title: NEG Chronic D14 H3K27ac Input

description:
NEG Chronic D14 H3K27ac Input
macs2-H3K27ac_regions_of_enrichment_NEG_Chronic_Day14_NEG_Day0_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_NEG_Chronic_Day14_Tram_NEG_Day0_DMSO_control.txt


title: POS Acute DMSO H3K27ac Replicate 2

status: Public on Nov 09 2021

type: SRA

city: Cambridge

first: Daniel

middle: Robert

last: Goulet

state: MA

address: 500 Main St

department: Koch Institute

country: USA

institute: Massachusetts Institute of Technology

description:
POS Acute DMSO H3K27ac Replicate 2
macs2-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control_union.txt
macs2-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control_union.txt
macs2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control.txt
DESeq2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
Raw_counts-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt

library_source: genomic

data_processing:
ChIP-seq fastq: Cutadapt (v.1.12) was used to remove adaptor sequences from reads. Reads were filtered with FASTX-Toolkit (v0.0.12) including options -Q 33, -p 90, and q 20.  Reads were then aligned to the hg19 genome using STAR (v2.5.2b) with the following parameters: --outFilterMismatchNmax 2, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, --outFilterScoreMin 1, --outFilterMultimapNmax 1.
Raw Counts tables: Number of reads for given set of genomic coordinates was tabulated using the featureCounts function in the Rsubread R package (v. 1.34.7)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain total read depth normalized signal. txt-MACS2 contain narrowpeak calls for JUNB ChIP-seq data, and refinePeaks summits of H3K27ac ChIP-seq with +/- 500 bp window. txt-DESEQ2 contains all results from differential signal analysis by DESeq2 for regions of H3K27ac signal enrichment. txt-Raw_counts represent the unnormalized read counts used for DESeq2 analyses.

molecule: genomic DNA

organism: Homo sapiens

source_name: Pleural effusion

growth_protocol: Low passage SUM-229PE and isolated subpopulations were cultured in Ham’s F-12 Media (Gibco cat. # 11765-054) with 5% fetal bovine serum (VWR cat. # 97068-085), 5 ug/mL insulin (Gibco cat. # 12585-014), 1 ug/mL hydrocortisone (Sigma cat. # H0396), 1% penicillin-streptomycin solution (Gibco cat. # 15140-014) and 5 mM HEPES (Corning cat. # 25-060-CI)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature, then quenched for five minutes using 1 mM Glycine. Media was discarded and cells were scraped on ice using a cell lifter. Cells were centrifuged 3K RPM at 4C, then supernatant was aspirated and the pellet was flash frozen in liquid nitrogen. Antibody was conjugated to Protein A Dynabeads (Life Technologies cat. # 1002D) for 4 hours at 4C in PBS + 0.5% BSA. Crosslinked pellets were resuspended in lysis buffer 1 to permeabilize plasma membrane, and centrifuged for 5 minutes at 4C at 200 x g. Nuclei were resuspended in lysis buffer, and centrifuged for 5 minutes at 4C at 200 x g. Chromatin was resuspended in sonication buffer, sonication beads added and chromatin was sonicated at 4C for 15 cycles; 30 seconds on, 30 seconds off. Beads were then washed three times with a low salt sonication buffer, then washed once with a high salt sonication buffer, then washed once with a LiCl wash buffer, then washed once with TE buffer. Fragmented chromatin was eluted from the beads with elution buffer at 65C for 15 minutes, vortexing every two minutes. Eluted chromatin and Dynabeads were placed on the magnet, and eluted chromatin was transferred to a fresh tube. Crosslinking was reversed by incubating the eluted chromatin at 65C overnight. The following day, 0.2 ug/mL RNase A (Sigma cat. # R4642) was added to the samples and incubated for 1 hr at 37C. Protein in the sample was digested using 0.2 ug/mL Proteinase K (Ambion cat. # 25530-015) at 55C. Fragmented DNA was purified using the Qiagen MinElute Kit (Qiagen cat. # 28004).
50 ng of DNA was used for library preparation using the KAPA stranded HyperPrep Kit (Roche cat. # 07962347001) and Illumina TruSeq Indexed Adapters according to the manufacturer’s instructions. Dual size selection was performed after 18 cycles of PCR amplification of the cDNA library according to manufacturer recommendations. A multiplexed pool of 12 libraries was sequenced using the 75-cycle NextSeq 500/550 High Output v2 sequencing kit (Illumina cat. # FC-404-2005) on the Illumina NextSeq500 to yield approximately 3.5 x 107 reads per sample.

treatment_protocol: DMSO Control, Acute 30 nM Trametinib for 24 hrs, Chronic 10 nM Trametinib for 0-5 weeks

tag: cell line

tag: cell type

value: Triple-Negative Breast Cancer Cell Line

tag: passages

tag: subpopulation

value: POS

tag: treatment

value: DMSO

tag: chip antibody

value: H3K27ac (Active Motif cat. # 39133)


title: NEG Acute DMSO H3K27ac Replicate 1

description:
NEG Acute DMSO H3K27ac Replicate 1
macs2-H3K27ac_regions_of_enrichment_NEG_Acute_Tram_NEG_DMSO_control_union.txt
macs2-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_NEG_Acute_Tram_NEG_DMSO_control.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_NEG_Acute_Tram_NEG_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control.txt

value: NEG


description:
Isolated POS Cells 30 nM Tram 24h RNA-Seq
POS_ISO_30nM_Tram

library_source: transcriptomic

data_processing:
Reads were aligned using mapsplice, sorted and indexed using samtools sort, samtools flagstat, and samtools index.
Indexed bam files were then filtered for indels, large inserts, and zero mapping quality
Aligned and filtered reads were used to quantify gene expression by RSEM. Raw read counts reported in txt file below.
Genome_build: hg19
Supplementary_files_format_and_content: *_Mapsplice.txt: Tab-delimited text files containing gene names and raw read counts.

molecule: total RNA

extract_protocol:
Approximately 1 million cells were rinsed with PBS and scraped from the dish with a cell lifter into 600 ul of RLT Buffer Plus w/ BME. RNA was isolated using the RNeasy Plus RNA isolation kit (Qiagen cat. # 74134), then RNA was converted to cDNA using the High Capacity cDNA Reverse Transcription kit (Applied Biosystems cat. # 4368813).
RNA Sequencing library was prepared with 4 mg of total RNA using KAPA stranded mRNA Sequencing kit (Roche cat. # 07962193001) and Illumina TruSeq sample indexes following the manufacturer’s protocol

treatment_protocol: DMSO Control, Acute 30 nM Trametinib for 24 hrs, Chronic 10 nM Trametinib for 0-5 weeks, siRNA knockdown for 72 hours + drug treatment as indicated


title: NEG Chronic D0 H3K27ac Replicate 1

description:
NEG Chronic D0 H3K27ac Replicate 1
macs2-H3K27ac_regions_of_enrichment_NEG_Chronic_Day14_NEG_Day0_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_NEG_Chronic_Day14_Tram_NEG_Day0_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_NEG_Chronic_Day14_Tram_NEG_Day0_DMSO_control.txt

value: Chronic Trametinib D0


title: NEG Acute DMSO H3K27ac Replicate 2

description:
NEG Acute DMSO H3K27ac Replicate 2
macs2-H3K27ac_regions_of_enrichment_NEG_Acute_Tram_NEG_DMSO_control_union.txt
macs2-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_NEG_Acute_Tram_NEG_DMSO_control.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_NEG_Acute_Tram_NEG_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control.txt


title: NEG Chronic D0 H3K27ac Input

description:
NEG Chronic D0 H3K27ac Input
macs2-H3K27ac_regions_of_enrichment_NEG_Chronic_Day14_NEG_Day0_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_NEG_Chronic_Day14_Tram_NEG_Day0_DMSO_control.txt


title: NEG Acute Tram H3K27ac Replicate 2

description:
NEG Acute Tram H3K27ac Replicate 2
macs2-H3K27ac_regions_of_enrichment_NEG_Acute_Tram_NEG_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_NEG_Acute_Tram_NEG_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_NEG_Acute_Tram_NEG_DMSO_control.txt

value: Acute Trametinib


title: NEG Acute Tram H3K27ac Replicate 1

description:
NEG Acute Tram H3K27ac Replicate 1
macs2-H3K27ac_regions_of_enrichment_NEG_Acute_Tram_NEG_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_NEG_Acute_Tram_NEG_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_NEG_Acute_Tram_NEG_DMSO_control.txt


title: NEG Acute Tram H3K27ac Input

description:
NEG Acute Tram H3K27ac Input
macs2-H3K27ac_regions_of_enrichment_NEG_Acute_Tram_NEG_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_NEG_Acute_Tram_NEG_DMSO_control.txt


title: Uncontrolled 200569440030_L

type: RNA

city: Taipei

first: Yungling

middle: Leo

last: Lee

address: Sec. 2, Academia Rd.

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

description: Uncontrolled

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Initial quality assessment of the whole genome gene expression data was performed using Illumina’s GenomeStudio Gene Expression module (San Diego, CA). Raw expression data were applied by log2‐transformation and quantile‐transformation.

label: biotin

source_name: whole blood

label_protocol: Standard Illumina protocol

extract_protocol: RNA samples were isolated from whole blood and then extracted by Direct-zolTM RNA MiniPrep (Zymo Research).

tag: gender

value: female


title: Uncontrolled 3999927051_F

description: Uncontrolled

value: male


title: Controlled 3999927051_H

description: Controlled


title: Uncontrolled 3999927051_K

description: Uncontrolled


title: NEG Acute DMSO JUNB Replicate 2

description:
NEG Acute DMSO JUNB Replicate 2
macs2-JUNB_regions_of_enrichment_POS_NEG_DMSO_control_union.txt
DESeq2-JUNB_regions_of_enrichment_POS_DMSO_NEG_DMSO_control.txt
Raw_counts-JUNB_regions_of_enrichment_POS_DMSO_NEG_DMSO_control.txt

value: JUNB (Cell Signaling cat. #3753S)


title: NEG Acute DMSO JUNB Replicate 1

description:
NEG Acute DMSO JUNB Replicate 1
macs2-JUNB_regions_of_enrichment_POS_NEG_DMSO_control_union.txt
DESeq2-JUNB_regions_of_enrichment_POS_DMSO_NEG_DMSO_control.txt
Raw_counts-JUNB_regions_of_enrichment_POS_DMSO_NEG_DMSO_control.txt


description:
FACS-Sorted NEG Subpopulation DMSO RNA-Seq
NEG_FACS_DMSO


title: Controlled 200569440030_K

description: Controlled


title: Isolated NEG Cells DMSO RNA-Seq

description:
Isolated NEG Cells DMSO RNA-Seq
NEG_ISO_DMSO


description:
FACS-Sorted POS Subpopulation 30 nM Tram 24h RNA-Seq
POS_FACS_30nM_Tram


title: Isolated POS Cells DMSO RNA-Seq

description:
Isolated POS Cells DMSO RNA-Seq
POS_ISO_DMSO


title: Uncontrolled 200757700032_J

description: Uncontrolled


title: Uncontrolled 200769890056_E

description: Uncontrolled


title: Uncontrolled 200769890056_J

description: Uncontrolled


title: Controlled 200569440030_I

description: Controlled


title: Controlled 200569440030_G

description: Controlled


title: POS Acute DMSO FAIRE Replicate 1

description:
Goulet_POS_DMSO_FAIRE_1
Replicate 1 of FAIRE-seq of POS cells treated with DMSO for 24 hours
processed data file: Goulet_POS_DMSO_Faire_Peaks.txt

data_processing:
Following removal of adaptor sequences (cutadapt v1.12), reads were filtered for quality using fastq_quality_filter in FASTX-Toolkit (v0.0.12) with options -Q 33, -p 90, and q 20.
Regions of FAIRE signal enrichment (ROE) were identified in each sample (MACS2 v2.1.2). Score per million (SPM) was calculated for each region of enrichment by dividing the MACS2 derived -log10(p-value) by the total -log10(p-value) then by 1,000,000 for each sample.
For each experimental condition ROE were ranked by SPM and the top 15% were used for downstream analysis. Replicate samples for the POS_DMSO and NEG_DMSO experimental conditions were combined by identifying regions of enrichment with a 30% signal overlap (bedtools v2.27.1).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_Faire_Peaks.txt: Tab-delimited text files containing peak locations and normalized read counts.

