-020-JS_exome_tumor


title: PD1-004-SS_exome_tumor


title: PD1-027-SD_RNA


title: PD1-005-ET_exome_normal


title: PD1-005-ET_RNA


title: PD1-017-JH_exome_normal


title: PD1-017-JH_RNA


title: PD1-032-AR_exome_normal


title: PD1-003-TF2_RNA


title: PD1-017-JH_exome_tumor


title: PD1-020-JS_exome_normal


title: WT_3

description: FACS sorted


title: PD1-019-WC_exome_tumor


title: PD1-011-MD_exome_tumor


title: PD1-004-SS_exome_normal


title: PD1-027-SD_exome_normal


title: PD1-003-TF2_exome_tumor


title: PD1-019-WC_exome_normal


title: WT_2

description: FACS sorted


title: PD1-003-TF2_exome_normal


title: PD1-001-KH_RNA


title: KO_4

description: FACS sorted


title: PD1-001-KH_exome_tumor


title: KO_2

description: FACS sorted


title: c-Rel -/-_IgM

city: Doha

first: Nico

last: Marr

address: Education City

country: Qatar

institute: Hamad Bin Khalifa University

description: c-Rel _IgM_BCell

data_processing:
Raw RNA-seq reads were aligned with UCSC human genome assembly version hg38, with STAR aligner (Dobin et al., 2013).
HTseq-count (Anders et al., 2015) was used to count the reads mapping to each gene feature. Downstream analysis and heatmap generation were performed with an in-house script in R [R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.], with DESEq2 (Love et al., 2014), and ComplexHeatmap (Gu et al., 2016)
Downstream analysis and heatmap generation were performed with an in-house script in R [R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.], with DESEq2 (Love et al., 2014), and ComplexHeatmap (Gu et al., 2016)
Genome_build: hg38
Supplementary_files_format_and_content: HTSeq-count is used to get the count files, followed by DESeq2 package in R for normalization and log2 transformation.

source_name: primary CD19+ B cells

growth_protocol: primary B and T cells: thawed and negatively sorted CD19+ primary B cells or CD4+ naive T-cells were rested overnight in x-vivo20 prior stimulation.

extract_protocol:
RNeasy plus micro kit (Qiagen): cDNA was prepared with the SMART-Seq RNA kit (Takara Bio) for low-input RNA and DNA library preparation and used the Nextera XT DNA Library Preparation Kit (Illumina) and the Nextera XT Index Kit v2 set A (Illumina), respectively
cDNA

treatment_protocol: Naïve CD4+ T cells: Stimulation of cells from the patient and 4 unrelated controls for two hours with the indicated combination of mAb coated beads (anti-CD2/3/28) or left untreated. Primary CD19+ B cells: Stimulation of cells from the patient and 4 unrelated controls for two hours with PMA, CD40L, F(ab')2 goat anti-IgM or left untreated.

value: CD19+ B cells

tag: disease state

value: patient with AR c-Rel deficiency

tag: treatment

value: IgM


title: c-Rel -/-_PMA

description: c-Rel _PMA_BCell

value: PMA


title: KO_3

description: FACS sorted


title: KO_1

description: FACS sorted


title: c-Rel -/-_NS

description: c-Rel _NS_BCell

value: unstimulated


title: Control B_IgM

value: healthy control


title: CD40-/-_NS


title: Control B_CD40 Li

description: CtrlB_CD40 Li_BCell

value: CD40 Li


title: PD1-001-KH_exome_normal


title: WT_1

description: FACS sorted


title: CD40-/-_CD40 Li

description: CD40_CD40 Li_BCell


title: Control B_PMA


title: Control A_PMA


title: Control A_IgM


title: c-Rel -/-_CD40 Li

description: c-Rel _CD40 Li_BCell


title: Control A_CD40 Li

description: CtrlA_CD40 Li_BCell


title: Control A_NS


title: Control 2_PMA


title: Control 2_IgM


title: 12m_D_P_51 [rGen01-167]

city: Rochester

first: Walter

last: Park

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

description:
replicate 1
rGen01-167

hyb_protocol: Standard Illumina hybridization protocol (hybridized to a Human HT-12v4.0 Expression (illumina Inc., San Diego, CA, USA)). Briefly, 750 ng labeled RNA/sample was hybridized to HT-12v4 Expression BeadChips (Illumina, Inc.) for 16 hours. The BeadChip underwent a washing and streptavidin-Cy3 (GE Healthcare Bio-Sciences) conjugate staining protocol.

