title: mouse_palate, replicate 1, scRNAseq

city: Philadelphia

first: Kang

middle: I

last: Ko

state: Pennsylvania

address: 240 S. 40th Street

department: Department of Periodontics

institute: University of Pennsylvania

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10 for mouse; hg18 for human
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hard palate soft tissue

extract_protocol:
Hard palate soft tissues were isolated, minced, and enzymatically digested in dispase and collagenase aMEM buffer (0.5% FBS). ACK buffer was used to lyse red blood cells. For mouse sample, hematopoetic cells were excluded by fluorescent-activated cell sorting to collect CD45-DAPI- cells. For human samples, DAPI- cells were collected to capture all live cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: CD45- cells

value: Hard palate soft tissue

value: 8 weeks old


title: ESC, Control, rep2

status: Public on Dec 19 2022

type: SRA

city: Edinburgh

first: Keisuke

last: Kaji

state: Midlothian

address: 47 Little France Crescent

department: MRC Centre for Reproductive Health

country: United Kingdom

institute: University of Edinburgh

description:
condition_ESC_KO_vs_ESC_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
ESC_2

library_source: transcriptomic

data_processing:
Quality control of reads using FastQC
Read trimming and adapter removal using Cutadapt
Quality control of trimmed reads using FastQC
Read mapping to GRCM38.p6 reference genome using STAR
Assign reads to genomic features using Rsubread
Differential expression analysis using DESeq2
Assembly: GRCm38.p6
Supplementary files format and content: CSV, RDS

molecule: total RNA

organism: Mus musculus

source_name: mESC_Control_parental line (Clone J) of Zfp266 KO ESC clones

growth_protocol: For MEFs, 1x10^5 cells were transduced with either a non-targeting control sgRNA or Zfp266 sgRNA. 96 hours after transduction, MEFs were harvested for RNA extraction. For reprogramming samples, cells were transduced with either a non-targeting control or Zfp266 sgRNA 24 hours prior to the beginning of reprogramming. OSKM expression was induced by adding reprogramming media to the transduced cells (ESC media + 300ng/ml doxycycline + 10ug/ml Vitamin C). Cells were harvested at D3, D5 and D7 of reprogramming and 1x10^5 cells were sorted per sample, per timepoint for RNA extraction. iPSCs were lifted at D15 of reprogramming and individual iPSCs were sorted into single wells. Clones were grow in ESC media without doxycycline and 1ug/ml Puromycin to select for stable iPSCs and Zfp266 KO was confirmed by genotyping. KO ESCs were generated by transfecting cells with a Zfp266 gRNA plasmid expressing BFP. Individual BFP+ ESCs were sorted into single wells and genotyped to confirm Zfp266 KO. 1x10^5 iPSCs or ESCs were use for RNA extraction.

extract_protocol:
Cells were homogenised with the Qiashredder kit (Qiagen) and total RNA was extracted with the RNeasy Plus Micro Kit (Qiagen).
RNA-Seq libraries were prepared using the NEB Ultra II stranded mRNA Library prep kit (NEB).
Bulk mRNA-Seq

treatment_protocol: Transduction with either a non-targeting control or Zfp266 sgRNA.

tag: genotype

value: wild type

tag: cell type

value: Embryonic Stem Cells


title: ESC, Control, rep1

description:
condition_ESC_KO_vs_ESC_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
ESC_1


title: LZ_Double_1

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Germinal center B cells Isolated from Spleen Using Facs sorting

data_processing:
The reads with good quality were firstly aligned to several mouse reference databases including mm10 mouse genome, exon, splicing junction segment and contamination database including ribosome and mitochondria sequences using BWA alignment algorithm. After filtering reads mapped to contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 mis-matches for each transcript were then counted as expression level for corresponding transcript.  After filtering out of the transcripts with low read (<100) across all samples, the read counts were log2 transformed and quantile-normalized at an equal global median value in order to compare transcription level across samples.
Genome_build: mm10
Supplementary_files_format_and_content: text file of raw counts

source_name: Spleen

extract_protocol:
Spleens removed and prepared into single cell suspension using frosted slides. Lysed Spenocytes were stained negatively selected for B cells and stained with antibody for FACS Sorting of Germinal Center Dark zone and Germinal center Light zone. 1000 Cells were acquired for each sample and subjected to cDNA synthesis and amplification using SMART-Seq Ultra v4 Ultra kit.
 Sequencing libraries of the amplicons passing QC were constructed using the Nextera XT DNA Library Preparation Kit (Illumina, Inc.).

treatment_protocol: treated mice were given 6 doses each of 200ug and 250ug of CTLA4-IG and Anti-CD40L, respectively, over a 2 week period starting at 18 weeks of age.

tag: strain

tag: treatment

value: 6 Doses of CTLA4-IG and 6 doses of Anti-CD40L

tag: tissue

value: Spleen


title: iPS, Zfp266-KO, rep3

description:
condition_iPS_KO_vs_iPS_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
iPS_6

source_name: iPSC_Zfp266 KO_Clone3

value: Zfp266 KO

value: induced Pluripotent Stem Cells


title: LZ_Control_1

value: untreated


title: Staphylococcus aureus, ArlRS+, glucose+, Replicate 1

city: Urbana

first: Thomas

middle: E

last: Kehl-Fie

state: Il

address: 601 South Goodwin Avenue, MC-110

department: Microbiology

institute: University of Illinois at Urbana-Champaign

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).
Adapters were trimmed from the 3' end of reads using Trimmomatic. Sequences matching the first 33 nt of the adapters used in library preparation were trimmed.
Rockhopper v2.0.3, with kentUtils v353 and SAMtools v1.9, was used for aligning reads to the genome, generating transcript counts, and predicting operons.
TMM normalization of transcript counts was performed with edgeR v3.34.0.  Transcripts were filtered if they did not have at least 0.5 counts per million in all three samples of at least one experimental group.  TMM normalization was re-done after filtering.
Assembly: GCF_000010465.1_ASM1046v1
Supplementary files format and content: Log-counts-per-million values after filtering are provided in tab-delimited text. Transcript metadata is included, including transcript and gene name, strand, transcription and translation start and stop sites, locus tag identifiers from the previous genome version, and KEGG pathways.
Supplementary files format and content: Raw counts before filtering are provided in tab-delimited text. Transcript metadata is included, including transcript and gene name, strand, transcription and translation start and stop sites, locus tag identifiers from the previous genome version, and KEGG pathways.

organism: Staphylococcus aureus

source_name: bacterial liquid culture

extract_protocol:
RNA was isolates using LETS buffer.
Ribosomal RNA was removed with the Ribozero kit (Illumina). The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).