growth_protocol: Low passage SUM-229PE and isolated subpopulations were cultured in Ham’s F-12 Media (Gibco cat. # 11765-054) with 5% fetal bovine serum (VWR cat. # 97068-085), 5 ug/mL insulin (Gibco cat. # 12585-014), 1 ug/mL hydrocortisone (Sigma cat. # H0396), 1% penicillin-streptomycin solution (Gibco cat. # 15140-014) and 5 mM HEPES (Corning cat. # 25-060-CI).

extract_protocol:
Cells were crosslinked and nuclei were prepared using the Active Motif Chromatin Preparation kit (53046) according to manufacturer’s instructions except that 0.25 million formaldehyde crosslinked Drosophila S2 cells were spiked into the SUM-229 cells just prior to nuclei preparation. Nuclei were resuspended in 90 uL Lysis Buffer A (Simon et al., 2012) and 10 uL of MegaShear (Triangle Biotechnology, Inc.) was added to each tube prior to sonication. Sonication was performed in a Covaris E110 instrument for 4 minutes per sample using conditions described in (Chiarella et al., 2018). Following sonication, insoluble debris was removed by centrifugation and samples were digested with 200 ug RNase (Qiagen) at 37˚C for 30 minutes. Ten uL of sample was removed for input and digested with 40 mg Proteinase K (Worthington) for 1 hour at 55˚C, followed by 2 hours at 80˚C to reverse the crosslinks, then purified using a silica matrix column (Zymo Research, ChIP DNA Clean and Concentrate kit, D5201). FAIRE was performed on the remaining 90 uL of sonicated chromatin by purification on a silica matrix column as described in (Pattenden et al., 2016). DNA was quantitated using fluorometry (Qubit dsDNA High Sensitivity Assay Kit, Invitrogen). Average peak fragment size of input and FAIRE DNA was confirmed using gel electrophoresis.
Approximately 50 ng of fragmented DNA was adapter ligated and purified using the KAPA stranded HyperPrep Kit (Roche cat. # 07962347001) and Illumina TruSeq Indexed Adapters according to the manufacturer’s instructions. Dual size selection was performed after 18 cycles of PCR amplification of the cDNA library according to manufacturer recommendations. A multiplexed pool of libraries was sequenced using the 75-cycle NextSeq 500/550 High Output v2 sequencing kit (Illumina cat. # FC-404-2005) on the Illumina NextSeq500 to yield approximately 5.0 x 10e7 75 bp single-ended reads per sample.

treatment_protocol: Cells were treated with DMSO or 30 nM Trametinib for 24 hours.


title: Uncontrolled 200769890047_D

description: Uncontrolled


title: Controlled 3999545107_G

description: Controlled


title: Uncontrolled 200569440030_H

description: Uncontrolled


title: Uncontrolled 200769890047_F

description: Uncontrolled


description:
FACS-Sorted POS Subpopulation DMSO RNA-Seq
POS_FACS_DMSO


title: Uncontrolled 200769890056_A

description: Uncontrolled


title: Uncontrolled 200769890056_D

description: Uncontrolled


title: Uncontrolled 200769890056_C

description: Uncontrolled


title: NEG Acute DMSO FAIRE Replicate 1

description:
Goulet_NEG_DMSO_FAIRE_1
Replicate 1 of FAIRE-seq of NEG cells treated with DMSO for 24 hours
processed data file: Goulet_NEG_DMSO_Faire_Peaks.txt


title: NEG Acute DMSO H3K27ac Input

description:
NEG Acute DMSO H3K27ac Input
macs2-H3K27ac_regions_of_enrichment_NEG_Acute_Tram_NEG_DMSO_control_union.txt
macs2-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_NEG_Acute_Tram_NEG_DMSO_control.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control.txt


description:
Isolated NEG Cells 30 nM Tram 24h RNA-Seq
NEG_ISO_30nM_Tram


title: NEG Acute Tram FAIRE Replicate 2

description:
Goulet_NEG_30nM_Tram_FAIRE_2
Replicate 2 of FAIRE-seq of NEG cells treated with 30 nM trametinib for 24 hours
processed data file: Goulet_NEG_Tram_Faire_Peaks.txt


title: NEG Acute Tram FAIRE Replicate 1

description:
Goulet_NEG_30nM_Tram_FAIRE_1
Replicate 1 of FAIRE-seq of NEG cells treated with 30 nM trametinib for 24 hours
processed data file: Goulet_NEG_Tram_Faire_Peaks.txt


description:
FACS-Sorted NEG Subpopulation 30 nM Tram 24h RNA-Seq
NEG_FACS_30nM_Tram


title: POS Acute DMSO FAIRE Replicate 2

description:
Goulet_POS_DMSO_FAIRE_2
Replicate 2 of FAIRE-seq of POS cells treated with DMSO for 24 hours
processed data file: Goulet_POS_DMSO_Faire_Peaks.txt


title: POS Acute Tram FAIRE Replicate 2

description:
Goulet_POS_30nM_Tram_FAIRE_2
Replicate 2 of FAIRE-seq of POS cells treated with 30 nM trametinib for 24 hours
processed data file: Goulet_POS_Tram_Faire_Peaks.txt


title: Controlled 200162410130_K

description: Controlled


title: Controlled 200569440030_C

description: Controlled


title: POS Acute Tram FAIRE Replicate 1

description:
Goulet_POS_30nM_Tram_FAIRE_1
Replicate 1 of FAIRE-seq of POS cells treated with 30 nM trametinib for 24 hours
processed data file: Goulet_POS_Tram_Faire_Peaks.txt


title: SUM159 Acute DMSO RNA-seq Replicate 1

description:
SUM159_DMSO_RNA_1
mRNA

data_processing:
Reads were aligned using mapsplice, sorted and indexed using samtools sort, samtools flagstat, and samtools index.
Indexed bam files were then filtered for indels, large inserts, and zero mapping quality.
Aligned and filtered reads were used to quantify gene expression by RSEM. Raw read counts reported in txt file below.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_Mapsplice.txt: Tab-delimited text files containing gene names and raw read counts.

source_name: Primary Tumor

growth_protocol:
Low passage SUM-229PE and isolated subpopulations were cultured in Ham’s F-12 Media (Gibco cat. # 11765-054) with 5% fetal bovine serum (VWR cat. # 97068-085), 5 ug/mL insulin (Gibco cat. # 12585-014), 1 ug/mL hydrocortisone (Sigma cat. # H0396), 1% penicillin-streptomycin solution (Gibco cat. # 15140-014) and 5 mM HEPES (Corning cat. # 25-060-CI).
POSR1 and POSR2 are trametinib-resistant cell lines established by continuous treatment for 6 weeks with 10 nM trametinib, followed by dose escalation to 30 nM trametinib. These cells now proliferate in 30 nM trametinib.

extract_protocol:
Approximately 1 million cells were rinsed with PBS and scraped from the dish with a cell lifter into 600 ul of RLT Buffer Plus w/ BME. RNA was isolated using the RNeasy Plus RNA isolation kit (Qiagen cat. # 74134), then RNA was converted to cDNA using the High Capacity cDNA Reverse Transcription kit (Applied Biosystems cat. # 4368813).
RNA Sequencing library was prepared with 4 mg of total RNA using KAPA stranded mRNA Sequencing kit (Roche cat. # 07962193001) and Illumina TruSeq sample indexes following the manufacturer’s protocol.

treatment_protocol: DMSO Control, Acute 30 nM Trametinib for 24 hrs, Chronic 10 nM Trametinib for 0-5 weeks, siRNA knockdown for 72 hours + drug treatment as indicated.

value: Mesenchymal Breast Cancer


title: POSR2 RNA-seq Replicate 3

description:
POSR2_RNA_3
mRNA


title: Controlled 200757700032_I

description: Controlled


title: NEG Acute DMSO FAIRE Replicate 2

description:
Goulet_NEG_DMSO_FAIRE_2
Replicate 2 of FAIRE-seq of NEG cells treated with DMSO for 24 hours
processed data file: Goulet_NEG_DMSO_Faire_Peaks.txt


title: POSR2 RNA-seq Replicate 1

description:
POSR2_RNA_1
mRNA


title: Controlled 200569440030_F

description: Controlled


title: Uncontrolled 200757700032_H

description: Uncontrolled


title: Controlled 200569440030_E

description: Controlled


title: Controlled 200569440030_D

description: Controlled


title: POSR1 RNA-seq Replicate 3

description:
POSR1_RNA_3
mRNA


title: POSR1 RNA-seq Replicate 1

description:
POSR1_RNA_1
mRNA


title: SUM159 Acute DMSO RNA-seq Replicate 3

description:
SUM159_DMSO_RNA_3
mRNA


title: Controlled 200569440030_B

description: Controlled


title: Uncontrolled 200569440030_A

description: Uncontrolled


title: Controlled 3999545107_E

description: Controlled


title: Uncontrolled 9999593126_E

description: Uncontrolled


title: POS Acute DMSO RNA-seq Replicate 5

description:
POS_DMSO_RNA_5
mRNA


title: POS Acute DMSO RNA-seq Replicate 3

description:
POS_DMSO_RNA_3
mRNA


title: POSR2 RNA-seq Replicate 2

description:
POSR2_RNA_2
mRNA


title: Uncontrolled 9999593126_L

description: Uncontrolled


title: POS Acute DMSO RNA-seq Replicate 2

description:
POS_DMSO_RNA_2
mRNA


title: POS Chronic 10 nM Trametinib Day 35 RNA-seq Replicate 3

description:
POS_Chronic_10nM_Tram_D35_RNA_3
mRNA

value: Chronic Trametinib

tag: time point

value: Day 35


title: POSR1 RNA-seq Replicate 2

description:
POSR1_RNA_2
mRNA


title: Controlled 200162410130_H

description: Controlled


title: Controlled 9999593126_D

description: Controlled


title: Controlled 9999593126_A

description: Controlled


title: Uncontrolled 200162410130_I

description: Uncontrolled


title: Controlled 3999927049_D

description: Controlled


title: SUM159 Acute DMSO RNA-seq Replicate 2

description:
SUM159_DMSO_RNA_2
mRNA


title: Uncontrolled 3999545107_B

description: Uncontrolled


title: POS Chronic 10 nM Trametinib Day 35 RNA-seq Replicate 1

description:
POS_Chronic_10nM_Tram_D35_RNA_1
mRNA


title: Controlled 200162410130_J

description: Controlled


title: Uncontrolled 3999927049_B

description: Uncontrolled


title: Uncontrolled 3999545107_C

description: Uncontrolled


title: Controlled 3999545107_D

description: Controlled


title: Controlled 9999593126_B

description: Controlled


title: POS Acute DMSO RNA-seq Replicate 4

description:
POS_DMSO_RNA_4
mRNA


title: POS Chronic 10 nM Trametinib Day 35 RNA-seq Replicate 2

description:
POS_Chronic_10nM_Tram_D35_RNA_2
mRNA


title: Controlled 3999890003_H

description: Controlled


title: POS Acute DMSO RNA-seq Replicate 6

description:
POS_DMSO_RNA_6
mRNA


title: POS Chronic 10 nM Trametinib Day 0 RNA-seq Replicate 3

description:
POS_Chronic_10nM_Tram_D0_RNA_3
mRNA

value: Day 0


title: POS Chronic 10 nM Trametinib Day 14 RNA-seq Replicate 3

description:
POS_Chronic_10nM_Tram_D14_RNA_3
mRNA

value: Day 14


title: Uncontrolled 3999927049_J

description: Uncontrolled


title: POS Acute DMSO RNA-seq Replicate 1

description:
POS_DMSO_RNA_1
mRNA


title: POS Chronic 10 nM Trametinib Day 14 RNA-seq Replicate 2

description:
POS_Chronic_10nM_Tram_D14_RNA_2
mRNA


title: POS Chronic 10 nM Trametinib Day 0 RNA-seq Replicate 1

description:
POS_Chronic_10nM_Tram_D0_RNA_1
mRNA


title: POS Chronic 10 nM Trametinib Day 1 RNA-seq Replicate 3

description:
POS_Chronic_10nM_Tram_D1_RNA_3
mRNA

value: Day 1


title: POS Acute 30 nM Trametinib RNA-seq Replicate 2

description:
POS_30nM_Tram_RNA_5
mRNA


title: POS Chronic 10 nM Trametinib Day 14 RNA-seq Replicate 1

description:
POS_Chronic_10nM_Tram_D14_RNA_1
mRNA


title: POS Chronic 10 nM Trametinib Day 1 RNA-seq Replicate 2

description:
POS_Chronic_10nM_Tram_D1_RNA_2
mRNA


title: Controlled 3999890003_F

description: Controlled


title: POS Chronic 10 nM Trametinib Day 0 RNA-seq Replicate 2

description:
POS_Chronic_10nM_Tram_D0_RNA_2
mRNA


title: Uncontrolled 200162410130_D

description: Uncontrolled


title: inact C

city: University Park

first: Emily

last: Weinert

state: PA

address: 306 Althouse Laboratory

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

data_processing:
Each sample was sequenced to approximate depth of 8-12 million reads.
RNA-Seq reads were aligned to the GenBank Salmonella enterica subsp. enterica serovar Typhimurium 14028s (CP001363.1) using the STAR Aligner v2.5.2b
Transcript abundance was estimated using htseq-count v0.6.1p1.
Differential expression analysis was performed with DESeq2
Genome_build: The NCBI index (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/750/555/GCA_000750555.1_ASM75055v1) was utilized for gene annotation.
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: S. Typhimurium culture