scan_protocol: Standard Illumina scanning protocol

data_processing: normalization performed using R.

source_name: 18-gauge kidney allograft biopsy

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep Amplification kit (Ambion-Life technologies). 200 ng of total RNA was reverse transcribed, biotin labeled. Biotinylated cRNA was prepared according to the standard Illumina protocol

extract_protocol: RNA isolation performed using TRIzol, followed by Qiagen clean-up.

treatment_protocol: Specimens are frozen in RNALater and stored at -80 oC until use.

tag: patient

value: Kidney transplant

tag: protocol

value: 1 year surveillance biopsy

tag: phenotype

value: Progressor

tag: cohort

value: Discovery


title: Control 1_PMA


title: Control 1_IgM


title: Control 2_NS


title: 12m_D_P_49 [rGen01-165]

description:
replicate 1
rGen01-165


title: Control 2_CD40 Li

description: Ctrl2_CD40 Li_BCell


title: Control 1_CD40 Li

description: Ctrl1_CD40 Li_BCell


title: 12m_D_P_54 [rGen01-170]

description:
replicate 1
rGen01-170


title: 12m_D_P_53 [rGen01-169]

description:
replicate 1
rGen01-169


title: 12m_D_P_50 [rGen01-166]

description:
replicate 1
rGen01-166


title: 12m_D_P_44 [rGen01-160]

description:
replicate 1
rGen01-160


title: 12m_D_P_48 [rGen01-164]

description:
replicate 1
rGen01-164


title: 12m_D_P_47 [rGen01-163]

description:
replicate 1
rGen01-163


title: 12m_D_P_42 [rGen01-158]

description:
replicate 1
rGen01-158


title: 12m_D_P_39 [rGen01-155]

description:
replicate 1
rGen01-155


title: 12m_D_P_46 [rGen01-162]

description:
replicate 1
rGen01-162


title: 12m_D_P_45 [rGen01-161]

description:
replicate 1
rGen01-161


title: 12m_D_P_52 [rGen01-168]

description:
replicate 1
rGen01-168


title: 12m_D_P_43 [rGen01-159]

description:
replicate 1
rGen01-159


title: 12m_D_P_41 [rGen01-157]

description:
replicate 1
rGen01-157


title: 12m_D_P_40 [rGen01-156]

description:
replicate 1
rGen01-156


title: 12m_D_P_35 [rGen01-136]

description:
replicate 1
rGen01-136


title: REL_HW_6357_CD3+CD28

source_name: primary CD4+ T cells

value: CD4+ T cells


title: 12m_D_P_38 [rGen01-139]

description:
replicate 1
rGen01-139


title: REL_HW_6357_CD28


title: REL_HW_6357_PMA


title: REL_HW_6357_CD3+CD2


title: 12m_D_P_34 [rGen01-135]

description:
replicate 1
rGen01-135


title: 12m_D_P_36 [rGen01-137]

description:
replicate 1
rGen01-137


title: Control 1_NS


title: 12m_D_P_37 [rGen01-138]

description:
replicate 1
rGen01-138


title: REL_HW_6357_CD3


title: REL_HW_6357_CD2


title: REL_HW_6357_NS


title: Ctl5_PMA


title: 12m_D_P_33 [rGen01-134]

description:
replicate 1
rGen01-134


title: 12m_D_P_32 [rGen01-133]

description:
replicate 1
rGen01-133


title: 12m_D_P_31 [rGen01-132]

description:
replicate 1
rGen01-132


title: Ctl5_CD28


title: Ctl5_CD3+CD2


title: Ctl5_CD3


title: Ctl5_CD2


title: Ctl2_PMA


title: Ctl5_NS


title: Ctl2_CD3+CD28


title: Ctl5_CD3+CD28


title: 12m_D_P_30 [rGen01-131]

description:
replicate 1
rGen01-131


title: Ctl2_CD3+CD2


title: 12m_D_P_28 [rGen01-129]

description:
replicate 1
rGen01-129


title: 12m_D_P_24 [rGen01-125]

description:
replicate 1
rGen01-125


title: 12m_D_P_27 [rGen01-128]

description:
replicate 1
rGen01-128


title: Ctl2_CD28


title: Ctl2_CD3


title: 12m_D_P_29 [rGen01-130]

description:
replicate 1
rGen01-130


title: Ctl2_CD2


title: Ctl2_NS


title: Ctl1_CD3+CD28


title: 12m_D_P_18 [rGen01-119]