value: Newman

value: bacterial liquid culture

value: ArlRS+

value: glucose+


title: ESC, Zfp266-KO, rep2

description:
condition_ESC_KO_vs_ESC_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
ESC_5

source_name: mESC_Zfp266 KO_Clone2


title: iPS, Zfp266-KO, rep2

description:
condition_iPS_KO_vs_iPS_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
iPS_5

source_name: iPSC_Zfp266 KO_Clone2


title: 88-4-PanCK-

city: Tucson

first: Bonnie

last: LaFleur

state: AZ

address: 4151 W Speedway Blvd

institute: University of Arizona

description: SAZT20088-1.SATZ20088-3.|.004.|.panckNeg

data_processing:
Data from the Nanostring DSP instrument were Q3 normalized. Data from expirement 1 (UACC_dermal_transcriptional_change_from_sunProtected_to_actinic_kertosis_expirement_1.txt) and expirement 2 (UACC_dermal_transcriptional_change_from_sunProtected_to_actinic_kertosis_expirement_2.txt) were combined after log2 transformation using Combat (linear empirical Bayes) to remove the batch effect from samples 88/99 versus 7, 15, 80, and 86 that were run in two batches points in time. The Q3 log2 batch corrected data can be found in UACC_SKin_Transcriptomics_log2_Q3_BatchCorrected.txt
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Q3 normalized reads (UACC_dermal_transcriptional_change_from_sunProtected_to_actinic_kertosis_expirement_1.txt) and the combined experiment 1 and experiment 2 log2 batch corrected Q3 reads ( UACC_SKin_Transcriptomics_log2_Q3_BatchCorrected.txt).

organism: Homo sapiens

source_name: Skin

extract_protocol:
All human tissue was sourced from the Skin Cancer Prevention Program Biorepository at the University of Arizona Cancer Center. The protocol has been approved by the Institutional Review Board at the University of Arizona (Protocol Title: Biomarker development for early phase melanoma prevention trials; Protocol Number: 2012277005). A set of matched sun protected and actinic keratosis from two individuals were used for in this study. Tissue blocks were sectioned with a 5 µm thickness and mounted in the center of the slide (Superfrost Plus Micro slides, VWR) within an area of 35.3 mm long by 14.1 mm wide to allow detection by the NanoString GeoMx DSP instrument.
Sample preparation was performed following Leica Biosystems Bond RX FFPE RNA Slide Preparation Protocol in the GeoMx NGS Slide Preparation User Manual (NanoString, MAN-10115-03 for software version v2.1). This assay relies upon photocleavable RNA probes coupled to oligonucleotide tags that allow the selection of tissue compartments of interest for RNA analysis. Slides were baked at 60°C for 60 minutes. Samples were loaded into Leica Bond Rx for deparaffinization and antigen retrieval with the following settings; Bake and Dewax preparation program, 150µl buffer dispense volume, HIER 20 minutes with ER2 at 100°C, 1µ/mL proteinase K for 15 minutes. Slides were briefly stored in 1x PBS. Excess PBS was removed from slides before the addition of 200µL Whole Transcriptome Assay (WTA) probe sets diluted 1:10 in Buffer R (NanoString), covered with Hybrislips (Grace Biolabs, 714022) and incubated at 37°C overnight in a hybridization chamber lined with Kimwipes moistened with 2x SSC. Unbound probes were removed by washing twice at 37°C for 25 minutes in 50% Formamide (ThermoFisher, AM9324)/2x SSC followed by two washes at room temperature in 2x SSC for 2 minutes. Slides were blocked with 200µL Buffer W (NanoString) for 30 minutes followed by 1 hour incubation at room temperature in a humidity chamber with morphology marker solution comprised of 1µL PMEL17 (Novus Biologicals, NBP2-34638AF647), 2µL CD45 (Cell Signaling Technology, 13917BF), 0.66µL Pan-cytokeratin (Novus Biologicals, NBP2-33200AF488), 10µL Syto83 (ThermoFisher, S11364) in Buffer W (NanoString) to 200µL per slide. Slides were subsequently washed twice with 2x SSC before loading onto NanoString GeoMx DSP instrument.
Slides were loaded and scanned on GeoMx instrument according to GeoMx DSP Instrument User Manual (NanoString, MAN-10116-03 for software version v2.1) with the following scan exposure times; 200ms FITC/525nm, 60ms Cy3/568nm, 250ms Texas Red/615nm, 300ms Cy5/666nm. 12 polygonal regions of interest (ROI) were selected per slide with segmentation masks applied to each ROI selecting Pan-cytokeratin positive and Pan-cytokeratin negative areas within each ROI. Channel thresholds were adjusted to maximize inclusion of signal areas and minimize inclusion of non-signal areas with default settings for erode, N-dilate, hole size and particle size

value: Skin

tag: aoi

value: PanCK-

tag: region

value: AK Edge

tag: region label

tag: sample

tag: race/ethnicity

value: White/non-Hispanic

tag: Sex

value: Male

tag: age

value: 67 years


title: 88-4-PanCK+

description: SAZT20088-1.SATZ20088-3.|.004.|.panckPos

value: PanCK+


title: 88-3-PanCK-

description: SAZT20088-1.SATZ20088-3.|.003.|.panckNeg

value: AK Center


title: 88-3-PanCK+

description: SAZT20088-1.SATZ20088-3.|.003.|.panckPos


title: 88-2-PanCK-

description: SAZT20088-1.SATZ20088-3.|.002.|.panckNeg


title: 88-2-PanCK+

description: SAZT20088-1.SATZ20088-3.|.002.|.panckPos


title: LZ_Double_2

value: 6 Doses of CTLA4-IG and 6 doses of Anti-CD40L


title: 88-1-PanCK+

description: SAZT20088-1.SATZ20088-3.|.001.|.panckPos


title: 88-1-PanCK-

description: SAZT20088-1.SATZ20088-3.|.001.|.panckNeg


title: iPS, Zfp266-KO, rep1

description:
condition_iPS_KO_vs_iPS_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
iPS_4

source_name: iPSC_Zfp266 KO_Clone1


title: DZ_Double_2

value: Spleen


title: parental_INH1 [mIDH1INH1 ]

city: Ann Arbor

first: Maria

middle: G

last: Castro

state: MI

address: 1150 East Medical Center Drive

department: Neurosurgery

institute: University of Michigan Medical School

description:
raw_counts_parental_INH.txt
Sample_130942

data_processing:
Sequence reads were aligned to the reference genome using Bowtie2 (version 2.2.1).
Expression quantitation was performed with HTSeq (version 0.6.1), set to count non-ambiguously mapped reads only.
Data were pre-filtered to remove genes with 0 counts in all samples.
Normalization and differential expression was performed with DESeq2 (version 1.14.1).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RNA counts for all samples

source_name: glioma neurospheres

growth_protocol: Human SF10602 cells were grown in NeuroCult NS-A Basal Medium supplemented with 100units/mL antibiotic-antimycotic, 10mL B-27 without vitamin A, 5mL N-2, 100µg/ml Normocin, 20ng/mL FGF, 20ng/mL EGF, and 20ng/mL PDGF-AA.

extract_protocol:
SF10602 cells were collected and suspended in digestion buffer. Digestion was performed using microccocal nuclease to obtain 150 pb DNA fragments. Histone-DNA complexes were isolated with the desired antibody.
Libraries for ChIP-seq were prepared using the TruSeq ChIP Sample Preparation Kit. Input and IP DNA was blunt-ended and phosphorylated, followed by the addition of a single adenine nucleotide prior to ligation with an adapter duplex with a T overhang. Ligated products were size selected by agarose gel electrophoresis, purified and PCR amplified for the final library preparation.

treatment_protocol: SF10602 cells were treated with mIDH1 inhibitor (AGI-5198) for 1 week.