growth_protocol: Overnight cultures of S. Typhimurium 14028s cells containing pKT-CNP or pKT-CNP-inact were grown in 3 mL M9 media (0.4% glucose, 0.2% casitone) with carbenicillin to maintain plasmids. Cells were subcultured 1:100 in 10 mL of the same M9 media in 50 mL conical tubes and were grown at 37 °C with shaking. When cultures reached OD600 = 0.1, expression of CNPase or CNP-Inact was induced with 25 ng/mL anhydrotetracycline. Cultures were returned to the incubator until cultures reached OD600 = 0.5-0.6. At this stage, samples were collected for both RNA-seq and 2´,3´-cNMP quantification.

extract_protocol:
Total RNA (2 µg) was extracted and subjected to ribosomal RNA depletion using the Bacterial Ribo-Zero™ rRNA Removal Kit (EpiCentre, Madison, WI, USA) following the manufacturer's instructions.
Complementary DNA (cDNA) libraries were prepared with the ScriptSeq v2 RNA-Seq library preparation kit (Epicentre, Madison, WI, USA)

treatment_protocol: 2 mL of culture were collected and cells were pelleted at 7000 g for 7 min. The media was decanted and pellets were resuspended in 0.5 mL RNAlater (Ambion, Austin, TX, USA). Cells were re-pelleted as described. Samples were frozen in a dry ice/ethanol bath, and pellets were stored at -80 °C.

tag: strain

value: ATCC 14028s

tag: growth phase

value: Logarithmic

tag: plasmid

value: pKT-CNP inact


title: NEG Acute DMSO RNA-seq Replicate 6

description:
NEG_DMSO_RNA_6
mRNA

value: Triple-Negative Breast Cancer Cell Line

value: DMSO


title: POS Acute 30 nM Trametinib RNA-seq Replicate 3

description:
POS_30nM_Tram_RNA_6
mRNA

value: POS


title: NEG Acute DMSO RNA-seq Replicate 5

description:
NEG_DMSO_RNA_5
mRNA

value: NEG


title: Uncontrolled 3999545107_A

description: Uncontrolled


title: POS Chronic 10 nM Trametinib Day 1 RNA-seq Replicate 1

description:
POS_Chronic_10nM_Tram_D1_RNA_1
mRNA


title: NEG Acute DMSO RNA-seq Replicate 4

description:
NEG_DMSO_RNA_4
mRNA


title: Uncontrolled 200769890047_B

description: Uncontrolled


title: POS Acute 30 nM Trametinib RNA-seq Replicate 1

description:
POS_30nM_Tram_RNA_4
mRNA

value: Acute Trametinib


title: Uncontrolled 3999927049_H

description: Uncontrolled


title: Uncontrolled 200162410130_E

description: Uncontrolled

value: female


title: Uncontrolled 200769980006_L

description: Uncontrolled

value: male


title: Uncontrolled 9999593137_E

description: Uncontrolled


title: Controlled 200544710005_L

description: Controlled


title: Uncontrolled 3999890003_L

description: Uncontrolled


title: Controlled 3999538003_I

description: Controlled


title: Controlled 200544710005_E

description: Controlled


title: inact B

organism: Salmonella enterica subsp. enterica serovar Typhimurium


title: Controlled 200162410130_A

description: Controlled


title: Controlled 200544710005_K

description: Controlled


title: Controlled 200757700032_F

description: Controlled


title: Uncontrolled 200162410130_C

description: Uncontrolled


title: NEG Acute DMSO RNA-seq Replicate 1

description:
NEG_DMSO_RNA_1
mRNA


title: Uncontrolled 3999538003_K

description: Uncontrolled


title: CNP B

value: pKT-CNP


title: CNP C


title: VA2_2

city: Beijing

first: Luming

last: Zou

state: PR

address: Haidian strict, Xiang Mountain South Road, Xiang Mountain South Village 20#

department: Institute of Botany

country: China

institute: University of Chinese Academy of Sciences

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to grape genome using STAR
Read counts were calculated by using htseq-count
Differential gene expression analysis was done using R package DESeq2
Genome_build: 12X grape genome of IGGP
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample

organism: Vitis amurensis

source_name: in vitro plants_cold

growth_protocol: In vitro plants of V. amurensis were subcultured monthly in half strength B5 medium (PhytoTech Lab, USA)supplemented with 0.2 mg/L IBA under 16/8 (light/dark) condition

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: in vitro plants with uniform growth status were transferred to a prechilled incubator set to 4°C and constant light (approximately 100 μmol m-2 s-1). Samples were collected at 2 h after cold treatment (CT2). Untreated plants cultured at 26°C under the same light condition were sampled as the control (WT0).

tag: tissue

value: leaf

tag: genotype

value: Wild-type

tag: age

value: one-month-old


title: NEG Acute DMSO RNA-seq Replicate 3

description:
NEG_DMSO_RNA_3
mRNA


title: CNP A


title: NEG Acute DMSO RNA-seq Replicate 2

description:
NEG_DMSO_RNA_2
mRNA


title: Controlled 9999593126_H

description: Controlled


title: Uncontrolled 200162410130_B

description: Uncontrolled


title: VA2_3


title: NEG Chronic 10 nM Trametinib Day 35 RNA-seq Replicate 1

description:
NEG_Chronic_10nM_Tram_D35_RNA_1
mRNA

value: Chronic Trametinib

value: Day 35


title: NEG Chronic 10 nM Trametinib Day 35 RNA-seq Replicate 3

description:
NEG_Chronic_10nM_Tram_D35_RNA_3
mRNA


title: inact A


title: VA0_2

source_name: in vitro plants_control


title: Controlled 9999593126_G

description: Controlled


title: VA2_1


title: Controlled 9999593137_G

description: Controlled


title: NEG Chronic 10 nM Trametinib Day 14 RNA-seq Replicate 3

description:
NEG_Chronic_10nM_Tram_D14_RNA_3
mRNA

value: Day 14


title: Controlled 200544710005_D

description: Controlled


title: Controlled 200544710005_J

description: Controlled


title: Controlled 200757700032_D

description: Controlled


title: Controlled 200544710005_C

description: Controlled


title: Controlled 3999538003_G

description: Controlled


title: NEG Chronic 10 nM Trametinib Day 14 RNA-seq Replicate 1

description:
NEG_Chronic_10nM_Tram_D14_RNA_1
mRNA


title: NEG Chronic 10 nM Trametinib Day 1 RNA-seq Replicate 2

description:
NEG_Chronic_10nM_Tram_D1_RNA_2
mRNA

value: Day 1


title: NEG Chronic 10 nM Trametinib Day 1 RNA-seq Replicate 3

description:
NEG_Chronic_10nM_Tram_D1_RNA_3
mRNA


title: VA0_1


title: VA0_3


title: NEG Chronic 10 nM Trametinib Day 0 RNA-seq Replicate 3

description:
NEG_Chronic_10nM_Tram_D0_RNA_3
mRNA

value: Day 0


title: ZfnB-VPR Rep 2

city: Duarte

first: Denis

last: OMeally

state: California

address: 1500 E Duarte Rd

department: Arthur Riggs Diabetes & Metabolism Research Institute

institute: City of Hope

data_processing:
nf-core rnaseq pipeline v1.4
Reads were mapped using STAR and counted using featureCounts, both with the default settings for the nf-core rnaseq v1.4 pipeline
Genome_build: GRCh37 with constructs included in STAR index
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: HEK293 cells

growth_protocol: pMo-HEK were seeded at 100000 cells per well in a 24-well plate and maintained in Dulbecco's modified Eagle's medium (Thermo Fisher Scientific, MA, USA) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific, M, USA) and 50 μg/ml Pen/Strep (Thermo Fisher Scientific, Waltham, MA) at 37 °C and 5% CO2.

extract_protocol:
Total cellular RNA was isolated 48 hrs post-transfection from cells using the Maxwell RC simplyRNA Cells Kit (Promega, WI, USA)
RNA libraries were prepared for sequencing by GeneWiz (South Plainfield, NJ) using standard un-stranded Illumina protocols

treatment_protocol: Cells were transfected with ZFP-362-VPR, dCas9-VPR+sgF2-362 or pcDNA3.1 control plasmids in quadruplicate using calcium phosphate transfection

tag: transfection


title: Controlled 200757700032_C

description: Controlled


title: pcDNA3-1 Rep 4

value: control


title: Uncontrolled 3999890003_D

description: Uncontrolled


title: NEG Chronic 10 nM Trametinib Day 0 RNA-seq Replicate 2

description:
NEG_Chronic_10nM_Tram_D0_RNA_2
mRNA

value: Triple-Negative Breast Cancer Cell Line


title: ZfnB-VPR Rep 1


title: NEG Chronic 10 nM Trametinib Day 14 RNA-seq Replicate 2

description:
NEG_Chronic_10nM_Tram_D14_RNA_2
mRNA


title: ZfnB-VPR Rep 4


title: pcDNA3-1 Rep 3


title: pcDNA3-1 Rep 2


title: Uncontrolled 3999538003_F

description: Uncontrolled


title: Controlled 3999538003_E

description: Controlled


title: Controlled 9999593137_J

description: Controlled


title: NEG Acute 30 nM Trametinib RNA-seq Replicate 3

description:
NEG_30nM_Tram_RNA_6
mRNA


title: Controlled 3999538003_D

description: Controlled


title: dCas9-VPR Rep 4

value: dCAs-VPR


title: NEG Acute 30 nM Trametinib RNA-seq Replicate 2

description:
NEG_30nM_Tram_RNA_5
mRNA


title: ZfnB-VPR Rep 3


title: Controlled 200544710005_B

description: Controlled


title: pcDNA3-1 Rep 1


title: NEG Acute 30 nM Trametinib RNA-seq Replicate 1

description:
NEG_30nM_Tram_RNA_4
mRNA


title: dCas9-VPR Rep 1


title: dCas9-VPR Rep 3


title: dCas9-VPR Rep 2


title: HCC1806 Acute DMSO RNA-seq Replicate 1

description:
HCC1806_DMSO_RNA_1
mRNA

value: Epithelial Breast Cancer

value: DMSO


title: HCC1806 Acute DMSO RNA-seq Replicate 2

description:
HCC1806_DMSO_RNA_2
mRNA


title: POS whole exome sequencing replicate 2

description:
Whole exome sequencing
processed data file: Goulet_229_snpEff_all.txt
processed data file: Goulet_229_snpEff_Q30_unique_calls.txt

data_processing:
Library strategy: WES
Nextera Rapid Capture whole exome sequencing data for SUM229 EpCAM/CD49f positive or negative sorted populations was aligned to GRCh37/hg19 using BWA-MEM v 0.7.9a using -Y -M -R options and duplicates were subsequently marked using Biobambam v 0.0.172.
ABRA (Mose et al., 2014) realignment was employed for indel detection and to improve variant allele frequency estimation.
The resulting ABRA .bam files were piped to FreeBayes (Garrison and Marth, 2012) v 1.1.0-54 for generation of a germline variant call file whereby SUM-229 positive and negative samples were unified by nucleotide variant position.
VCFtools (Danecek et al., 2011) v 0.1.15 was employed to limit variant call file entries to Nextera Rapid Capture targeted regions. Variants were annotated using SNPEff (Cingolani et al., 2012) v 4.3t and only variants supported by a Quality score of > 30 were considered for tabulation and plotting.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Text output of processing pipeline.