description:
replicate 1
rGen01-119


title: Ctl1_PMA


title: 12m_D_P_19 [rGen01-120]

description:
replicate 1
rGen01-120


title: 12m_D_P_25 [rGen01-126]

description:
replicate 1
rGen01-126


title: 12m_D_P_20 [rGen01-121]

description:
replicate 1
rGen01-121


title: 12m_D_P_22 [rGen01-123]

description:
replicate 1
rGen01-123


title: 12m_D_P_23 [rGen01-124]

description:
replicate 1
rGen01-124


title: Ctl1_CD3+CD2


title: 12m_D_P_21 [rGen01-122]

description:
replicate 1
rGen01-122


title: 12m_D_P_14 [rGen01-115]

description:
replicate 1
rGen01-115


title: 12m_D_P_13 [rGen01-114]

description:
replicate 1
rGen01-114


title: Ctl1_CD3


title: 12m_D_P_26 [rGen01-127]

description:
replicate 1
rGen01-127


title: Ctl1_CD2


title: 12m_D_P_12 [rGen01-113]

description:
replicate 1
rGen01-113


title: 12m_D_P_11 [rGen01-112]

description:
replicate 1
rGen01-112


title: 12m_D_P_15 [rGen01-116]

description:
replicate 1
rGen01-116


title: Ctl3_PMA


title: Ctl1_NS


title: 12m_D_P_10 [rGen01-111]

description:
replicate 1
rGen01-111


title: 12m_D_P_8 [rGen01-109]

description:
replicate 1
rGen01-109


title: Ctl3_CD3+CD2


title: 12m_D_P_9 [rGen01-110]

description:
replicate 1
rGen01-110


title: Ctl3_CD28


title: 12m_D_P_4 [rGen01-105]

description:
replicate 1
rGen01-105


title: Ctl3_NS


title: Pooled sample 4

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

description:
S4
Single-cell RNA-seq
RNA and HTO data are present in the submitted raw and processed data files.
covid_control_RNA_counts.csv
cap_control_RNA_counts.csv
covid_cap_RNA_counts.csv

data_processing:
Sample demultiplexing: We demultiplexed the pooled samples into individual samples based on the Hashtag antibodies, using the R package Seurat (v3) (Stuart et al., 2019).
Deconvolution: To deconvolute the cells belonging to each sample we used the R package Seurat (v3) (Stuart et al., 2019). The outputs derived from CellRanger were used to create two separate objects (one with the transcriptome alignment and one with the antibody plus hashtags (HTO) alignment). Initial objects were created using the function “Read10X”. We filtered both objects based on the cell barcode to keep only cells which were identified in both the transcriptome and in the antibody alignments. After this cell filtering, we used the function “CreateSeuratObject” to create a transcriptome-based Seurat object. The antibody derived data was filtered to maintain only the hashtag counts; later it was appended as a specific assay using the “CreateAssayObject” function. Antibody reads were normalized using the CLR method.
Cell demultiplexing: For cell demultiplexing we used the function “HTODemux” with the parameters “init=9”, “nsamples=10000” and “positive quantile” ranging between 0.999 and 0.9999999 per each sample, in order to maximize the number of singlets detected. Individual single cells were finally filtered based on their assigned “HTO_classification.global”= “Singlet”.
Normalizing HTO data: Antibody data was normalized using the Seurat function “NormalizeData” with the parameters “normalization.method” = "CLR" and “margin”=”2”, to indicate a normalization across cells.
Filtering: Cells were filtered based on number of features, number of genes and percentage of mitochondrial reads using Seurat “subset(object, subset = nCount_RNA > 1000 &nCount_RNA < 10000 & nFeature_RNA > 200 & percent.mt < 20)”.
Cell cycle correction and normalizing: We calculated cell cycle scores as following (“CellCycleScoring(Healthy_object_Cycle, s.features = s.genes, g2m.features = g2m.genes, set.ident = TRUE”) using a list of S phase and G2M phase genes preloaded in Seurat. Cells were then scaled and normalized using the function “SCTransform(object, vars.to.regress = c("nCount_RNA","percent.mt","S.Score", "G2M.Score"))”.
Genome_build: GRCh38
Supplementary_files_format_and_content: Each comparison (Covid - control, CAP - control, Covid-CAP) has a count and metadata file.
Supplementary_files_format_and_content: *_RNA_counts.csv: Comma-separated text file includes counts. HTO data are included in these files.
Supplementary_files_format_and_content: *_count_metadata.csv: Comma-separated text file includes metadata.