value: glioma neurospheres

tag: cell line

value: radioresistant patient-derived glioma cell culture

value: IDH1 mutant


title: parental_INH2 [mIDH1INH2 ]

description:
raw_counts_parental_INH.txt
Sample_130943


title: parental_INH3 [mIDH1INH3]

description:
raw_counts_parental_INH.txt
Sample_130944


title: ESC, Control, rep3

description:
condition_ESC_KO_vs_ESC_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
ESC_3

value: wild type

value: Embryonic Stem Cells


title: parental3 [basal3 ]

description:
raw_counts_parental_INH.txt
Sample_130941

value: untreated


title: LZ_Control_3

description: Germinal center B cells Isolated from Spleen Using Facs sorting


title: iPS, Control, rep3

description:
condition_iPS_KO_vs_iPS_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
iPS_3

value: induced Pluripotent Stem Cells


title: parental2 [basal2 ]

description:
raw_counts_parental_INH.txt
Sample_130940


title: iPS, Control, rep2

description:
condition_iPS_KO_vs_iPS_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
iPS_2


title: parental1 [basal1 ]

description:
raw_counts_parental_INH.txt
Sample_130939


title: INH_input_1

library_source: genomic

data_processing:
Sequence reads were trimmed with TrimGalore (TrimGalore) (v0.4.5) and cutadapt (Martin) (v1.15) with the following parameters: –adapter AGATCGGAAGAGC -e 0.1 –stringency 6 –length 20 –nextseq 20.
Trimmed reads to hg19 with Bowtie2  (v2.3.4.1) with the following parameters: -X 2000, and defaults multi-seed length of 20bp with 0 mismatches. Duplicate reads are marked and removed with Picard (Picard).
Alignments below a MAPQ threshold are removed. These filtering steps are performed with samtools (v1.2) and the flags: -q 10 -F 1024.
Sample-wise peaks are called with macs2 (v2.1.2) with flags: –format BAM –gsize hs.
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

extract_protocol:
SF10602 cells were collected and suspended in digestion buffer. Digestion was performed using microccocal nuclease to obtain 150 pb DNA fragments. Histone-DNA complexes were isolated with the desired antibody.
The ChIP-Seq libraries are prepared using the Swift ACCEL-NGS 2S Plus DNA Library Kit, with dual indexing. We used 5.4ng dna/library, and 7 cycles for the final PCR library amplification step. Quality control is performed on each Input/IP libraries using Qubit and Agilent TapeStation HS D1000. Libraries were quantitated using the KAPA Illumina Library Quantitation kit, pooled, and sent to the UM Advanced Genomics Core for PE-50 sequencing on Illumina’s NovaSeq6000

treatment_protocol: SF10602 cells were treated with mIDH1 inhibitor (AGI-5198) for 10 days

tag: chip antibody


title: INH_input_2


title: LZ_Control_2


title: DZ_Double_1


title: DZ_Control_3


title: iPS, Control, rep1

description:
condition_iPS_KO_vs_iPS_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
iPS_1


title: INH_H3K36me3_2


title: INH_H3K27me3_2


title: DZ_Double_3


title: INH_H3K36me3_1


title: D7-reprogramminng, Zfp266-KO, rep3

description:
condition_D7_KO_vs_D7_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D7_6

source_name: Zfp266 sgRNA transduced cells, at D7 of reprogramming

value: Zfp266 KO

value: Reprogramming Cells

tag: time


title: human_palatal_ruga, replicate 2, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

source_name: Ruga tissue from anterior palate

value: All cells

value: Ruga tissue from anterior palate

value: 32 years old


title: INH_H3K27ac_1


title: D7-reprogramminng, Zfp266-KO, rep1

description:
condition_D7_KO_vs_D7_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D7_4


title: DZ_Control_2


title: INH_H3K4me3_2


title: D7-reprogramminng, Zfp266-KO, rep2

description:
condition_D7_KO_vs_D7_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D7_5


title: DZ_Control_1


title: D7-reprogramminng, Control, rep3

description:
condition_D7_KO_vs_D7_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D7_3

source_name: control sgRNA transduced cells, at D7 of reprogramming


title: INH_H3K4me1_2


title: INH_H3K4me1_1


title: CHP212, FAM193A KO, Nutlin, replicate 2

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

description: poly(A)+ RNA from CHP212 FAM193AKO cells Nutlin treated

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the HiSeq 4000 RTA software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
FASTQC (v0.11.5) was used to assess sequence data quality.
fastq files from 2 separate lanes were merged for each sample to obtain sufficient read depth.
Low quality bases (Q <10) were trimmed from the 3' end of reads and short reads (<30 nt after trimming) and adaptor sequences were removed using the fastqc-mcf(v1.05) tool from EAutils.
FastQ Screen (v0.9.1) was used to check for common sequencing contaminants
Alignment to the Human reference genome (GRCh37/hg19) was carried out using TopHat2 (v2.1.1, --b2-sensitive --keep-fasta-order --no-coverage-search --max-multihits 10 --library-type fr-firststrand) and Bowtie2 (v2.2.9.0) with the UCSC hg19 GTF annotation file provided in the iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were then filtered to remove low quality mapped reads (MAPQ < 10) using SAMtools (v1.5)
Reads were coordinate sorted and duplicates were marked using Picard (v2.9.4)
Quality assessment of final mapped reads was performed using RSeQC (v2.6.4)
Raw gene-level count data was generated using HTSeq (v0.8.0) with the following options (--stranded=reverse –minaqual=10 –type=exon –idattr=gene_id --mode=intersection-nonempty) using the GTF provided in the UCSC hg19-based igenomes bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Genome_build: GRCh37/hg19; Bowtie2 index and GTF from iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Supplementary_files_format_and_content: Tab delimited text files containing raw gene-level counts for each sample

molecule: polyA RNA

source_name: CHP212 FAM193AKO

growth_protocol: Cells were cultivated in DMEM:F12 supplemented with 10% fetal bovine serum and 1x antibiotic-antimycotic in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
TRI reagent
Strand-specific poly(A)+-enriched mRNA (Illumina TruSEQ mRNA)

treatment_protocol: Cells were treated with either 0.2% DMSO (control treatment) or 10 uM Nutlin-3a  for 12h

value: Neuroblastoma

tag: genetic modification

value: 12h 10 uM Nutlin-3a

tag: library type

value: strand-specific


title: INH_H3K4me3_1

tag: genotype


title: D7-reprogramminng, Control, rep2

description:
condition_D7_KO_vs_D7_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D7_2

tag: cell type


title: human_palatal_ruga, replicate 1, scRNAseq

description: 10x Genomics

tag: strain

value: 34 years old


title: D7-reprogramminng, Control, rep1

description:
condition_D7_KO_vs_D7_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D7_1


title: CHP212, FAM193A KO, Nutlin, replicate 1

tag: treatment


title: CHP212, FAM193A KO, DMSO, replicate 2

description: poly(A)+ RNA from CHP212 FAM193AKO cells vehicle control

value: DMSO


title: INH_H3K27me3_1

tag: tissue

value: glioma neurospheres


title: INH_H3K27ac_2


title: S602_H3K36me3_1


title: S602_H3K27me3_2


title: S602_H3K36me3_2


title: D5-reprogramminng, Zfp266-KO, rep3

description:
condition_D5_KO_vs_D5_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D5_6

source_name: Zfp266 sgRNA transduced cells, at D5 of reprogramming


title: CHP212, FAM193A KO, DMSO, replicate 1


title: S602_H3K27me3_1


title: S602_H3K27ac_2


title: S602_H3K27ac_1


title: D5-reprogramminng, Zfp266-KO, rep1

description:
condition_D5_KO_vs_D5_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D5_4