extract_protocol:
Approximately 1 million cells were rinsed with PBS and scraped off the plate with a cell lifter.
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 HiSeq 4000 following the manufacturer's protocols.

value: POS


title: NEG Chronic 10 nM Trametinib Day 0 RNA-seq Replicate 1

description:
NEG_Chronic_10nM_Tram_D0_RNA_1
mRNA

value: NEG


title: GluN3A BDNF1h rep2

city: San Juan de Alicante

first: Sergio

last: Niñerola

state: Alicante

address: Avenida Santiago Ramon y Cajal, s/n

department: Molecular Neurobiology and Neuropathology

country: Spain

institute: CSIC-Instituto de Neurociencias de Alicante

data_processing:
Adapters were trimmed using trim_galore v0.6.4_dev and reads with longer length than 40 bp were selected.
Trimmed reads were aligned using star c2.6.1b to the mouse genome (mm10). Reads with mapq> 30 were selected using Samtools v1.9.
Mapped reads were quantified using R scripts (R version 4.0.3, 2020), Rsubread v2.4.3 and the Mus_musculus.GRCm38.99.gtf annotation data.
Differential expression analysis was performed using DESeq2 1.31.1 and limma 3.46.0.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and  sample
Supplementary_files_format_and_content: Bigwig files were done with DeepTools v3.5.0, normalized with RPKM.

molecule: polyA RNA

organism: Mus musculus

source_name: Primary cortical neuron culture

growth_protocol: Cortices were dissected  from E17.5 mice pups and dissociated with papain (Worthington Biochemical).  Neurons were plated at 500,000 cells per well on 6-wells  plates coated with laminin and poly-D-lysine and grown  in Neurobasal Medium supplemented with B27 (ThermoFisher).

extract_protocol:
Total RNA from cultured rat cortical neurons was isolated using the Nucleospin RNA (Macherey-  Nagel). RNA concentration and purity were assessed with NanoDrop™. RNA quality was  determined by the RNA Integrity Number (RIN) algorithm using the Agilent® 2100 Bionalyzer  Instrument; only samples with RIN>9 matched our standard.
For RNAseq experiments, we performed bulk mRNA sequencing single-end with a length of  50bp using the RNAseq Illumina Hiseq2500.

treatment_protocol: Neurons were infected with lentiviruses 5 days prior to collection. Neurotrophic factors and other drugs were used at the following  concentrations: Recombinant human BDNF (100 ng/ml,  PeproTech 450-02) and bicuculline (50 µM, Abcam Ab120108).

value: Primary cortical neuron culture


title: NEG whole exome sequencing replicate 2


title: GFP BDNF1h rep3

value: GFP;BDNF


title: Controlled 200536850027_J

description: Controlled

value: female


title: HCC1806 Acute DMSO RNA-seq Replicate 3

description:
HCC1806_DMSO_RNA_3
mRNA


title: GFP BDNF1h rep2


title: GluN3A BDNF1h rep1


title: Controlled 3999890003_E

description: Controlled

value: male


title: Controlled 200757700032_B

description: Controlled


title: Controlled 200536850027_K

description: Controlled


title: Controlled 3999927049_L

description: Controlled


title: Uncontrolled 3999927049_G

description: Uncontrolled


title: Controlled 200536850027_F

description: Controlled


title: RIP in flag-taged IRF3 macrophages

city: Shanghai

first: Junfang

last: Xu

address: 800 Xiangyin Road

institute: national key laboratory of medical immunology

data_processing:
Raw reads were aligned to the reference genome (mm10) using TopHat (v2.0.14) (Kim et al. 2013) after removing adapter.
RPKM were calculated by Cuffnorm.
The mm10 genome annotation (RefSeq gene) is download form UCSC. tdf files are generated by IGVtools.
Genome_build: mm10
Supplementary_files_format_and_content: tdf files with whole genomic peaks

source_name: peritoneal macrophages

growth_protocol: Peritoneal macrophages were harvested from mice 4 days after thioglycollate treatment and cultured in DMEM medium.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were fixed with 1% formaldehyde for 30 min which was terminated using 0.125 M Glycine for 5 min. Then cells were lysed with CLB supplemented with Protease inhibitor cocktail, recombinant RNase inhibitor (RRI, Takara) and 2% SDS, followed by sonication with high level until the cell lysate was clarified. Then the sonicated lysate was centrifuged at 12,000 rpm for 15 min at 4℃ and mixed the supernatant with IP buffer (0.01% SDS, 1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH8.1, 167 mM NaCl) followed by precipitated with anti-Flag magnetic beads (ThermoFisher) for 4-6 hours. After that, the beads were washed with low salt wash buffer once followed with one wash using high salt wash buffer. The IRF3-RNA complex on beads were decrosslinked at 65 ℃ for 3 hours and digested with Protease K for 30 min. Lastly, RNA isolated with TRIzol reagent from beads was subjected to RNA sequencing.

value: peritoneal macrophages

tag: rip antibody and beads

value: anti-flag antibody (SIGMA-ANTI-FLAG M2 Magnetic Beads (M8823))


title: Uncontrolled 200757700032_A

description: Uncontrolled


title: Controlled 3999890003_G

description: Controlled


title: GFP BDNF1h rep1


title: POS whole exome sequencing replicate 1


title: GluN3A Bic1h rep3


title: Controlled 3999927049_E

description: Controlled


title: NEG whole exome sequencing replicate 1


title: RIP in WT macrophages

value: WT


title: NEG Chronic 10 nM Trametinib Day 1 RNA-seq Replicate 1

description:
NEG_Chronic_10nM_Tram_D1_RNA_1
mRNA

value: Chronic Trametinib


title: RNA-seq for transcriptome in lnc-IRF3-/- spleen tissue

data_processing:
BGISEQ-500 basecalling software
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped clean reads to whole mm10 gene using Bowtie2 and to mm10 genome using HISAT.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by RSEM.
Genome_build: mm10
Supplementary_files_format_and_content: text file with FPKM values for NCBI Gene IDs.

source_name: spleen

extract_protocol:
spleen were removed, and RNA was harvested using Trizol reagent.1 μg of total RNA for the construction of sequencing libraries.  RNA libraries were prepared for sequencing using standard Illumina protocols    RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were intraperitoneally infected with VSV (1*10^7 PFU/g) for 12 hours.

value: spleen

value: 8 weeks

tag: infected with

value: VSV


title: GluN3A Bic1h rep2


title: PfBDP1HA::PfBDP7BirATy_Input_mature S

city: Erlangen

first: Michaela

last: Petter

address: Wassertrumstr. 3-5

department: Mirkobiologisches Institut

country: Germany

institute: Univeritätsklinikum Erlangen

description: Accel2S Ultra DNA library kit

data_processing:
Quality control of samples using FastQC version 0.11.8
Trimming using TrimGalore version 0.6.5 and Cutadapt version 2.8
Mapping with Bowtie2 version 2.3.5.1 against Plasmdium genome version 28
BAM files with Samtools version 1.2
Bigwig files of log2 ratios with Deeptools version 3.3.1
Genome_build: PlasmoDB-28_Pfalciparum3D7_Genome.fasta / PlasmoDB-28_Pfalciparum3D7.gff (available on PlasmoDB)
Supplementary_files_format_and_content: Bigwig files with Log2 ratio ChIP/Input

organism: Plasmodium falciparum

source_name: P. falciparum in vitro culture

growth_protocol: Plasmodium falciparum parasites were cultured in RPMI-HEPES medium containing 5% O+ red blood cells, 0.2% sodium bicarbonate and 0.25% Albumax (Gibco) and 5% human serum (AB+). Parasitaemia was maintained at 0.5%-10%. Parasites cultures were incubated at 37ºC in 1% O2, 5% CO2 and 94% N2.

extract_protocol:
Cultures were fixed with 1% PFA and nuclei were isolated. Chromatin was fragmented by sonication before immunoprecipitation of Protein/DNA complexes.
Libraries were generated using the Accel2S PLUS DNA Library kit (Swift Biosciences). Library amplification was performed using the KAPA Hifi PCR kit (KK2101) according to published procedures (PMID: 26067602).

tag: parasite line

tag: Stage

value: mature schizont


title: PfBDP1HA::PfBDP7BirATy_anti-Ty_mature S

description: Accel2S Ultra DNA library kit


title: PfBDP1HA::PfBDP7BirATy_Input_early S

description: Accel2S Ultra DNA library kit

value: early schizont


title: Human umbilical vein endothelial cells (HUVEC) R183Q #3

city: Bethesda

first: Jonathan

last: Pevsner

state: MD

address: 6001 Executive Blvd

institute: NIMH

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for systemcontrol and base calling through an integrated primary analysis software called RTA (Real Time Analysis).
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Adapters are not trimmed away from the reads.
FASTQ files were aligned with HiSAT2 (2.0.4) to the human reference (hg19).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human umbilical vein endothelial cells

extract_protocol:
Total RNA was isolated using standard protocols
RNA libraries were prepared for sequencing using standard Illumina protocols using a TruSeq Stranded Total RNA LT Sample Prep Kit.

tag: cell type

value: HUVEC


title: PfBDP1HA::PfBDP7BirATy_anti-HA_mature S

description: Accel2S Ultra DNA library kit


title: Human umbilical vein endothelial cells (HUVEC) R183Q #2


title: PfBDP1HA::PfBDP7BirATy_anti-HA_early S

description: Accel2S Ultra DNA library kit


title: PfBDP1HA::PfBDP7BirATy_anti-Ty_early S

description: Accel2S Ultra DNA library kit


title: Human umbilical vein endothelial cells (HUVEC) R183Q #1


title: Human umbilical vein endothelial cells (HUVEC) WT #3


title: GluN3A Bic1h rep4


title: GluN3A Bic1h rep1


title: GFP Bic1h rep3

value: GFP;Bicuculine


title: PfBDP7Ty_GlmS_Input_early S

description: Accel2S Ultra DNA library kit


title: PfBDP7Ty_GlmS_Input_mature S

description: Accel2S Ultra DNA library kit


title: Human umbilical vein endothelial cells (HUVEC) WT #1


title: NEG Chronic 10 nM Trametinib Day 35 RNA-seq Replicate 2

description:
NEG_Chronic_10nM_Tram_D35_RNA_2
mRNA

tag: cell line

value: Triple-Negative Breast Cancer Cell Line

tag: passages

tag: subpopulation

value: Day 35


title: Human umbilical vein endothelial cells (HUVEC) WT #2


title: rep2-plate2

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. For Illunima platform cellbarcode: In read1, the bases 1-6,22-27,43-48,92-101 merge (28bp); UMI: In read1, the　bases　84-91 (8bp). For MGI platform (rep1-plate1-2, rep1-plate2-2, rep2-plate1-1, rep2-plate1-2, rep2-plate2-1, rep2-plate2-2) cell barcode: In read1, the bases 1-18, 27-36 merge (28bp), UMI: In read1, the bases 19-26 (8bp). For MGI platform (rep1-plate1-1, rep1-plate2-1) cell barcode: In read1, the bases 1-18, 33-42 merge (28bp), UMI: In read1, the bases 25-32 (8bp).
ScRNA-seq reads were aligned to the mix genome (human hg19 and mouse mm10), Homo_sapiens.GRCH39, Mus_musculus.GRCm38.88 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cell barcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: mix genome (human hg19 and mouse mm10), Homo_sapiens.GRCH39, Mus_musculus.GRCm38.88 genome
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.
Supplementary_files_format_and_content: The file chemical_annotation.xlsx is the  metadata file with the cell barcode, cluster, perturbation information for rep1 and rep2.