source_name: PBMCs

extract_protocol:
For all patients and controls, heparin anticoagulated whole-blood was processed within 4 hours of sampling. PBMCs were separated by density gradient centrifugation using Ficoll-Paque Plus medium (GE Healthcare Life science, Little Chalfont, UK) and washed twice, first with cold PBS and then with cold PBS supplemented with 0.5% sterile endotoxin-free bovine serum albumin (Divbio Science Europe, Breda, the Netherlands). PBMC’s were resuspended in PBS containing 0.5% BSA and 2mm EDTA and the concentration PBMCs was determined using a Coulter Counter. PBMCs were resuspended in IMDM medium containing 20% filter-sterilized fetal calf serum and pen/strep, after which an equal part of the same medium containing 20% DMSO was slowly added while continuously stirring and working on ice. 3-5 million PBMCs were viably stored in 1.8 ml cryogenic vials (Corning #430388), which were steadily brought to -80 degrees Celsius. After 24-72 hours, the cells were transferred to liquid nitrogen storage until further analysis. After thawing, all samples averaged 90% viability as determined by FACS analysis. PBMCs were thawed, stained with viability dye and 500,000 cells were sorted using a FACS Sony Sorter selecting alive, singlet cells. The cells were incubated with FC blocker for 10 minutes, after which each sample was incubated with TotalSeq Hashtag antibody tags to enable multiplexing and subsequent deconvoluting. After Hashtag staining the cells were pooled into four pools of five samples, each sample contributing equally to their respective pool. Cells were counted manually by light microscopy and Neubauer chambers. Each pooled sample was then incubated for 30 minutes with our TotalSeq oligo-conjugated antibody panel (see the Key Resources Table) for later surface protein marker quantification.
Libraries were generated using the Chromium Single Cell 5′ Library & Gel Bead Kit v1.1 (10X genomics, Pleasanton, CA) following the manufacturer’s instructions. In short, pooled cells were loaded aiming the capture of 10,000 cells per pool. Libraries were generated according to standard protocol (Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 rev E). The amplified mRNA and antibody-derived tags were divided by size and sequenced separately.

value: PBMC


title: Ctl3_CD3


title: Ctl3_CD2


title: 12m_D_P_7 [rGen01-108]

description:
replicate 1
rGen01-108


title: Pooled sample 2

description:
S2
Single-cell RNA-seq
RNA and HTO data are present in the submitted raw and processed data files.
covid_control_RNA_counts.csv
cap_control_RNA_counts.csv
covid_cap_RNA_counts.csv


title: Ctl1_CD28


title: 12m_D_P_17 [rGen01-118]

description:
replicate 1
rGen01-118


title: Pooled sample 1

description:
S1
Single-cell RNA-seq
RNA and HTO data are present in the submitted raw and processed data files.
covid_control_RNA_counts.csv
cap_control_RNA_counts.csv
covid_cap_RNA_counts.csv


title: 12m_D_P_5 [rGen01-106]

description:
replicate 1
rGen01-106


title: 12m_D_P_6 [rGen01-107]

description:
replicate 1
rGen01-107


title: 12m_D_P_1 [rGen01-102]

description:
replicate 1
rGen01-102


title: 12m_D_P_2 [rGen01-103]

description:
replicate 1
rGen01-103


title: 12m_V_P_43 [Gen04-44-091]

description:
replicate 1
Gen04-44-091

value: Validation


title: 12m_V_P_42 [Gen04-44-086]

description:
replicate 1
Gen04-44-086


title: A-5_REL(-/-) + REL vector

description: REL(-/-) + REL vector

source_name: EBV-B

growth_protocol: For Epstein-Barr virus (EBV)-transformed B-cell lines (EBV-B), fresh blood samples were obtained from patients and controls, and after PBMC isolation, cells were subsequently infected with EBV and cultured in RPMI medium supplemented with 10% FCS. EBV-B clones appear in culture in about 15 days.

treatment_protocol: EBV B-cells: Stimulation for 2h with PDBU or left untreated.

tag: disease stage

value: c-REL deficient cells

value: medium

tag: transfection

value: wildtype c-REL rescue vector


title: A-3_REL(-/-) + Empty vector

description: REL(-/-) + Empty vector

tag: timepoint

value: empty control vector


title: A-4_REL(-/-) + Empty vector

description: REL(-/-) + Empty vector

value: PDBU


title: A-6_REL(-/-) + REL vector

description: REL(-/-) + REL vector


title: A-1_REL(-/-)

description: REL(-/-)

value: untreated


title: A-2_REL(-/-)

description: REL(-/-)


title: 12m_D_P_16 [rGen01-117]

description:
replicate 1
rGen01-117


title: CF, transduced with HIV-GFP [CFB_14_19_GFP]