title: CHP212, WT, Nutlin, replicate 2

description: poly(A)+ RNA from CHP212 cells Nutlin treated

source_name: CHP212 WT

value: WT


title: S602_H3K4me3_2

value: IDH1 mutant


title: S602_H3K4me3_1


title: S602_input_2


title: D5-reprogramminng, Control, rep3

description:
condition_D5_KO_vs_D5_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D5_3

source_name: control sgRNA transduced cells, at D5 of reprogramming

value: wild type


title: CHP212, WT, Nutlin, replicate 1


title: S602_H3K4me1_2


title: S602_input_1


title: S602_H3K4me1_1


title: D5-reprogramminng, Control, rep2

description:
condition_D5_KO_vs_D5_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D5_2


title: CHP212, WT, DMSO, replicate 1

description: poly(A)+ RNA from CHP212 cells vehicle control


title: Sorted cells, TCR(VDJ)-derived cDNA [Pam1-cite-TCR04]

city: Bethesda

first: Qin

last: Xu

state: Maryland

address: 4 Memorial Drive

department: Laboratory of Immune System Biology

institute: National Institute of Allergy and Infectious Diseases

description:
T cell receptor VDJ region reads from mulitmodal scRNAseq
TCR V(D)J sequence
Pam1_CITE_multi5P12_raw_feature_bc_matrix.h5
Pam1-cite-TCR04

data_processing:
fastq generation: Illumina bcl2fastq 2.20
T cell receptor VDJ and B cell receptor VDJ analysis: CellRanger 6.0.0
CellRanger (10x Genomics) version 6.0.0 was used to map cDNA libraries to the hg19 genome reference (10x genomics hg19 cellranger reference, version 1.2.0) and to count antibody tag features. Data were further processed using Seurat (v.4.0.1) running in R v4.0.3. After transforming the surface protein library counts using dsb, we demultiplexed the pooled samples using manual cutoffs on the hashtag antibody staining. We removed cells with less than 100 detected genes, greater than 30% mitochondrial reads, or mRNA counts greater than 25,000. To exclude cells with extremely high surface antibody counts, we also removed the top 0.05% of cells in the surface antibody total count distribution.
Cell clustering was performed by applying the FindNeighbors() function from Seurat on a distance matrix generated from the dsb-transformed surface protein data, followed by Louvain clustering on the resulting SNN graph using Seurat’s FindClusters() algorithm, with a resolution parameter of 1. Expression of selected genes were visualized using the ComplexHeatmap package87, and the percentage of cells per cluster for the S1+ and S1- cells and T cell populations of interest was plotted using ggplot2.
Assembly: hg19
Supplementary files format and content: CellRanger count matrices in h5 data format
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: Pooled Adenoid,Tonsil, PBMC

extract_protocol:
PBMCs were isolated the day after collection by density gradient centrifugation. If red blood cell contamination was present, cells were lysed with ACK buffer. Tonsil and adenoid tissues were stored in RPMI media with 5% FBS (VWR), gentamicin 50mg/mL (Gibco), and 1X antibiotic/antimycotic solution (Gibco) on ice immediately after collection. They were processed the next day, mechanically disrupted and filtered through a 100μm cell strainer to create a single cell suspension, lysed with ACK buffer and washed with PBS three times. The processed cells were stored in liquid nitrogen in the presence of FBS (VWR) with 10% DMSO. Banked PBMC, tonsils and adenoids from 2 donors with history of COVID-19 (CNMC 71 and 89) and one uninfected control (CNMC 99) were thawed from liquid nitrogen in a 37°C water bath for 2-3 mins. 2 mL of media consisting of RPMI with 10% of fetal bovine serum, 0.1mg/ml DNase I (Roche) and 10mM HEPES was added drop-by-drop to the thawed cells. Cells were further diluted by incremental addition of a 1:1 volume of media up to 8 mL, then centrifuged at 300 x g for 5 min. Cells were then resuspended in 300 μL of media, incubated at room temperature for 5 min, washed with media without DNase I, and filtered through a 100μm strainer before spinning down and resuspending in staining buffer (PBS + 1% BSA). Cells were then incubated with Fc blocker (Human TruStain FcX, BioLegend), stained with TotalSeq-C human hashtag antibodies (BioLegend) to uniquely label the sample origin (by tissue and donor), and washed with PBS + 0.04% BSA. Adenoids and tonsils from the 3 donors (6 samples in total) were pooled together and PBMCs from 3 were pooled together separately. The number of cells to pool from each tissue and donor was calculated with the aim of pooling a similar number of Spike1+ positive B cells from each sample. Pooled cells were first incubated with Fc blocker at 4°C for 10 min followed by CITE-seq and sorting antibody cocktails in the following order at 4°C: TotalSeq anti-CXCR3 antibody for 10 min, TotalSeq chemokine cocktail (anti-CCR7, CCR6, CXCR5 antibodies) for 10 min, and the rest of CITE-seq antibodies and fluorescence-labeled sorting antibodies and viability dye (Aqua) for 30 min. Cells were then washed with PBS+0.04% BSA and resuspended in PBS+2% FBS. S1+ and S1- B cells and CD95+ CD4+ and CD95+ CD8+ T cells were sorted from each pool on a BD FACS Aria Fusion sorter for tonsil/adenoid pool and FACS Aria Ill sorter for the PBMC pool. Cells were sorted into PBS+2% FBS.
Library was prepared using Chromium Single Cell 5ʹ v2 (CG000330, Dual Index) kit (10x Genomics). V(D)J, mRNA and cell surface protein (CSP) were captured and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 5’ v2 protocol. SPRI bead size selection was performed in order to separate cDNAs from CSP Feature Barcode tagged DNA fragments. GEX libraries, CSP libraries and V(D)J libraries were separately constructed according to the manufacturer’s instructions.
Three types of libraries were pooled separately at the same molar concentration. The final pool composed of  80% GEX library, 10%V(D)J library and 10% CSP library for sequencing on NovaSeq 6000.
Reference for feature surface markers was listed in Feature reference.xlsx.

value: Pooled Adenoid,Tonsil, PBMC

value: CD8+CD95+ cells

value: V(D)J

tag: antibodies/tags


title: Sorted cells, TCR(VDJ)-derived cDNA [Pam1-cite-TCR03]

description:
T cell receptor VDJ region reads from mulitmodal scRNAseq
TCR V(D)J sequence
Pam1_CITE_multi5P11_raw_feature_bc_matrix.h5
Pam1-cite-TCR03


title: Sorted cells, TCR(VDJ)-derived cDNA [Pam1-cite-TCR02]

description:
T cell receptor VDJ region reads from mulitmodal scRNAseq
TCR V(D)J sequence
Pam1_CITE_multi5P10_raw_feature_bc_matrix.h5
Pam1-cite-TCR02

value: CD4+CD95+ cells


title: D5-reprogramminng, Zfp266-KO, rep2

description:
condition_D5_KO_vs_D5_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D5_5

value: Zfp266 KO

value: Reprogramming Cells


title: Sorted cells, BCR(VDJ)--derived cDNA [Pam1-cite-BCR03]

description:
B cell receptor VDJ region reads from mulitmodal scRNAseq
BCR V(D)J sequence
Pam1_CITE_multi5P08_raw_feature_bc_matrix.h5
Pam1-cite-BCR03

value: Spike1- B cells


title: D3-reprogramminng, Zfp266-KO, rep3

description:
condition_D3_KO_vs_D3_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D3_6

source_name: Zfp266 sgRNA transduced cells, at D3 of reprogramming


title: RNA_seq_the other ECs

city: Suita

first: Hiroyuki

last: Nakajima

state: Osaka

address: 6-1 Kishibeshinmachi

department: Department of Cell Biology

country: Japan

institute: National Cerebral and Cardiovascular Center Research Institute

description: scRNAseq

data_processing:
The 10x Genomics Cell Ranger pipeline (version 5.0.0) was used to perform sample demultiplexing, alignment to the reference genome (Danio rerio GRCz11) and reporter sequences (EGFP and RFP) with the gene annotation file (Danio_rerio.GRCz11.99.chr.gtf.gz), barcode/UMI processing, and gene counting for each cell.
Genome_build: GRCz11
Supplementary_files_format_and_content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI counts for each sample.