source_name: HESCs(H9) with chemical perturbation

growth_protocol: H9 human embryonic stem cells (ESCs) were maintained in mTeSRTM1 media (STEMCELL Technologies) on 6-well tissue culture plates coated with Matrigel (BD Bioscience) routinely.

extract_protocol: Library preparations were performed with the Microwell-seq 2.0 protocol

treatment_protocol: Day 0, 96-well plate was coated using 50 μL Matrigel (25 μg protein/well). The 96-well plate was incubated at room temperature for 1 hour. H9 cells were dissociated into single-cell suspension with Accutase (Gibco) and resuspended in 1 mL mTeSR™1 (with 10 μg Y-27632). Excess Matrigel solution was removed from the well and 5000 cells (200μL) were seeded per well using a multi-channel pipettor. Cells were pipetted up and down several times with the multi-channel pipettor. After mixing, the plate was undisturbed inside the bench for 10 min. Then the plate was incubated at 37°C and 5% CO2 with 95% humidity overnight. Day 1, culture medium was removed and 100 μL fresh mTeSR™1 (with 25 μg protein/well Matrigel) was added. The plate was incubated at 37°C and 5% CO2 with 95% humidity overnight. Day 2, a full medium change was performed using 100 μL fresh mTeSR™1. Day 3, a full medium change was performed using 200 μL fresh E6 (STEMCELL Technologies) with different compounds (47 perturbations + 1 vehicle, two repetitions). Day 5, cells were dissociated into single-cell suspension with Accutase. Cells were collected into a 96-well PCR plate for washing and fixation. The fixed cells were stored at -80℃.

tag: culture medium

value: M6 medium with chemical perturbation


title: rep2-plate1


title: human endothelial colony forming cells (EC-R183Q) #3

source_name: human endothelial colony forming cells


title: rep1-plate2


title: GFP Bic1h rep2

tag: treatment

value: Primary cortical neuron culture


title: GFP Bic1h rep4

tag: strain


title: GFP Bic1h rep1


title: GluN3A Control rep3


title: human endothelial colony forming cells (EC-WT) #3

value: EC-WT


title: Kelly_AP2B_2_H3K27ac

city: Memphis

first: Brian

middle: J

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Library strategy: CUT&RUN
Reads were aligned to the NC_008253.1 version of the E. coli reference genome using bowtie v1.2.2 in single-end mode with parameter -k 1 –best. Reads not aligned to E. coli were retained and aligned to the hg19 revision of the human reference genome using bowtie v1.2.2 in single-end mode with parameters -k 2 -m 2 –best.
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are normalized to millions of mapped reads

source_name: Neuroblastoma

growth_protocol: Human cell lines were cultured in RPMI media containing 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin. All cell lines were routinely validated to be free of Mycoplasma species and used within 10 passages after thawing.

extract_protocol: CUT&RUN sequencing was performed by standard methodology, using reagents from Epicypher Inc. H3K27ac and IgG CUT&RUN validated antibodies were obtained from Epicypher Inc. Briefly, Kelly-cas9 expressing cells were infected with lentiviruses encoding sgRNAs to TFAP2b (TFAP2b-1,2) or control loci (ch2.2, LACZ) and grown in selection media containing puromycin at 5ug/mL. At day 6 post-infection, 500,000 live cells per sample were permeabilized and processed by CUT&RUN by standard protocols. Samples were internally controlled by spiking in exogenous E.coli DNA relative to cell number, per the manufacturer’s protocol.

value: Kelly

value: Neuroblastoma

tag: chip antibody

tag: antibody manu.

value: Millipore

tag: antibody catalog

tag: antibody lot


title: GluN3A Control rep1

tag: tissue


title: human endothelial colony forming cells (EC-R183Q) #2


title: Kelly_2_2_H3K27ac


title: RNA-seq for transcriptome in WT spleen tissue

tag: genotype

value: WT

tag: age


title: GluN3A Control rep2


title: sch9Δ_Day4_Rep2

city: Stanford

first: Kevin

middle: C.

last: Stein

address: Clark Center E200, 318 Campus Drive

department: Biology

institute: Stanford University

description: Ribosome protected mRNA

data_processing:
Library strategy: Ribo-Seq
Illumina CASAVA 1.8 was used for base calling and demultiplexing.
Adaptor sequences (CTGTAGGCACCATCAAT) were trimmed using Cutadapt v1.4.2, followed by removal of the 5' nucleotide using FASTX-Trimmer.
Ribosomal RNA reads were removed by alignment using Bowtie v1.0.0.
Remaining reads were aligned using Bowtie v1.0.0 (parameters "-y -a -m 1 -v 2 --norc --best --strata") to a library of coding sequences. For worms, this CDS library included only the longest transcript of each gene, and for yeast, the library excluded dubious ORFs and ORFs that overlapped with other genes.
A nucleotide offset was empirically calculated from the 5' end of each fragment length that displayed three nucleotide periodicity, thereby assigning each read to a specific A-site nucleotide. Nucleotide reads were then summed for each codon.
Genome_build: Worms: ce11 WBcel235; Yeast: sacCer3 R64-1-1
Supplementary_files_format_and_content: Tab-delimited text files include: Column1: ORF; Column2: codon position of each ORF, including 21 flanking nucleotides (7 triplets) before the start codon and after the stop codon; Column3: codon; Column4: counts of ribosome reads.

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Synchronized populations of worms were grown at 20°C on NGM plates. Adult worms were washed off plates at the indicated ages, briefly pelleted at low speed in a microcentrifuge, aspirated, and flash frozen in liquid nitrogen. Yeast were grown at 30°C in synthetic complete media with supplemented nutrients to account for genetic auxotrophies. Yeast were harvested at the indicated chronological ages using fast filtration and flash freezing in liquid nitrogen.

extract_protocol:
Following lysis, samples were digested with RNase I. Ribosomal pellets were isolated by ultracentrifugation using a sucrose gradient. RNA was extracted using hot phenol/chloroform.
RNA fragments in the range of ~20-35 nucleotides were gel purified. After dephosphorylation, a DNA linker (CTGTAGGCACCATCAAT) was ligated to the 3' end of the RNA footprints. Samples were then depleted of rRNA using Ribo-Zero kits (Illumina), followed by reverse transcription into cDNA, and circularization. Libraries were barcoded during PCR amplification and sent for sequencing.

value: Day 4

tag: tissue/cell type

value: Whole cells


title: GFP Control rep3

value: GFP;Saline


title: Kelly_AP2B_1_H3K27ac


title: Kelly_AP2B_2_IgG

value: IgG

value: Epicypher Inc


title: sch9Δ_Day2_Rep1

description: Ribosome protected mRNA

value: Day 2


title: sch9Δ_Day4_Rep1

description: Ribosome protected mRNA


title: human endothelial colony forming cells (EC-WT) #2


title: sch9Δ_Day2_Rep2

description: Ribosome protected mRNA


title: human endothelial colony forming cells (EC-WT) #1


title: Kelly_AP2B_1_IgG


title: hTERT-RPE1_Ko8h-2

city: Augusta

first: Chunhong

last: Yan

state: GA

address: 1410 Laney Walker Blvd

department: Georgia Cancer Center

institute: Augusta University

data_processing:
TopHat aligner in Tuxedo Suite
Cufflinks and Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: hTERT-RPE1 immortalized cells

growth_protocol: Cells were first cultured in the complete medium for 2 days, washed twice with PBS, and then cultured in the serine/glycine-free medium for 8 h.

extract_protocol:
RNAs were prepared using the RNeasy Min Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: serine/glycine-free medium

tag: batch


title: GFP Control rep1


title: Kelly_lacZ_H3K27ac


title: sch9Δ_Day0_Rep2

description: Ribosome protected mRNA

value: Day 0


title: rep1-plate1


title: npr1_TNX_biorep3

city: Yokohama

first: Shuta

last: Asai

address: 1-7-22, Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN

data_processing:
Illumina sequence was quality filtered using FASTX Toolkit 0.0.13 with parameters -q20 and -p50, and reads containing “N” are discarded.
Quality-filtered libraries were aligned to Arabidopsis TAIR10 genome using Bowtie version 0.12.8.
Unaligned reads from previous step were aligned to transcript sequences of Arabidopsis Col-0 (ftp://ftp.Arabidopsis.org/home/tair/Sequences/blast_datasets/TAIR10_blastsets/TAIR10_cdna_20101214_updated) using Bowtie version 0.12.8.
The uniquely aligned reads were used for downstream analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw read counts for each gene and each sample.

organism: Arabidopsis thaliana

source_name: whole plant

extract_protocol:
RNAs were extracted by RNeasy Plant Mini Kit (QIAGEN).
Library was constructed using EXPRSS tag-seq protocol (BMC Genomics 2014, 15:341).

value: seedling

tag: genotype/variation

value: TNX


title: Kelly_lacZ_IgG

tag: cell type


title: hTERT-RPE1_Ko0h-2

tag: cell line

value: complete medium


title: GFP Control rep2

value: Primary cortical neuron culture


title: Kelly_2_2_IgG


title: hTERT-RPE1_Ko0h-1


title: hTERT-RPE1_Ko8h-1


title: human endothelial colony forming cells (EC-R183Q) #1


title: sch9Δ_Day0_Rep1

description: Ribosome protected mRNA


title: npr1_SA_TNX_biorep3

value: SA+TNX


title: N2_Day12_Rep2

description: Ribosome protected mRNA

organism: Caenorhabditis elegans

source_name: Worms

value: wild-type

value: Day 12 adult

value: Whole animals


title: hTERT-RPE1_Wt8h-1

value: wildtype


title: WT_Day2_Rep1

description: Ribosome protected mRNA


title: hTERT-RPE1_Wt0h-2


title: N2_Day1_Rep2

description: Ribosome protected mRNA

value: Day 1 adult


title: WT_Day4_Rep1

description: Ribosome protected mRNA

value: Day 4

value: Whole cells


title: npr1_TNX_biorep1


title: N2_Day12_Rep1

description: Ribosome protected mRNA


title: WT_Day4_Rep2

description: Ribosome protected mRNA


title: hTERT-RPE1_Wt8h-2


title: WT_Day2_Rep2

description: Ribosome protected mRNA


title: Controlled 3999927049_A

description: Controlled

data_processing: Initial quality assessment of the whole genome gene expression data was performed using Illumina’s GenomeStudio Gene Expression module (San Diego, CA). Raw expression data were applied by log2‐transformation and quantile‐transformation.

source_name: whole blood

extract_protocol: RNA samples were isolated from whole blood and then extracted by Direct-zolTM RNA MiniPrep (Zymo Research).

tag: gender

value: female


title: npr1_TNX_biorep2


title: 25T_VN

value: 10% DMEM


title: WT_Day0_Rep2

description: Ribosome protected mRNA


title: N2_Day6

description: Ribosome protected mRNA

value: Day 6 adult


title: npr1_SA_TNX_biorep1


title: npr1_SA_TNX_biorep2


title: N2_Day1_Rep1

description: Ribosome protected mRNA


title: hTERT-RPE1_Wt0h-1


title: No_EXO

source_name: Mouse testis

value: C57BL/6 mouse testis cell

value: primary cell


title: npr1_Mock_biorep3

value: seedling

value: Mock


title: npr1_SA_biorep3

value: SA


title: WT_Day0_Rep1

description: Ribosome protected mRNA

value: Day 0


title: npr1_SA_biorep2


title: npr1_SA_biorep1


title: drna pKT-Inact5

description: Total RNA depleted of rRNA

data_processing:
Each sample was sequenced to an approximate depth of 12 million reads.
Quality control and adapter trimming was performed with bcl2fastq (ver. 2.20.0.445) on default parameters.
RNA-Seq reads were mapped to the GenBank accession CP001363.1 using HISAT2 (version 2.2.0) on default parameters + '--very-sensitive'
Read quantification was performed using Subread’s featureCounts functionality (ver. 2.0.1) on default parameters + '-Q 20'
Read counts loaded into R (ver. 4.0.2) and were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm (ver. 1.14.5) with default parameters.
Subsequent values were then converted to counts per million (cpm).
Differential expression analysis was performed using edgeR’s Quasi-Linear F-Test (qlfTest) functionality against treatment groups (ver. 1.14.5) with default parameters.
Genome_build: The NCBI index (CP001363.1) was used for gene annotation. https://www.ncbi.nlm.nih.gov/nuccore/CP001363.1/
Supplementary_files_format_and_content: Table with raw counts for each locus and sample
Supplementary_files_format_and_content: A table containing normalized read counts for each sample (in columns) and each annotated transcript (in rows). Includes statistics for differential expression between samples expressing pKT-CNP and pKT-CNP-inactive.