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

data_processing:
Raw fastq files were aligned to a hybrid genome consisting of human genome assembly GRCh38.p13 and lentivirus genome sequence. Filtering, barcode counting, and UMI counting were performed with 10x CellRanger software version 3.0.2 with the argument --expect-cells=5000.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: HDF5 format file containing counts for each gene (row) and cell barcode (column)

source_name: CF_transduced with HIV-GFP

extract_protocol:
Cultured cells were rinsed in PBS -/- and lifted in TrypLE for 45 min at 37C. Cells were centrifuged for 5 min at 200xrcf, supernatent was removed, and cells were resuspended in Phenol red-free DMEM:F12 with 0.04% non-acetylated BSA and counted.
10x Genomics Chromium Single Cell 3’ Reagent Kits v3 system

tag: subject id

tag: subject status

value: cystic fibrosis (CF)

tag: tissue

value: lung

value: primary basal cells

value: HIV-GFP


title: CF, untreated [CFB_14_19_untreated]


title: 12m_V_P_37 [Gen04-06-038]

description:
replicate 1
Gen04-06-038

value: Kidney transplant


title: 12m_V_P_38 [Gen04-44-028]

description:
replicate 1
Gen04-44-028

value: 1 year surveillance biopsy


title: 12m_V_P_39 [Gen04-44-069]

description:
replicate 1
Gen04-44-069

value: Progressor


title: 12m_V_P_34 [Gen04-05-189]

description:
replicate 1
Gen04-05-189


title: 12m_V_P_35 [Gen04-05-197]

description:
replicate 1
Gen04-05-197


title: 12m_V_P_33 [Gen04-05-185]

description:
replicate 1
Gen04-05-185


title: CF, transduced with HIV-GFP [CFB_13_19_GFP]


title: non-CF, untreated [B_20_19_untreated]

value: non-cystic fibrosis (non-CF)


title: 12m_D_P_3 [rGen01-104]

description:
replicate 1
rGen01-104

value: Discovery


title: CF, transduced with HIV-CFTR [CFB_13_19_CFTR]

source_name: CF_transduced with HIV-CFTR

value: HIV-CFTR


title: CF, transduced with HIV-CFTR [CFB_14_19_CFTR]


title: 12m_V_P_31 [Gen04-05-164]

description:
replicate 1
Gen04-05-164

value: Validation


title: CF, untreated [CFB_13_19_untreated]


title: non-CF, transduced with HIV-GFP [B_20_19_GFP]

source_name: non-CF_transduced with HIV-GFP


title: non-CF, transduced with HIV-CFTR [B_20_19_CFTR]

source_name: non-CF_transduced with HIV-CFTR


title: non-CF, transduced with HIV-GFP [B_18_19_GFP]


title: non-CF, transduced with HIV-CFTR [B_18_19_CFTR]


title: non-CF, untreated [B_19_19_untreated]


title: 12m_V_P_26 [Gen04-05-089]

description:
replicate 1
Gen04-05-089


title: 12m_V_P_29 [Gen04-05-121]

description:
replicate 1
Gen04-05-121


title: 12m_V_P_27 [Gen04-05-106]

description:
replicate 1
Gen04-05-106


title: M6

city: New York

first: Jessica

middle: Esther

last: Treisman

state: NY

address: SKI 4/9, 540 First Avenue

department: Skirball Institute/Cell Biology

institute: NYU School of Medicine

data_processing:
Sequence quality was assessed with FastQC
Sequencing adapters were removed with Trimmomatic
Cleaned reads were aligned to the Drosophila reference genome (dm3) with Tophat2 v2.1.1 1.
Per sample gene expression profiles were computed using Cufflinks v2.2.1 1
Differential gene expression was computed for various contrasts between genotypes with the Cufflinks protocol  with default thresholds.
Genome_build: dm3
Supplementary_files_format_and_content: Excel spreadsheet with FPKM for each sample, log fold change between control and btz mutant samples and significance values

organism: Drosophila melanogaster

source_name: Third instar larval carcass

growth_protocol: Larvae were maintained in uncrowded conditions on standard cornnmeal-agar medium at 25 degrees C.