organism: Danio rerio

source_name: resected tails (posterior to the yolk end)

extract_protocol:
Tails resected from TgBAC(isl1:TagRFP);Tg(dab2:EGFP) embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution (TrypLE Express with 2.7 mg/ml Collagenase P) and incubated at 28 °C until full dissociation (~15 min). Cells were pelleted (3000 rpm, 5 minutes at 4 °C) and resuspended in suspension medium (phenol red free Dulbecco’s modified Eagle’s medium with 1% FBS and 0.8 mM calcium chloride) twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP-/EGFP+ cells separately. For scRNA-seq, single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller (10x Genomics).
RNA from the barcoded cells for each sample was subsequently reverse-transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit (10x Genomics). Sequencing was performed with Illumina NovaSeq6000.

value: AB

tag: developmental stage

value: 48 hours post fertilization (hpf)

value: Tail

value: other ECs (TagRFP-/EGFP+)


title: D3-reprogramminng, Zfp266-KO, rep2

description:
condition_D3_KO_vs_D3_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D3_5


title: Alg1E time point 30

city: Basel

first: Foivos

last: Gypas

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

description:
Alg1E_TP30
small RNA-sequencing

data_processing:
3' adapters (AACTGTAGGCACCATCAAT) were trimmed with cutadapt (version 2.3) with the following options (--error-rate 0.1, --minimum-length 15, --overlap 3).
Reads were mapped to the genome with bowtie (version 1.2.2) with the following options (-v 1, -m 100,--best, --strata, --fr).
Alignments were sorted and indexed with samtools (version 1.9).
Reads mapping to rRNA, rRNA_pseudogene, tRNA, tRNA_pseudogene or from the MT chromosome were excluded (based on the Wormbase WS270 annotation).
The mature miRNAs from miRBase (version 22) and reads were counted with HTSeq (version XXX) with the following options (--stranded yes, --type miRNA, --idattr Name, --mode union).
Genome_build: ce11
Supplementary_files_format_and_content: counts.tsv: Tab-delimited text file includes counts.

organism: Caenorhabditis elegans

source_name: Alg1E time point 30

growth_protocol: C. elegans were collected hourly between 18 and 30 hours at 25 degree after plating synchronized L1. Worms were washed off the plate(s) thrice in M9 buffer. After washing, 1ml Tri Reagent (MRC) was added, frozen in liquid nitrogen and stored overnight at -80°C.

extract_protocol:
Total RNA was extracted from protocol adapted from (Bethke et al., 2009).
The libraries were prepared from QIAseq miRNA Library Kit (cat. No- 331505), according to the manufacturer protocol.

tag: strain/background

value: Whole body

tag: time point

value: 30 hr


title: RNA_seq_isl1-derived ECs

description: scRNAseq

value: isl1-derived ECs (TagRFP+/EGFP+)


title: Sorted cells, BCR(VDJ)--derived cDNA [Pam1-cite-BCR01]

description:
B cell receptor VDJ region reads from mulitmodal scRNAseq
BCR V(D)J sequence
Pam1_CITE_multi5P06_raw_feature_bc_matrix.h5
Pam1-cite-BCR01

value: Spike1+ B cells


title: D3-reprogramminng, Zfp266-KO, rep1

description:
condition_D3_KO_vs_D3_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D3_4


title: CHP212, WT, DMSO, replicate 2

value: Neuroblastoma

value: WT

value: DMSO

value: strand-specific


title: Sorted cells, BCR(VDJ)--derived cDNA [Pam1-cite-BCR02]

description:
B cell receptor VDJ region reads from mulitmodal scRNAseq
BCR V(D)J sequence
Pam1_CITE_multi5P07_raw_feature_bc_matrix.h5
Pam1-cite-BCR02

value: Pooled Adenoid,Tonsil, PBMC

value: V(D)J


title: Alg1E time point 29

description:
Alg1E_TP29
small RNA-sequencing

source_name: Alg1E time point 29

value: 29 hr


title: Sorted cells, CSP-derived cDNA [Pam1-cite-CSP11]

description:
Cell Surface Protein Tag reads from mulitmodal scRNAseq
Cell Surface Protein-derived oligonucleotide
Pam1_CITE_multi5P11_raw_feature_bc_matrix.h5
Pam1-cite-CSP11

library_source: other

molecule: protein

value: CD8+CD95+ cells

value: CSP


title: D3-reprogramminng, Control, rep2

description:
condition_D3_KO_vs_D3_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D3_2

source_name: control sgRNA transduced cells, at D3 of reprogramming

value: wild type

value: Reprogramming Cells


title: Sorted cells, CSP-derived cDNA [Pam1-cite-CSP10]

description:
Cell Surface Protein Tag reads from mulitmodal scRNAseq
Cell Surface Protein-derived oligonucleotide
Pam1_CITE_multi5P10_raw_feature_bc_matrix.h5
Pam1-cite-CSP10

value: CD4+CD95+ cells


title: Sorted cells, CSP-derived cDNA [Pam1-cite-CSP07]

description:
Cell Surface Protein Tag reads from mulitmodal scRNAseq
Cell Surface Protein-derived oligonucleotide
Pam1_CITE_multi5P07_raw_feature_bc_matrix.h5
Pam1-cite-CSP07

value: Spike1- B cells


title: Sorted cells, CSP-derived cDNA [Pam1-cite-CSP08]

description:
Cell Surface Protein Tag reads from mulitmodal scRNAseq
Cell Surface Protein-derived oligonucleotide
Pam1_CITE_multi5P08_raw_feature_bc_matrix.h5
Pam1-cite-CSP08


title: Sorted cells, CSP-derived cDNA [Pam1-cite-CSP06]

description:
Cell Surface Protein Tag reads from mulitmodal scRNAseq
Cell Surface Protein-derived oligonucleotide
Pam1_CITE_multi5P06_raw_feature_bc_matrix.h5
Pam1-cite-CSP06


title: Sorted cells, CSP-derived cDNA [Pam1-cite-CSP09]

description:
Cell Surface Protein Tag reads from mulitmodal scRNAseq
Cell Surface Protein-derived oligonucleotide
Pam1_CITE_multi5P09_raw_feature_bc_matrix.h5
Pam1-cite-CSP09


title: Alg1E time point 27

description:
Alg1E_TP27
small RNA-sequencing

source_name: Alg1E time point 27

value: Whole body

value: 27 hr


title: Sorted cells, CSP-derived cDNA [Pam1-cite-GEX12]