source_name: S. Typhimurium culture

growth_protocol: Overnight cultures in M9 minimal medium (0.4% glucose, 0.2% casitone) were subcultured 1:100 in the same medium and grown at 37 degrees C with aeration; samples were collected at OD600 ~0.5.

extract_protocol:
RNA was isolated using the RNAsnap method, treated with Dnase I, and RNA quality checked as described in Kurasz et al. 2018. J. Bacteriol. 200(23):e00476-18.
Extracted RNA was sent on dry ice to the Microbial Genome Sequencing Center (Pittsburgh, PA, USA) where all following steps, incuding data processing, were completed. 300 ng RNA for each sample were subjected to ribosomal RNA depletion using the Ribo-Zero™ Plus rRNA Removal Kit and complementary DNA (cDNA) libraries were then prepared with the Illumina Stranded RNA library preparation kit.

treatment_protocol: Cultures of strains containing the pKT-CNP or pKT-CNP-Inactive plasmids were treated with 25 ng/mL anhydrotetracycline at OD600=0.1 and outgrown to OD600 ~0.5.

value: 14028s delta-rna

tag: growth phase

value: Logarithmic

tag: plasmid

value: plasmid:pKT-CNP inactive (H73L/H152L)


title: A925L lorlatinib-DT, biological rep3

city: Kyoto

first: Keiko

last: Tanimura

address: 465, Kajii-cho

institute: Kyoto-Prefetural University of Medicine

description: Gene expression data from A925L cells treated with lorlatinib for 9days

hyb_protocol: Biotin-labeled cDNA was injected into Genechip Human Clariom S Array and hybridized with probe in Genechip Hybridization Oven 640. The array was washed using Genechip Hybridization, Wash and Stain Kit and stained by phycoerythrin. These procedure was performed with GeneChip Fluidics Station 450.

scan_protocol: Fluorescent signal by phycoerythrin staining of cDNA hybridized to the probe in the array was measured using a GeneChip Scanner 3000 7G.  Data was acquired using Affymetrix GeneChip Command Console 4.0.

data_processing: Background-adjusted signals was normalized in a data mining software (Affymetrix Expression Console Software 1.4.1) using the SST-RMA algorithm.

source_name: A925L cells treated with lorlatinib for 9 days

label_protocol: 5.5 µg of sense-strand cDNA is fragmented by uracil-DNA glycosylase (UDG) and  apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues, and biotinylated.

growth_protocol: Cells were maintained in RPMI1640 medium with 10 % FBS, penicillin and streptomycin in a humidified 5% CO2 incubator at 37°C.

extract_protocol: Total RNA was extracted using NucleoSpin® RNA Plus (Takara Bio, Shiga, Japan) according to the manufacturer’s instructions.

treatment_protocol: H2228 and A925L cells were incubated with or without alectinib (3 µmol/L) or lorlatinib (1 or 10 µmol/L) for 9 days.

tag: treatment

value: Lorlatinib 1 umol/L


title: Mouse testis

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp)； UMI:In read1, the　bases　49-54 (6bp)
ScRNA-seq reads were aligned to the mix genome (human hg19 and mouse mm10), Homo_sapiens.GRCH39, Mus_musculus.GRCm38.88 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cell barcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: mix genome (human hg19 and mouse mm10), Homo_sapiens.GRCH39, Mus_musculus.GRCm38.88 genome
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

value: testis cell

tag: strain

tag: culture medium


title: drna pKT-Inact4

description: Total RNA depleted of rRNA


title: npr1_Mock_biorep2


title: npr1_Mock_biorep1


title: 6N


title: drna pKT-CNP2

description: Total RNA depleted of rRNA


title: drna pKT-CNP5

description: Total RNA depleted of rRNA


title: drna pKT-Inact1

description: Total RNA depleted of rRNA


title: EXO


title: drna pKT-CNP3

description: Total RNA depleted of rRNA


title: A925L alectinib-DT, biological rep3

description: Gene expression data from A925L cells treated with alectinib for 9days

source_name: A925L cells treated with alectinib for 9 days

value: Alectinib 3 umol/L


title: Col-0_TNX_biorep2

value: TNX


title: CK (control groups)

city: shanghai

first: xujiao

last: zhou

address: fenyang road 83

institute: Eye & ENT Hospital, Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained
(1) reads with 5’ adapter; (2) reads without 3’ adapter or insert sequence; (3) reads with more than 10% N; (4) reads with more than 50% nucleotides with Qphred<=20; (5) reads with ploy A/T/G/C.
Adapter trimming for the removal of adapter sequences from the 3’ ends of reads was also performed.
At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: mice corneas

extract_protocol:
Corneas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cornea

value: 6-8 weeks


title: TREAT (dry eye mice model groups)


title: Col-0_TNX_biorep3


title: WT2

description: Total RNA depleted of rRNA

data_processing:
Each sample was sequenced to an approximate depth of 12 million reads.
Quality control and adapter trimming was performed with bcl2fastq (ver. 2.20.0.445) on default parameters.
RNA-Seq reads were mapped to the GenBank accession CP001363.1 using HISAT2 (version 2.2.0) on default parameters + '--very-sensitive'
Read quantification was performed using Subread’s featureCounts functionality (ver. 2.0.1) on default parameters + '-Q 20'
Read counts loaded into R (ver. 4.0.2) and were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm (ver. 1.14.5) with default parameters.
Subsequent values were then converted to counts per million (cpm).
Differential expression analysis was performed using edgeR’s Quasi-Linear F-Test (qlfTest) functionality against treatment groups (ver. 1.14.5) with default parameters.
Genome_build: The NCBI index (CP001363.1) was used for gene annotation. https://www.ncbi.nlm.nih.gov/nuccore/CP001363.1/
Supplementary_files_format_and_content: Table with raw counts for each locus and sample
Supplementary_files_format_and_content: A table containing normalized read counts for each sample (in columns) and each annotated transcript (in rows). Includes statistics for differential expression between WT samples and the 'rna' deletion strain.


title: A925L lorlatinib-DT, biological rep1


title: A925L lorlatinib-DT, biological rep2


title: WT1

description: Total RNA depleted of rRNA


title: A925L alectinib-DT, biological rep2


title: LM61 d9 Nr. 15

city: Basel

first: Carolyn

last: King

address: Hebelstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description:
analysis d9
UMImatrix_Lm_GP61_d0.tsv.gz

data_processing:
Single-cell sequencing files (basecalls) were processed using the Cell Ranger Single Cell Software Suite (v3.1.0) to perform quality control, sample de-multiplexing, barcode processing, alignment to mm10 genome with STAR (version 2.6.1a_08-27), and read counting on Ensembl 93 gene model (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Default parameters were used for Cell Ranger, except for the STAR parameters outSAMmultNmax set to 1 and alignIntronMax set to 10000.
UMI were counted by extracting read counts from the raw_feature_bc_matrix generated by Cell Ranger, using R and DropletUtils. The UMI matrix was filtered to keep cells with log10 library size > 3.3 and < 4.78,  log number of features > 3, % mitochondrial reads >= 5, % ribosomal protein reads >= 20. Genes with average counts < .007 were removed.  The UMI counts matrices are tab-separated and gzipped in the processed data files.
Genome_build: mm10
Supplementary_files_format_and_content: UMImatrix*.tsv.gz; gzipped tab-separated values text file with UMI counts.  Rowname = Ensembl Stable ID.  Columns named as: CellBarcode-Immunization-Timepoint-SampleNum, e.g. AAACCCAAGAAACTGT-Lm_WT-d5-Sample2

source_name: splenocytes

extract_protocol:
GP66 specfic CD4 T cells were FACS sorted on day 9 or 14  days directly RPMI+FCS or pure FACS and processed immediately for 10x Genomics
10X: Chemistry = Single Cell 3' v3, Transcriptome = mm10-2.1.0, Pipeline Version = 3.1.0

treatment_protocol: On day 0, recipient mice were pre-immunized with either wildtype LM (mice 2-3) or LM61 (mice 7, 8, 14, 15).  On day 9 mouse 14 and 15 were used for analysis. All remaining mice (2, 3, 7, 8) received KL25HL B cells by adoptive transfer and were challenged with LCMV on day 9.  On day 14, GP66-77-specific CD4 T cells (CD4+ CD44hi, B220-, CD8-, F4/80-) were purified by FACS-sorting and were subject to scRNAseq.

value: LM61 immunization on d0

tag: ID


title: LM61 d9 Nr.14

description:
analysis d9
UMImatrix_Lm_GP61_d0.tsv.gz


title: A925L alectinib-DT, biological rep1


title: Col-0_SA_TNX_biorep3

value: SA+TNX


title: Col-0_TNX_biorep1


title: LM61 d14 Nr. 8

description:
d9 KL25HL B cell transfer and LCMV infection, analysis d14
UMImatrix_Lm_GP61_d5.tsv.gz


title: Col-0_SA_TNX_biorep2


title: drna2

description: Total RNA depleted of rRNA


title: drna3

description: Total RNA depleted of rRNA


title: A925L parent, biological rep3

description: Gene expression data from A925L cells as negative control

source_name: A925L parental cells

value: DMSO


title: WT3

description: Total RNA depleted of rRNA


title: LM61 d14 Nr. 7


title: Col-0_SA_TNX_biorep1


title: LM wt Nr. 3

description:
d9 KL25HL B cell transfer and LCMV infection, analysis d14
UMImatrix_Lm_WT_d5.tsv.gz

value: LM immunization on d0


title: A925L parent, biological rep2


title: A925L parent, biological rep1


title: deltainact 3

description: Total RNA depleted of rRNA

data_processing:
Each sample was sequenced to an approximate depth of 12 million reads.
Quality control and adapter trimming was performed with bcl2fastq (ver. 2.20.0.445) on default parameters.
RNA-Seq reads were mapped to the GenBank assembly GCA_015534855.1 using HISAT2 on default parameters + '--very-sensitive'
Read quantification was performed using Subread’s featureCounts functionality (ver. 2.0.1) on default parameters + '-Q 20'
Read counts loaded into R (ver. 4.0.2) and were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm (ver. 1.14.5) with default parameters.
Subsequent values were then converted to counts per million (cpm).
Differential expression analysis was performed using edgeR’s Quasi-Linear F-Test (qlfTest) functionality against treatment groups (ver. 1.14.5) with default parameters.
Genome_build: The NCBI index (https://www.ncbi.nlm.nih.gov/assembly/GCF_015534855.1/) was used for gene annotation.
Supplementary_files_format_and_content: Table with raw counts for each locus and sample
Supplementary_files_format_and_content: A table containing normalized read counts for each sample (in columns) and each annotated transcript (in rows). Includes statistics for differential expression between samples expressing pKT-CNP and pKT-CNP-inactive.

organism: Escherichia coli K-12

source_name: E. coli culture

growth_protocol: Overnight cultures of E coli BW25113 Δrna cells containing pKT-CNP or pKT-CNP-inact were grown in 3 mL M9 media (0.4% glucose, 0.2% casitone) with kanamycin and chloremphenicol to maintain plasmids and deletion strain, respectively. Cells were subcultured 1:100 in 10 mL of fresh M9 media in 50 mL conical tubes and were grown at 37 °C with shaking. When cultures reached OD600 = 0.1, expression of CNPase or CNP-Inact was induced with 25 ng/mL anhydrotetracycline. Cultures were returned to the incubator until cultures reached OD600 = 0.5-0.6. At this stage, samples were collected for both RNA-seq

extract_protocol:
Total RNA was extracted from half of the resuspended pellet using the Monarch® Total RNA Miniprep Kit #T2010S (NEB, Ipswich, MA, USA) following the manufacturer's instructions.
Extracted RNA was sent on dry ice to the Microbial Genome Sequencing Center (Pittsburgh, PA, USA) where all following steps, incuding data processing, were completed. Samples were subjected to ribosomal RNA depletion using the Ribo-Zero™ Plus rRNA Removal Kit and complementary DNA (cDNA) libraries were then prepared with the Illumina Stranded RNA library preparation kit.