extract_protocol:
Third instar larval central nervous systems were dissected out and other tissues removed. Larval carcasses were prepared by removing all internal tissues, leaving only muscle and cuticle. Total RNA was extracted using Trizol.
Libraries were constructed using the Illumina TruSeq RNA sample Prep Kit v2 (Cat #RS-122-2002), using 500 ng of total RNA as input.

value: Carcass

tag: developmental stage

value: Wandering third instar larva


title: 12m_V_P_32 [Gen04-05-182]

description:
replicate 1
Gen04-05-182


title: 12m_V_P_30 [Gen04-05-163]

description:
replicate 1
Gen04-05-163


title: M4


title: 12m_V_P_28 [Gen04-05-113]

description:
replicate 1
Gen04-05-113


title: M5

value: btz2/+ control


title: M3


title: 12m_V_P_22 [Gen04-05-062]

description:
replicate 1
Gen04-05-062


title: 12m_V_P_23 [Gen04-05-064]

description:
replicate 1
Gen04-05-064


title: 12m_V_P_24 [Gen04-05-082]

description:
replicate 1
Gen04-05-082


title: M2


title: C5

source_name: Third instar larval central nervous system

value: CNS


title: M1


title: C4


title: C6


title: C3


title: C2


title: 12m_V_P_21 [Gen04-05-053]

description:
replicate 1
Gen04-05-053


title: 12m_V_P_20 [Gen04-05-044]

description:
replicate 1
Gen04-05-044


title: 12m_V_P_25 [Gen04-05-086]

description:
replicate 1
Gen04-05-086


title: 12m_V_P_16 [Gen04-05-008]

description:
replicate 1
Gen04-05-008


title: 12m_V_P_36 [Gen04-06-010]

description:
replicate 1
Gen04-06-010


title: 12m_V_P_15 [Gen04-02-096]

description:
replicate 1
Gen04-02-096


title: 12m_V_P_18 [Gen04-05-031]

description:
replicate 1
Gen04-05-031


title: 12m_V_P_17 [Gen04-05-012]

description:
replicate 1
Gen04-05-012


title: 12m_V_P_13 [Gen04-02-089]

description:
replicate 1
Gen04-02-089


title: 12m_V_P_11 [Gen04-02-066]

description:
replicate 1
Gen04-02-066


title: Control B_NS

value: CD19+ B cells

value: healthy control

value: unstimulated


title: 12m_V_P_12 [Gen04-02-080]

description:
replicate 1
Gen04-02-080


title: 12m_V_P_14 [Gen04-02-090]

description:
replicate 1
Gen04-02-090


title: 12m_V_P_9 [Gen04-02-054]

description:
replicate 1
Gen04-02-054


title: 12m_V_P_19 [Gen04-05-042]

description:
replicate 1
Gen04-05-042


title: Ctl3_CD3+CD28

value: CD4+ T cells


title: 12m_V_P_8 [Gen04-02-053]

description:
replicate 1
Gen04-02-053


title: PRO301A384_S90_L003 H. poly infected enteric glia, rep 3

city: London

first: Vassilis

last: Pachnis

address: 1 Midland Rd

department: Development and Homeostasis of the Nervous System Laboratory

institute: The Francis Crick Institute

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A384_S90_L003

data_processing:
Nextera adapter sequences were removed from reads using Cutadapt (version 1.18).
Reads were aligned to the Ensembl GRCm38 genome using STAR (version 2.5.2a).
Gene counts were obtained using the featureCounts program (from Subread version 1.6.4).
Quality control, normalisation and downstream analysis were performed using the software Seurat (version 3.1.1).
Cells expressing more than 2000 genes and less than 10 percent mitochondrial reads were retained for further analysis. Contaminating macrophages (n=7) were removed based on the expression of Itgam (> 10 counts), and contaminating neurons (n=95) were removed based on expression of Elavl4 (> 30 counts). Genes detected in fewer than 3 cells or with total counts < 10 were omitted from further analysis. The dimension of the final data matrix was 18643 genes by 217 cells (134 cells from naïve mice and 83 from H. poly infected mice).
Counts were normalized to ten thousand counts per cell, natural-log transformed using log1p, and scaled.
Highly variable genes were identified using Seurat, and the top 1000 used for dimensionality reduction and clustering. The first 4 principal components were selected as input for dimensionality reduction using the UMAP algorithm and Louvain clustering at a resolution of 0.1.
Genome_build: GrCM38
Supplementary_files_format_and_content: Count matrices in .tsv format. Seurat object saved as an .rds file.