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
Pam1_CITE_multi5P12_raw_feature_bc_matrix.h5
Pam1-cite-GEX12

value: mRNA


title: D3-reprogramminng, Control, rep1

description:
condition_D3_KO_vs_D3_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D3_1


title: D5-reprogramminng, Control, rep1

description:
condition_D5_KO_vs_D5_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D5_1


title: Sorted cells, mRNA-derived cDNA [Pam1-cite-GEX11]

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
Pam1_CITE_multi5P11_raw_feature_bc_matrix.h5
Pam1-cite-GEX11


title: Sorted cells, TCR(VDJ)-derived cDNA [Pam1-cite-TCR01]

description:
T cell receptor VDJ region reads from mulitmodal scRNAseq
TCR V(D)J sequence
Pam1_CITE_multi5P09_raw_feature_bc_matrix.h5
Pam1-cite-TCR01


title: Sorted cells, mRNA-derived cDNA [Pam1-cite-GEX10]

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
Pam1_CITE_multi5P10_raw_feature_bc_matrix.h5
Pam1-cite-GEX10


title: Alg1E time point 26

description:
Alg1E_TP26
small RNA-sequencing

source_name: Alg1E time point 26

value: 26 hr


title: MEFs, Zfp266-KO, rep3

description:
condition_MEF_KO_vs_MEF_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
MEF_6

source_name: Zfp266 sgRNA transduced Mouse Embryonic Fibroblasts

value: Zfp266 KO

value: Mouse Embryonic Fibroblasts

tag: cell origin

value: P2 fibroblasts derived from E12.5 embryos


title: Sorted cells, CSP-derived cDNA [Pam1-cite-CSP12]

description:
Cell Surface Protein Tag reads from mulitmodal scRNAseq
Cell Surface Protein-derived oligonucleotide
Pam1_CITE_multi5P12_raw_feature_bc_matrix.h5
Pam1-cite-CSP12


title: Alg1E time point 25

description:
Alg1E_TP25
small RNA-sequencing

source_name: Alg1E time point 25

value: 25 hr


title: MEFs, Zfp266-KO, rep2

description:
condition_MEF_KO_vs_MEF_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
MEF_5


title: Alg1E time point 24

description:
Alg1E_TP24
small RNA-sequencing

source_name: Alg1E time point 24

value: 24 hr


title: Sorted cells, mRNA-derived cDNA [Pam1-cite-GEX09]

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
Pam1_CITE_multi5P09_raw_feature_bc_matrix.h5
Pam1-cite-GEX09

value: Pooled Adenoid,Tonsil, PBMC


title: Sorted cells, mRNA-derived cDNA [Pam1-cite-GEX07]

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
Pam1_CITE_multi5P07_raw_feature_bc_matrix.h5
Pam1-cite-GEX07

data_processing:
We performed unsupervised clustering based on cell surface markers. We also did RNA-based clustering of Spike1+ and Spike1- B cells; for this, we first downsampled the fastq files from the Spike1+ sequencing library to more closely match the reads-per-cell obtained in the Spike1- sequencing libraries using seqtk v1.3. Cells were then clustered using the top 15 PCs derived from the 2000 most variable genes, selected by Seurat’s FindVariableFeatures function using the “vst” method. Clustering was performed using the Louvain method and a resolution of 1.15 in Seurat’s FindClusters function. Corresponding processed file “Pam1_CITE_multi5P06_DS_raw_feature_bc_matrix.h5” was provided.
fastq generation: Illumina bcl2fastq 2.20
T cell receptor VDJ and B cell receptor VDJ analysis: CellRanger 6.0.0
CellRanger (10x Genomics) version 6.0.0 was used to map cDNA libraries to the hg19 genome reference (10x genomics hg19 cellranger reference, version 1.2.0) and to count antibody tag features. Data were further processed using Seurat (v.4.0.1) running in R v4.0.3. After transforming the surface protein library counts using dsb, we demultiplexed the pooled samples using manual cutoffs on the hashtag antibody staining. We removed cells with less than 100 detected genes, greater than 30% mitochondrial reads, or mRNA counts greater than 25,000. To exclude cells with extremely high surface antibody counts, we also removed the top 0.05% of cells in the surface antibody total count distribution.
Cell clustering was performed by applying the FindNeighbors() function from Seurat on a distance matrix generated from the dsb-transformed surface protein data, followed by Louvain clustering on the resulting SNN graph using Seurat’s FindClusters() algorithm, with a resolution parameter of 1. Expression of selected genes were visualized using the ComplexHeatmap package87, and the percentage of cells per cluster for the S1+ and S1- cells and T cell populations of interest was plotted using ggplot2.
Assembly: hg19
Supplementary files format and content: CellRanger count matrices in h5 data format
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)


title: Sorted cells, mRNA-derived cDNA [Pam1-cite-GEX08]

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
Pam1_CITE_multi5P08_raw_feature_bc_matrix.h5
Pam1-cite-GEX08


title: Alg1E time point 28

description:
Alg1E_TP28
small RNA-sequencing

source_name: Alg1E time point 28

value: 28 hr


title: Sorted cells, mRNA-derived cDNA [Pam1-cite-GEX06]

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
Pam1_CITE_multi5P06_raw_feature_bc_matrix.h5
Pam1-cite-GEX06

value: Spike1+ B cells


title: MEFs, Zfp266-KO, rep1

description:
condition_MEF_KO_vs_MEF_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
MEF_4


title: Alg1E time point 23

description:
Alg1E_TP23
small RNA-sequencing

source_name: Alg1E time point 23

value: 23 hr


title: D3-reprogramminng, Control, rep3

description:
condition_D3_KO_vs_D3_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
D3_3

value: wild type


title: MEFs, Control, rep3

description:
condition_MEF_KO_vs_MEF_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
MEF_3

source_name: control sgRNA transduced Mouse Embryonic Fibroblasts


title: hTCEpi, SPARC 5, rep5

city: Saint Louis

first: Joseph

middle: B

last: Lin

state: MO

address: 660 South Euclid Ave, MSC-8096-06-07

department: Ophthalmology & Visual Sciences

institute: Washington University School of Medicine

description: sample 20

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.2.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.0.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights function and were fitted using a Limma generalized linear model with additional unknown latent effects as determined by surrogate variable analysis (SVA).  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
For each contrast extracted with Limma, global perturbations in known Gene Ontology (GO) terms, MSigDb, and KEGG pathways were detected using the R/Bioconductor package GAGE to test for changes in expression of the reported log 2 fold-changes reported by Limma in each term versus the background log 2 fold-changes of all genes found outside the respective term.  The R/Bioconductor package heatmap3 was used to display heatmaps across groups of samples for each GO or MSigDb term with a Benjamini-Hochberg false-discovery rate adjusted p-value less than or equal to 0.05.  Perturbed KEGG pathways where the observed log 2 fold-changes of genes within the term were significantly perturbed in a single-direction versus background or in any direction compared to other genes within a given term with p-values less than or equal to 0.05 were rendered as annotated KEGG graphs with the R/Bioconductor package Pathview.
To find the most critical genes, the Limma voomWithQualityWeights transformed log 2 counts-per-million expression data was then analyzed via weighted gene correlation network analysis with the R/Bioconductor package WGCNA.  Briefly, all genes were correlated across each other by Pearson correlations and clustered by expression similarity into unsigned modules using a power threshold empirically determined from the data.  An eigengene was then created for each de novo cluster and its expression profile was then correlated across all coefficients of the model matrix.  Because these clusters of genes were created by expression profile rather than known functional similarity, the clustered modules were given the names of random colors where grey is the only module that has any pre-existing definition of containing genes that do not cluster well with others. These de-novo clustered genes were then tested for functional enrichment of known GO terms with hypergeometric tests available in the R/Bioconductor package clusterProfiler.  Significant terms with Benjamini-Hochberg adjusted p-values less than 0.05 were then collapsed by similarity into clusterProfiler category network plots to display the most significant terms for each module of hub genes in order to interpolate the function of each significant module.  The information for all clustered genes for each module were then combined with their respective statistical significance results from Limma to determine whether or not those features were also found to be significantly differentially expressed.
Assembly: Human Ensembl GRCh38.101
Supplementary files format and content: group_SPARC_0p05-group_Control_Differential_Expression.tsv: Differential gene expression performed comparing control vs. SPARC 0.05.
Supplementary files format and content: group_SPARC_0p5-group_Control_Differential_Expression.tsv: Differential gene expression performed comparing control vs. SPARC 0.5.
Supplementary files format and content: group_SPARC_5-group_Control_Differential_Expression.tsv: Differential gene expression performed comparing control vs. SPARC 5.
Supplementary files format and content: all.gene_counts.tsv: Raw counts.