treatment_protocol: 10 mL of culture were collected at OD600 = 0.5 and cells were pelleted at 4500 rpm for 15 min. Supernatent was removed and the pellets were flash frozen in liquid nitrogen. The pellets were stored at -80 °C.

value: K12 BW25113 delta_rna

value: pKT-CNP inactive (H73L/H152L)


title: Col-0_SA_biorep3

value: seedling

value: SA


title: deltainact 2

description: Total RNA depleted of rRNA


title: H2228 lorlatinib-DT, biological rep2

description: Gene expression data from H2228 cells treated with lorlatinib for 9days

source_name: H2228 cells treated with lorlatinib for 9 days

value: Lorlatinib 10 umol/L


title: LM wt Nr.2


title: Col-0_SA_biorep2


title: H2228 lorlatinib-DT, biological rep3


title: deltainact 1

description: Total RNA depleted of rRNA

value: Logarithmic


title: Col-0_SA_biorep1


title: Microglia_P15_cKO_rep2

city: Boston

first: Emilia

last: Favuzzi

address: 220 Longwood Avenue, Armenise 217

department: Neurobiology

institute: Harvard Medical School

description: GABAB1R cKO

data_processing:
Raw scRNA-seq data were processed using the standard CellRanger v3.0.0 pipeline (10x Genomics). Reads were aligned to the GRCm38 (mm10) mus musculus genome.
Doublets, cells with low quality or likely undergoing stress and putative non-microglia were excluded from the analysis. Criteria for exclusion were: fraction of reads mapping to mitochondrial genes greater than 10%, less than 800 genes detected, more than 20,000 total UMI detected and no reads mapping to Fcrls and Cx3cr1 genes.
Monocle3 R package was used to perform unsupervised clustering analysis on scRNA-seq data (Cao et al., 2019). Briefly, a gene by cell expression matrix was generated for wild-type and GABAB1R KO and annotated by sample (WT_1 and WT_2, KO_2 and KO_3 respectively), preprocessed using default parameters (normalized by log and size factor, and reduced to a 50 dimensions lower space with PCA), batch effect were removed with align_cds using sample as the alignment group, UMAP was computed using reduce_dimension, clusters were computed using the Leiden community detection with cluster_cells. Cre-Het data were preprocessed in the same manner.
A gene by cell expression matrix was generated for wild-type and GABAB1R KO and annotated by sample (WT_1 and WT_2, KO_2 and KO_3) and condition (WT and KO). Data were then preprocessed using default parameters (normalized by log and size factor, and reduced to a 50 dimensions lower space with PCA). Batch effect were removed with align_cds using condition as the alignment group. UMAP was computed using reduce_dimension and clusters were computed using the Leiden community detection with cluster_cells.
Lists of genes enriched in each cluster were generated using the top_markers function in the Monocle3 R package (marker score > 0.15). Additionally, clusters from Monocle3 were transferred to Seurat (Satija et al., 2015) and lists of genes enriched in each cluster were generated using the FindAllMarkers function in the Seurat R package with Wilcoxon rank sum tests (default parameters: absolute value of the average log2FC >0.25 and p value ≤ 0.01).
For each cluster composed of both wild-type and GABAB1R cKO microglia in similar proportions (i.e. clusters 1, 2, 3, 4, 6 and 8), a differential expression analysis was performed between wild-type and cKO cells. For this “within cluster” wild-type versus cKO differential expression analysis, first, clusters from Monocle were transferred to Seurat. Then, for cells belonging to each cluster, a differential expression analysis was performed using the FindMarkers function in the Seurat R package with Wilcoxon rank sum tests (absolute value of the average log2 fold change > 0.25) and the identity class set on condition (wild-type or cKO).
Genome_build: mm10
Supplementary_files_format_and_content: per-molecule information for all molecules that contain a valid barcode and valid UMI and were assigned with high confidence to a gene or Feature Barcode. This HDF5 file contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis.

source_name: 6 females, 1 male

extract_protocol:
mice were transcardially perfused using ice-cold Hank’s balanced salt solution (1X HBSS), S1 was dissected and a single cell suspension was generated, the suspension was enriced for microglia using Percoll gradient centrifugation, microglia were then blocked, stained for Cd11b-PE, CD45-APC-Cy7 and Cx3cr1-APC and purified from the suspension by fluorescence-activated cell sorting (FACS) using a 100 μm chip on a SH800S Sony sorter.
Single-cell RNA-seq libraries were prepared on the 10x Genomics platform using the Chromium Single Cell 3’ Library and Gel Bead Kit v3.0 (PN-1000075), Chromium Single Cell 3’ Library Construction Kit v3.0 (PN-1000078), Chromium Chip B Single Cell kit (PN-1000154) and Chromium i7 Multiplex Kit (PN-120262) as instructed by the manufacturer. Libraries were sequenced using the Nova-Seq 100 cycle kit (Illumina) by Broad Institute Genomic Services

value: Microglia

tag: developmental stage

value: Cx3cr1 Cre/+; Gabab fl/fl (cKO)

tag: brain region

tag: Sex

value: pooled male and female

value: C57BL/6 x Balb/c


title: drna1

description: Total RNA depleted of rRNA

value: 14028s delta-rna


title: deltaCNP 3

description: Total RNA depleted of rRNA

value: pKT-CNP


title: Microglia_P15_cKO_rep1

description: GABAB1R cKO

source_name: 3 females, 3 males

tag: tissue

tag: genotype


title: deltaCNP 1

description: Total RNA depleted of rRNA


title: Col-0_Mock_biorep1

value: Mock


title: Col-0_Mock_biorep3


title: Microglia_P15_Cre-Het

description: Cre-Het microglia

source_name: 8 females, 2 males

value: Cx3cr1 Cre/+; Gabab +/+


title: deltaCNP 2

description: Total RNA depleted of rRNA


title: Microglia_P15_WT_rep2

description: WT microglia

source_name: 1 female, 7 males

value: Cx3cr1 +/+; Gabab +/+ (wild-type)


title: H2228 lorlatinib-DT, biological rep1


title: H2228 alectinib-DT, biological rep2

description: Gene expression data from H2228 cells treated with alectinib for 9days

source_name: H2228 cells treated with alectinib for 9 days

value: Alectinib 3 umol/L


title: Microglia_P15_WT_rep1

description: WT microglia

source_name: 2 females, 2 males


title: zebrafish_24hpf_embryo_hMeDIPseq_rep2

status: Public on Nov 08 2021

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute

data_processing:
Library strategy: hMeDIP-seq
hMeDIP-seq raw data was processed using the NGSANE framework v0.5.2.0 (Buske et al, 2014). Sequenced hMeDIP-seq reads in fastq format were trimmed using Trimmomatic software (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:5:20).
Trimmed reads were mapped to Spur_v3.1, Bl71nemr and danRer10 reference genomes for sea urchin, lancelet and zebrafish, respectively, using bowtie2 v2.1.0 with the following parameters: bowtie2 --end-to-end -R 2 -p 10 -N 1 --very-sensitive -X 1000 --no-mixed --no-discordant (Langmead et al, 2012)
Optical and PCR duplicates were removed using Picard Tools’s function MarkDuplicates REMOVE_DUPLICATES=true.
Genome_build: sea urchin: Spur_v3.1; lancelet: Bl71nemr; zabrafish: danRer10
Supplementary_files_format_and_content: bigwig

organism: Danio rerio

source_name: 24 hpf zebrafish embryo DNA subjected to hMeDIP-seq rep2

extract_protocol: hMeDIP-seq library preparation for the DNA hydroxymethylation profiling was performed  according to the Active Motif protocol (hMeDIP, Cat No 55010).

treatment_protocol: no treatment

tag: age

value: 24 hpf embryo

value: embryo


title: zebrafish_24hpf_embryo_ACEseq

data_processing:
Library strategy: ACE-seq
Adapter clipping and read quality trimming using Trimmomatic (ILLUMINACLIP:NEXTflex.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:5 TRAILING:5 MINLEN:50 CROP:140 HEADCROP:10) (Bolger et al, 2014)
Trimmed reads were mapped to Spur_v3.1, Bl71nemr, danRer10 and mm10 genome references for sea urchin, lancelet, zebrafish and mouse, respectively, (all containing the λ phage genome as chrLambda and pUC19 plasmid genome as chrPUC) using WALT (Chen et al, 2016) with the following settings: -m 10 -t 24 -N 10000000 -L 2000.
Optical and PCR duplicates were removed using Picard Tools’s function MarkDuplicates REMOVE_DUPLICATES=true (http://broadinstitute.github.io/picard/).
Reads with more than three consecutive non-converted cytosines in the CC, CA and CT context were removed using Picard Tools’ function FilterSamReads, in order to eliminate DNA molecules not efficiently deaminated by APOBEC3A
The numbers of hydroxymethylated and unmethylated cytosines at each genomic CpG position were called using the MethylDackel extract genome.fasta input.bam -o output --mergeContext. Additional MethylDackel extract parameters --minOppositeDepth 5 --maxVariantFrac 0.5 were used for the genotype correction (in order to exclude C-to-T nucleotide transitions in the genomic DNA of interest, which could be incorrectly considered as unmodified cytosines) (https://github.com/dpryan79/MethylDackel)
Genome_build: sea urchin: Spur_v3.1; lancelet: Bl71nemr; zabrafish: danRer10
Supplementary_files_format_and_content: bed / The file contains 1. Chromosome / Scaffold; 2. CpG start coordinate; 3. CpG end coordinate; 4. The methylation percentage rounded to an integer; 5. The number of alignments/pairs reporting hydroxymethylated bases; 6. The number of alignments/pairs reporting unmethylated bases

source_name: 24 hpf zebrafish embryo DNA subjected to ACE-seq rep1

extract_protocol: ACE-seq library preparation for the DNA hydroxymethylation profiling was performed as previously described {Schutsky et al, 2018 PMID: 30295673;Wang et al, 2021 PMID: 32822044}. Briefly, 100 ng of genomic DNA extracted from sea urchin, lancelet and zebrafish embryos and adult tissues was spiked with 1ng of CpG methylated λ phage DNA (Wisegene) and 0.5 ng of all-C hydroxymethylated pUC19 plasmid DNA (Wisegene) and sonicated to ~300 bp fragments using a M220 focused ultrasonicator (Covaris) with the following parameters: peak incident power, 50W; duty factor, 20%; cycles per burst, 200; treatment time, 75 sec. Sonicated DNA (125 ul total volume) was concentrated to 16.6 ul using AMPure beads (1 volume DNA : 2 volumes AMPure beads). 5hmC protection reaction was performed using β-glucosetransferase (10U/ul, New England Biolabs) in Cutsmart Buffer according to manufacturer’s instructions at 37°C for 1 hr, followed by 10 min at 65°C. The DNA was denatured in DMSO at 95°C for 10 min and immediately placed on dry ice for 2 mins allowing the samples to freeze. C and 5mC deamination reaction was performed using the APOBEC3A enzyme (NEBNext® Enzymatic Methyl-seq Kit, New England Biolabs) with the following ramping conditions: 4°C for 10 min, 4°C - 50°C 2:15 min per degree of the ramp, 50°C for 10 min. Deaminated DNA was then purified using AMPure beads (1 volume DNA : 1 volume AMPure beads) and subjected to low input library preparation using Accel-NGS Methyl-Seq DNA kit (Swift Biosciences). Briefly, DNA was denatured and subjected to an adaptase reaction, followed by primer extension, adapter ligation, and 15 cycles of indexing PCR. Library size and consistency was determined by the Agilent 4200 Tapestation system. The libraries were quantified using the KAPA library quantification kit (Roche).