source_name: Enteric glia

growth_protocol: Mice used in this study were maintained according to standard practices and all procedures were approved by The Francis Crick Institute Animal Ethics Committee and conformed to UK Home Office requirements (ASPA 1986) and the ARRIVE guidelines.

extract_protocol:
For isolation of EGCs, the longitudinal smooth muscle layer and associated myenteric plexus were peeled off the wall of the smal intestineand subjected to enzymatic digestion to prepare a single-cell suspension. Single-cell suspensions were subjected to fluorescence activated cell sorting and live EGCs were isolated based on tdT expression DAPI exclusion. 200-1000 cells were loaded into a Fluidigm C1 Single Cell Auto Prep IFC for mRNA-seq for use with the Fluidigm C1 system. After the cell load program cells were imagined using the JuliStage to identify wells that contain 1 single cell.
The SMART-Seq v4 Ultra Low Input RNA Kit for the Fluidigm C1 System, IFCs was used to reverse transcribe and amplify cDNA. cDNA was quantified using the Glomax (Promega). Libraries were prepared from cDNA generated from single cells using the Nextera XT kit from Illumina. Final libraries were pooled and sequenced on the HiSeq 4000.

treatment_protocol: All mice were injected with tamoxifen 24 hours prior single cell isolation and some mice were infected with H. poly 7 days prior single cell isolation.

tag: Stage

value: Adult

tag: strain

value: Infected


title: PRO301A383_S130_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A383_S130_L003


title: PRO301A382_S170_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A382_S170_L003


title: C1

tag: genotype


title: PRO301A379_S194_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A379_S194_L003


title: 12m_V_P_7 [Gen04-02-043]

description:
replicate 1
Gen04-02-043

value: Kidney transplant


title: PRO301A377_S52_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A377_S52_L003


title: 12m_V_P_10 [Gen04-02-060]

description:
replicate 1
Gen04-02-060

value: 1 year surveillance biopsy


title: PRO301A378_S182_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A378_S182_L003


title: PRO301A376_S186_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A376_S186_L003


title: 12m_V_P_5 [Gen04-02-024]

description:
replicate 1
Gen04-02-024

value: Progressor


title: PRO301A380_S5_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A380_S5_L003


title: 12m_V_P_6 [Gen04-02-029]

description:
replicate 1
Gen04-02-029


title: PRO301A374_S124_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A374_S124_L003


title: 12m_V_P_4 [Gen04-02-012]

description:
replicate 1
Gen04-02-012


title: PRO301A375_S44_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A375_S44_L003


title: 12m_V_P_41 [Gen04-44-079]

description:
replicate 1
Gen04-44-079


title: PRO301A370_S65_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A370_S65_L003


title: PRO301A371_S33_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A371_S33_L003


title: PRO301A367_S138_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A367_S138_L003


title: PRO301A365_S192_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A365_S192_L003


title: 12m_V_P_3 [Gen04-02-005]

description:
replicate 1
Gen04-02-005


title: Pooled sample 3

description:
S3
Single-cell RNA-seq
RNA and HTO data are present in the submitted raw and processed data files.
covid_control_RNA_counts.csv
cap_control_RNA_counts.csv
covid_cap_RNA_counts.csv

tag: cell type

value: PBMC


title: PRO301A364_S134_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A364_S134_L003

tag: disease state


title: PRO301A362_S57_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A362_S57_L003


title: PRO301A363_S183_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A363_S183_L003


title: 12m_V_P_1 [Gen04-02-001]

description:
replicate 1
Gen04-02-001


title: 12m_D_NP_114 [rGen01-152]

description:
replicate 1
rGen01-152

value: Non-Progressor

value: Discovery


title: PRO301A359_S168_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A359_S168_L003


title: PRO301A360_S167_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A360_S167_L003


title: PRO301A361_S196_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A361_S196_L003


title: 12m_D_NP_111 [rGen01-149]

description:
replicate 1
rGen01-149


title: PRO301A356_S14_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A356_S14_L003


title: 12m_D_NP_116 [rGen01-154]

description:
replicate 1
rGen01-154


title: 12m_D_NP_113 [rGen01-151]

description:
replicate 1
rGen01-151


title: 12m_V_P_2 [Gen04-02-003]

description:
replicate 1
Gen04-02-003

value: Validation


title: 12m_D_NP_108 [rGen01-146]

description:
replicate 1
rGen01-146


title: 12m_D_NP_115 [rGen01-153]

description:
replicate 1
rGen01-153


title: PRO301A357_S114_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A357_S114_L003