source_name: hTCEpi

growth_protocol: We used a telomerase-immortalized human corneal epithelial cell line (hTCEpi) that was graciously donated by Danielle Robertson (UT Southwestern). These cells were maintained in keratinocyte growth medium 2 (PromoCell C20011) supplemented with SupplementMix, 1% penicillin/streptomycin, and 0.15 mM calcium chloride.

extract_protocol:
After incubation, we washed cells twice with PBS, then used TRIzol (ambion) and RNeasy Plus Mini Kit (Qiagen) to extract RNA following the manufacturer's recommended protocol.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: We treated hTCEpi cells with recombinant human SPARC (PeproTech 120-36) in KGM media: 0.00, 0.05, 0.50, and 5.00 micrograms/ml for 24h.

value: hTCEpi

value: telomerase-immortalized human corneal epithelial cells

value: SPARC, 5.00 ug/ml


title: MEFs, Control, rep2

description:
condition_MEF_KO_vs_MEF_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
MEF_2


title: Alg1E time point 22

description:
Alg1E_TP22
small RNA-sequencing

source_name: Alg1E time point 22

value: Whole body

value: 22 hr


title: Alg1E time point 21

description:
Alg1E_TP21
small RNA-sequencing

source_name: Alg1E time point 21

value: 21 hr


title: hTCEpi, SPARC 5, rep4

description: sample 19


title: hTCEpi, SPARC 5, rep2

description: sample 17


title: hTCEpi, SPARC 5, rep3

description: sample 18


title: hTCEpi, SPARC 5, rep1

description: sample 16


title: Alg1E time point 20

description:
Alg1E_TP20
small RNA-sequencing

source_name: Alg1E time point 20

value: 20 hr


title: hTCEpi, SPARC 0.5, rep4

description: sample 14

value: SPARC, 0.50 ug/ml


title: MEFs, DamZfp266, 5

description:
bindSite.Ensembl.broadPeak
Zfp266-Dam.bigWig

data_processing:
Library strategy: DamID-Seq
Quality control of raw reads using FastQC
Read trimming and adapter removal using Cutadapt
Quality control of trimmed reads using FastQC
Read mapping to GRCm38.p6 using BWA
Peak calling using Dam
Assembly: GRCm38.p6
Supplementary files format and content: broadPeak, bigWig

source_name: mouse embryonic fibroblast

growth_protocol: MEFs were maintained in MEF media prior to nucleofectionn of DamID plasmids and during assay.

extract_protocol:
Genomic DNA was extrected from sorted cells using the Quick-gDNA Microprep kit (Zymo Research)
32 ng of genomic DNA per samples was used for preparation of the DamID-Seq libraries folloing the protocol published in Tosti, et al., Genome Research, 2018 (doi:  10.1101/gr.227124.117)

treatment_protocol: 1x10^5 MEFs were nucleofected with translation reinitiation-dependent Dam or Dam-Zfp266 expression vectors that have mOrange as a first open reading flame under the PGK promoter, using the P4 primary cell-4D-nucleofector x kit (Lonza). Following nucleofection cells were recovered in MEF media for 48hours before mOrnage+ cells were sorted for DNA extraction.

tag: damid plasmid

value: mouse embryonic fibroblast (MEF)


title: hTCEpi, SPARC 0.5, rep5

description: sample 15


title: Alg1E time point 19

description:
Alg1E_TP19
small RNA-sequencing

source_name: Alg1E time point 19

value: 19 hr


title: MEFs, Control, rep1

description:
condition_MEF_KO_vs_MEF_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
MEF_1

value: Mouse Embryonic Fibroblasts

value: P2 fibroblasts derived from E12.5 embryos


title: hTCEpi, SPARC 0.5, rep3

description: sample 13


title: MEFs, DamZfp266, 4


title: hTCEpi, SPARC 0.5, rep2

description: sample 12


title: hTCEpi, SPARC 0.05, rep5

description: sample 10

value: SPARC, 0.05 ug/ml


title: hTCEpi, SPARC 0.5, rep1

description: sample 11


title: Alg1E time point 18

description:
Alg1E_TP18
small RNA-sequencing

source_name: Alg1E time point 18

value: 18 hr


title: MEFs, DamZfp266, 3


title: hTCEpi, SPARC 0.05, rep4

description: sample 09


title: Alg1A time point 30

description:
Alg1A_TP30
small RNA-sequencing

source_name: Alg1A time point 30

value: 30 hr


title: MEFs, DamZfp266, 2


title: hTCEpi, SPARC 0.05, rep3

description: sample 08


title: hTCEpi, SPARC 0.05, rep2

description: sample 07


title: hTCEpi, SPARC 0.05, rep1

description: sample 06


title: Alg1A time point 29

description:
Alg1A_TP29
small RNA-sequencing

source_name: Alg1A time point 29

value: 29 hr


title: hTCEpi, control, rep5

description: sample 05

value: control


title: MEFs, DamZfp266, 1


title: hTCEpi, control, rep4

description: sample 04

value: hTCEpi


title: Alg1A time point 28

description:
Alg1A_TP28
small RNA-sequencing

source_name: Alg1A time point 28

value: 28 hr


title: MEFs, Dam, 5

value: PGK-mO-Dam


title: hTCEpi, control, rep2

description: sample 02

value: telomerase-immortalized human corneal epithelial cells


title: MEFs, Dam, 4


title: Alg1A time point 27

description:
Alg1A_TP27
small RNA-sequencing

source_name: Alg1A time point 27

value: Whole body

value: 27 hr


title: B12

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

data_processing:
Raw sequencing reads from human brain samples were mapped to hg38 using HISAT2.
Counts of reads mapping to genes were obtained using featureCounts software of Subread package against Ensembl v90 annotation.
Differential expression was done using the DESeq2 package.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing raw counts