title: H2228 alectinib-DT, biological rep3


title: zebrafish_24hpf_embryo_input_rep1

source_name: 24 hpf zebrafish embryo input DNA sequencing rep1


title: seaurchin_48hpf_embryo_ACEseq_rep2

organism: Strongylocentrotus purpuratus

source_name: 48 hpf sea urchin embryo DNA subjected to ACE-seq rep2

value: 48 hpf embryo


title: H2228 alectinib-DT, biological rep1


title: H2228 parent, biological rep3

description: Gene expression data from H2228 cells as negative control

source_name: H2228 parental cells

value: DMSO


title: seaurchin_adult_tubefeet_ACEseq_rep2

source_name: sea urchin adult tube feet DNA subjected to ACE-seq rep2

value: adult tube feet

value: tube feet


title: seaurchin_72hpf_embryo_ACEseq_rep2

source_name: 72 hpf sea urchin embryo DNA subjected to ACE-seq rep2

value: 72 hpf embryo


title: H2228 parent, biological rep2


title: seaurchin_24hpf_embryo_ACEseq_rep2

source_name: 24 hpf sea urchin embryo DNA subjected to ACE-seq rep2


title: H2228 parent, biological rep1


title: zebrafish_24hpf_embryo_input_rep2

source_name: 24 hpf zebrafish embryo input DNA sequencing rep2


title: fer rep3

first: Xin

last: Liu

address: NO. 3888 Chenhua Road, Shanghai, China

institute: CAS Center for Excellence in Molecular Plant Sciences

data_processing:
Paired-end reads were cleaned by Trimimomatic
Clean reads were mapped to the genome of Arabidopsis thaliana (TAIR 10) using HISAT2
The mapped reads on each gene were counted by htseq-count
The differentially expressed genes (DEGs) were identified using the R package edgeR (FDR (false discovery rate) < 0.05, log2FoldChange > 1.5)
Genome_build: TAIR 10
Supplementary_files_format_and_content: Tab separated values file include RPKM values for each sample and logFC (log2 fold change) and FDR (false discovery rate) of differentially expressed genes analysis in indicated sample.

source_name: Seedling

growth_protocol: Plants were grown in a growth chamber at 22 °C and under long day (16 h light/8 h dark) conditions for 8 days

extract_protocol:
Total RNAs were extracted from eight-day-old seedlings grown under the long-day condition using RNeasy Plant Mini Kit (Qiagen, Cat#74904) according to the manufacturer’s instructions. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Seedling

value: 8-day old

value: fer


title: WT rep1

value: Wild type


title: WT rep3


title: WT rep2


title: phybfer rep2

value: phybfer


title: phybfer rep1


title: fer rep2


title: zebrafish_24hpf_embryo_hMeDIPseq_rep1

source_name: 24 hpf zebrafish embryo DNA subjected to hMeDIP-seq rep1


title: TFAP2A-overexpressing_after_BMP_ActA_RNASeq [PREP0095_RHuan11781A_B02v1_10_RH_1018_S2]

city: Cambridge

first: Sharad

last: Ramanathan

address: 52 Oxford Street, Room 402

department: Molecular and Cellular Biology

institute: Harvard University

data_processing:
Reads were pseudoaligned using kallisto 0.45.1 to transcripts from the human genome build hg38.
Abundance matrix was extracted with sleuth 0.30.0
Genome_build: hg38
Supplementary_files_format_and_content: abundance_genes_overexpression.tsv contains the abundance estimates as output by sleuth for each gene

source_name: OCT4:RFP; SOX2:YFP H1 hESCs

growth_protocol: Cells were grown on polyester membrane filters (Sterlitech) with 3 µm pores that had been treated with Matrigel.

extract_protocol:
Total RNA was prepared from Accutase-dissociated cells with an RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA integrity was quantified with a TapeStation 4200 (Agilent). All RINe scores were ≥ 9.9.
Libraries were constructed from total RNA using a Kapa mRNA HyperPrep Kit (Roche) by the Bauer Core at Harvard University.

treatment_protocol: BMP4 + Activin A treatment was accomplished by treating cells with mTeSR supplemented with 3 ng/mL recombinant human BMP4 protein (R&D Systems) and 100 ng/mL recombinant human Activin A protein (R&D Systems).

value: Transduced with CFP:P2A:TFAP2A lentivirus before mesendoderm differentiation


title: POU2F3-overexpressing_after_BMP_ActA_RNASeq [PREP0095_RHuan11781A_A02v1_9_RH_973_S1]

value: Transduced with CFP:P2A:POU2F3 lentivirus before mesendoderm differentiation


title: TFAP2C-overexpressing_after_BMP_ActA_RNASeq [PREP0095_RHuan11781A_E02v1_13_RH_1053_S5]

value: Transduced with CFP:P2A:TFAP2C lentivirus before mesendoderm differentiation


title: JUNB-overexpressing_after_BMP_ActA_RNASeq [PREP0095_RHuan11781A_D02v1_12_RH_1028_S4]

value: Transduced with CFP:P2A:JUNB lentivirus before mesendoderm differentiation


title: hDRG6

first: Minh

middle: Q

last: Nguyen

state: MARYLAND

address: 9000, Rockville Pike

institute: NIDCR/NIH

data_processing:
bcl2fastq (v2.17) was used for basecalling
Sequence reads from 10x libraries were processed using Cell Ranger 2 and 3 from 10x Genomics (http://www.10xgenomics.com/)
Reads were aligned to a pre-mRNA GRCh38 genome.
Seurat (v3) was used for downstream analysis in R as described by the Satija lab (https://satijalab.org/)
Genome_build: GRCh38.v25.premRNA
Supplementary_files_format_and_content: csv files with cell barcodes and corresponding gene expression counts; only nuclei meeting minimum threshold of transcripts are included for analysis

source_name: dorsal root ganglia

extract_protocol:
Dorsal root ganglia were harvested and incubated in RNAlater (ThermoFisher) at 4oC overnight.  Tissues were then transferred and stored at -80oC until use.  Tissues were homogenized using a glass dounce homogenizer on ice.  Neuronal nuclei were isolated using rabbit anti-NeuN antibody (Abcam) followed by anti-rabbit IgG microbeads (Miltenyi Biotec) and LS column (Miltenyi Biotec).
Libraries construction were performed using 10x Genomics according to the manufacturer's instructions using v3 chemistry kits.

value: female

value: 55 years

value: dorsal root ganglia

tag: molecule subtype

value: pre-mRNA


title: phybfer rep3


title: hDRG5

value: 34 years


title: hDRG4

value: 35 years


title: HN18_PBL cells

city: Pittsburgh

first: Robert

middle: L

last: Ferris

address: 5500 Center Ave

institute: University of Pittsburgh

data_processing:
BCL to Fastq: Cellranger mkfastq
Fastq to Counts: Cellranger count
Aggregation of counts: Cellranger aggr
Genome_build: hg38
Supplementary_files_format_and_content: Matrix, barcode and features files for each sample

source_name: PBL

extract_protocol:
The Single Cell 3’ Reagent Kit Protocol
10x Genomics 3' kit v2

tag: tiisue

value: PBL

tag: sorting


title: fer rep1


title: HN18_CD45+ cells

source_name: Tumor

value: Tumor


title: HN17_CD45- cells


title: HN18_CD45- cells


title: HN17_CD45+ cells


title: Col-0_Mock_biorep2

source_name: whole plant

value: seedling

tag: genotype/variation

value: Mock


title: HN16_CD45- cells


title: HN17_PBL cells


title: GRHL1-overexpressing_after_BMP_ActA_RNASeq [PREP0095_RHuan11781A_C02v1_11_RH_1024_S3]

tag: cell type

value: Transduced with CFP:P2A:GRHL1 lentivirus before mesendoderm differentiation


title: HN15_CD45+ cells


title: HN15_CD45- cells


title: HN15_PBL cells


title: HN14_PBL cells


title: HN13_CD45- cells


title: HN14_CD45- cells


title: HN12_CD45+ cells


title: HN12_CD45- cells


title: HN12_PBL cells


title: HN14_CD45+ cells


title: HN11_CD45- cells


title: HN11_PBL cells


title: HN10_CD45- cells


title: HN10_PBL cells


title: HN08_CD45+ cells


title: HN09_CD45+ cells


title: HN09_PBL cells


title: HN16_CD45+ cells


title: HN08_PBL cells


title: HN16_PBL cells


title: HN07_CD45- cells


title: HN07_PBL cells


title: HN07_CD45+ cells


title: HN13_PBL cells


title: HN06_CD45- cells


title: HN05_CD45- cells


title: HN03_CD45+ cells


title: HN09_CD45- cells


title: HN10_CD45+ cells


title: RNA-Seq adult_miR29_ASO_rep3

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

description:
adult_miR29_ASO_rep3
Samples collected by University of Rochester Pediatric Processing Core (PI: Gloria Pryhuber)

data_processing:
trim_galore (with cutadapt v1.18) was used to trim and filter reads.
hisat2 (v2.2.0) was used to map reads to the mouse mm10.
featureCounts (v2.0.0) was used to count  reads to genes (-s 0 -Q 50).
Genome_build: hg38
Supplementary_files_format_and_content: raw counts: Matrix table with raw gene counts for every gene and every sample

source_name: CD8+ T cells

growth_protocol: 2x105 magnetically-enriched CD8+ T cells from human PBMCs were plated per well in RPMI-1640 complete media with 10% FBS, Pen/strep and L-glut with IL-7 (2 ng/mL).

extract_protocol:
Naïve CD8+ T cells were FACS sorted by staining for CD8, CD4, CD45RA, CD45RO and Viability Dye. Cells were sorted into PBS + 2% BSA  + 2mM EDTA. Cells were placed in Trizol and RNA was purified following the manufacturer's instructions, with the addition of a chloroform extraction, GlycoBlue addition when precipitating, and a second wash of the pelleted RNA in 70% ethanol. RNA integrity was confirmed on a Fragment Analyzer.
Libraries were prepared by the TREx core at Cornell University as follows: RNAseq libraries were generated with the non-directional NEBNext Ultra II RNA Library Prep Kit (New England Biolabs) using 10 ng of total RNA that was initially polyA-selected.

treatment_protocol: 100 µL of red blood cell EVs (RBCEVs) were added per well, and incubated at 37°C for 4-5 days. The media was changed every 48 hours.

tag: cell state

value: Naive

value: Enriched Adult Peripheral Blood Mononuclear Cells

value: treat with EV loaded with miR-29 ASO for 4-5 days


title: HN01_CD45+ cells


title: HN01_CD45- cells


title: HN05_CD45+ cells


title: HN05_PBL cells


title: HN02_PBL cells


title: HN06_PBL cells


title: RNA-Seq neonate_ctrl_rep3

description:
neonate_ctrl_rep3
Samples collected by University of Rochester Pediatric Processing Core (PI: Gloria Pryhuber)

value: Enriched Cord Blood Mononuclear Cells

value: treat with EV loaded with negative control (NC) mimic for 4-5 days


title: HN04_PBL cells


title: HN03_PBL cells


title: RNA-Seq adult_ctrl_rep3

description:
adult_ctrl_rep3
Samples collected by University of Rochester Pediatric Processing Core (PI: Gloria Pryhuber)

value: treat with EV loaded with negative control (NC) anti-sense oligonucleotides (ASO) for 4-5 days


title: HN01_PBL cells


title: HN11_CD45+ cells


title: HN06_CD45+ cells


title: RNA-Seq adult_miR29_ASO_rep2

description:
adult_miR29_ASO_rep2
Samples collected by University of Rochester Pediatric Processing Core (PI: Gloria Pryhuber)


title: RNA-Seq adult_ctrl_rep1

description:
adult_ctrl_rep1
Samples collected by University of Rochester Pediatric Processing Core (PI: Gloria Pryhuber)


title: HN13_CD45+ cells


title: RNA-Seq neonate_ctrl_rep2

description:
neonate_ctrl_rep2
Samples collected by University of Rochester Pediatric Processing Core (PI: Gloria Pryhuber)


title: RNA-Seq neonate_miR29_mimics_rep2

description:
neonate_miR29_mimics_rep2
Samples collected by University of Rochester Pediatric Processing Core (PI: Gloria Pryhuber)

value: treat with EV loaded with miR-29 mimic for 4-5 days


title: RNA-Seq neonate_miR29_mimics_rep1

description:
neonate_miR29_mimics_rep1
Samples collected by University of Rochester Pediatric Processing Core (PI: Gloria Pryhuber)


title: HN08_CD45- cells