title: 12m_D_NP_109 [rGen01-147]

description:
replicate 1
rGen01-147


title: 12m_D_NP_110 [rGen01-148]

description:
replicate 1
rGen01-148


title: PRO301A355_S160_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A355_S160_L003


title: PRO301A354_S99_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A354_S99_L003


title: 12m_D_NP_105 [rGen01-143]

description:
replicate 1
rGen01-143


title: PRO301A353_S50_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A353_S50_L003


title: 12m_D_NP_112 [rGen01-150]

description:
replicate 1
rGen01-150


title: PRO301A350_S175_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A350_S175_L003


title: PRO301A351_S97_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A351_S97_L003


title: PRO301A348_S155_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A348_S155_L003


title: PRO301A347_S162_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A347_S162_L003


title: 12m_D_NP_103 [rGen01-141]

description:
replicate 1
rGen01-141


title: PRO301A345_S39_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A345_S39_L003


title: PRO301A352_S131_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A352_S131_L003


title: 12m_D_NP_101 [rGen01-101]

description:
replicate 1
rGen01-101


title: 12m_D_NP_102 [rGen01-140]

description:
replicate 1
rGen01-140


title: 12m_D_NP_106 [rGen01-144]

description:
replicate 1
rGen01-144


title: 12m_D_NP_99 [rGen01-099]

description:
replicate 1
rGen01-099


title: 12m_D_NP_104 [rGen01-142]

description:
replicate 1
rGen01-142


title: 12m_D_NP_97 [rGen01-097]

description:
replicate 1
rGen01-097


title: PRO301A343_S140_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A343_S140_L003


title: PRO301A342_S103_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A342_S103_L003


title: PRO301A346_S126_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A346_S126_L003


title: 12m_D_NP_94 [rGen01-094]

description:
replicate 1
rGen01-094


title: PRO301A344_S54_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A344_S54_L003


title: 12m_D_NP_98 [rGen01-098]

description:
replicate 1
rGen01-098


title: PRO301A341_S4_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A341_S4_L003


title: PRO301A340_S12_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A340_S12_L003


title: 12m_D_NP_91 [rGen01-091]

description:
replicate 1
rGen01-091


title: 12m_D_NP_92 [rGen01-092]

description:
replicate 1
rGen01-092


title: 12m_V_P_40 [Gen04-44-072]

description:
replicate 1
Gen04-44-072


title: 12m_D_NP_93 [rGen01-093]

description:
replicate 1
rGen01-093


title: PRO301A334_S136_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A334_S136_L003


title: PRO301A331_S203_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A331_S203_L003


title: PRO301A330_S73_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A330_S73_L003


title: 12m_D_NP_95 [rGen01-095]

description:
replicate 1
rGen01-095


title: 12m_D_NP_100 [rGen01-100]

description:
replicate 1
rGen01-100


title: 12m_D_NP_96 [rGen01-096]

description:
replicate 1
rGen01-096


title: PRO301A339_S84_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A339_S84_L003


title: 12m_D_NP_88 [rGen01-088]

description:
replicate 1
rGen01-088


title: PRO301A336_S157_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A336_S157_L003


title: PRO301A329_S205_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A329_S205_L003


title: PRO301A328_S139_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A328_S139_L003


title: 12m_D_NP_89 [rGen01-089]

description:
replicate 1
rGen01-089


title: PRO301A324_S71_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A324_S71_L003


title: 12m_D_NP_83 [rGen01-083]

description:
replicate 1
rGen01-083


title: 12m_D_NP_82 [rGen01-082]

description:
replicate 1
rGen01-082


title: 12m_D_NP_107 [rGen01-145]

description:
replicate 1
rGen01-145


title: 12m_D_NP_81 [rGen01-081]

description:
replicate 1
rGen01-081


title: PRO301A337_S86_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A337_S86_L003


title: PRO301A323_S109_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A323_S109_L003


title: PRO301A322_S49_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A322_S49_L003


title: PRO301A321_S177_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A321_S177_L003


title: PRO301A325_S47_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A325_S47_L003


title: PRO301A317_S195_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A317_S195_L003


title: PRO301A316_S174_L003 H. poly infected enteric glia, rep 3

description:
H. poly infected enteric glia, rep 3
H. poly 3
PRO301A316_S174_L003


title: 12m_D_NP_78 [rGen01-078]

description:
replicate 1
rGen01-078


title: 12m_D_NP_90 [rGen01-090]

description:
replicate 1
rGen01-090