source_name: Brain

extract_protocol:
Biospecimens were provided by the University of Miami Brain Endowment Bank™, an IRB-approved biorepository that holds frozen brain tissue annotated with demographic information and clinical variables. Postmortem brain specimens were obtained from unaffected control subjects and from cocaine-related deaths that came to routine autopsy. Medicolegal investigations and certifications of the cocaine intoxication deaths were conducted by forensic pathologists to determine the cause and manner of death. The circumstances of death and blood and brain toxicology were reviewed to identify sudden deaths due to the toxic effects of chronic cocaine abuse in persons who met the criteria for cocaine use disorder (n = 25). Drug-free age-matched control subjects (n = 20) were selected from homicides, accidental or natural deaths that had negative urine screens for all common drugs in decedents with no history of licit or illicit drug use before death. The brain samples were matched for sex (male), age, race, smoking history, PMI and brain pH to normalize factors that can affect sample quality. This study used male samples only because of the preponderance of males in the available brain bank. Cocaine use still predominates in males overall and the incidence of cocaine intoxication deaths follows this pattern. Also, the rates of polydrug abuse and psychiatric comorbidity are higher among females, further excluding females based on the criteria for subject inclusion for the present study. To isolate RNA from the samples in Trizol LS, we used the Zymo Directzol RNA miniprep kit (Zymo Research; R2050). We performed DNase treatment on all samples to ensure the removal of genomic DNA before proceeding with library preparation. RNA was analyzed for size distribution and quantity using Bioanalyzer 2000 (Agilent Technologies, USA).
We used the Takara SMARTer Stranded Total RNA-seq library preparation kit to create indexed libraries from ribo-depleted RNA from each sample for sequencing (Takara; 634839). All libraries were generated simultaneously using a multiplexed library preparation strategy to ensure no variation in processing due to batch effects. Resulting libraries were analyzed for size distribution and quantity using the Agilent Bioanalyzer and Tape Station (Life Technologies) prior to sequencing.

value: Brain

tag: brain region

value: Nucleus accumbens

tag: group

value: Cocaine

tag: race

value: White

tag: Sex

value: male

tag: age

tag: pmi


title: Alg1A time point 26

description:
Alg1A_TP26
small RNA-sequencing

source_name: Alg1A time point 26

tag: genotype

value: 26 hr


title: MEFs, Dam, 3

tag: cell type

value: mouse embryonic fibroblast (MEF)


title: Alg1A time point 25

description:
Alg1A_TP25
small RNA-sequencing

source_name: Alg1A time point 25

value: 25 hr


title: MEFs, Dam, 2

tag: strain


title: hTCEpi, control, rep1

description: sample 01

tag: cell line

tag: treatment


title: Alg1A time point 24

description:
Alg1A_TP24
small RNA-sequencing

source_name: Alg1A time point 24

tag: tissue

value: 24 hr


title: MEFs, Dam, 1


title: E11

value: Black


title: A12


title: F11


title: G11


title: Alg1A time point 23

description:
Alg1A_TP23
small RNA-sequencing

source_name: Alg1A time point 23

value: 23 hr


title: D11


title: C11


title: 72 hours reprogramming, Zfp266-KO, rep3

description:
Rep_Zfp266.mRp.clN_peaks.broadPeak
Rep_Zfp266.mRp.clN_peaks.gappedPeak
Rep_Zfp266.mRp.clN.bigWig
Rep_ZeovsRep_Zfp266.mLb.deseq2.FDR0.05.results.bed
Rep_ZeovsRep_Zfp266.mLb.deseq2.FDR0.05.results.txt

data_processing:
Quality control of raw reads using FastQC
Read trimming and adapter removal using Cutadapt
Quality control of trimmed reads using FastQC
Read mapping to GRCm38.p6 using BWA
Alignments due to PCA duplicates removed using Picard's Mark Duplicates
Uninformative and spurious alignments filtered using BEDtools and SAMtools
Peak calling using MACS2
Differential accessibility analysis using DESeq2
Assembly: GRCm38.p6
Supplementary files format and content: broadPeak, gappedPeak, bigWig, BED, TXT

source_name: Zfp266 sgRNA transduced reprogramming cells

growth_protocol: Cells were cultured in MEF media  prior to gRNA transduction and for 24 hours after. 24 hours post transduction, cells for reprogramming samples were changed to reprogramming media (ESC media + 300ng/ml doxycycline and 10ug/ml Vitamin C) to begin reprogramming. MEF samples were maintained in MEF media. All samples were then harvested and cell sorted 96 hours after transduction, equal to 72 hours after OSKM induction by doxycycline.

extract_protocol:
DNA extraction and transposition from 50,000 startinng cells was performed according to the Omni-ATAC protocol. Briefly cells were lysed on ice in lysis buffer for 3 minutes before 1000ul resuspension buffer was added and tubes were centrifuged at 500 x g for 10 mins at 4oC. Supernatants were aspirated and pelleted nuclei were resuspended in 50ul transposition mix (2.5 ul Tn5 transposase, 25 ul 2x TD buffer (both Illumina), 0.5 ul 1% Digitonin (Promega), 0.5 ul 10% Tween-20 (Sigma), 16.5 ul 1x PBS, 5ul nuclease-free H2O) shaking at 37oC for 30mins at 1000rpm in a thermomixer. Tn5 transposed genomic DNA was then purified with the Zymo DNA Clean and Concentrator-5 kit (Zymo Research) and eluted in dH20
Purified and transposed DNA was PCR amplified with the NEBNext High Fidelity 2x MasterMix (NEB) . Illumina/Nextera i5/i7 common adaptors were used. PCR fragments  were purified with double-sided bead purification using AMPure XP magnetic beads (Beckman Coulter).
Omni ATAC-Seq

treatment_protocol: Transduction with either non-targeting control or Zfp266 sgRNA

value: Zfp266 KO

value: Reprogramming Cells

value: P2 fibroblasts from E12.5 embryos treated with doxycycline for 72 hours OSKM induction

value: Zfp266 sgRNA


title: Alg1A time point 22

description:
Alg1A_TP22
small RNA-sequencing

source_name: Alg1A time point 22

value: Whole body

value: 22 hr


title: B11

value: Brain


title: hTCEpi, control, rep3

description: sample 03

source_name: hTCEpi

value: hTCEpi

value: telomerase-immortalized human corneal epithelial cells

value: control


title: 72 hours reprogramming, Zfp266-KO, rep2


title: Alg1A time point 21

description:
Alg1A_TP21
small RNA-sequencing

source_name: Alg1A time point 21

value: 21 hr


title: Alg1A time point 20

description:
Alg1A_TP20
small RNA-sequencing

source_name: Alg1A time point 20

value: 20 hr


title: 72 hours reprogramming, Control, rep3

description:
Rep_Zeo.mRp.clN_peaks.broadPeak
Rep_Zeo.mRp.clN_peaks.gappedPeak
Rep_Zeo.mRp.clN.bigWig
Rep_ZeovsRep_Zfp266.mLb.deseq2.FDR0.05.results.bed
Rep_ZeovsRep_Zfp266.mLb.deseq2.FDR0.05.results.txt

source_name: control sgRNA transduced reprogramming cells

value: wild type

value: control sgRNA


title: 72 hours reprogramming, Zfp266-KO, rep1


title: H10

value: Nucleus accumbens

value: Cocaine

value: White

value: male


title: A11


title: Alg1A time point 19

description:
Alg1A_TP19
small RNA-sequencing

source_name: Alg1A time point 19

value: 19 hr


title: 72 hours reprogramming, Control, rep2

value: Reprogramming Cells

value: P2 fibroblasts from E12.5 embryos treated with doxycycline for 72 hours OSKM induction


title: H11

value: Black


title: Alg1A time point 18

description:
Alg1A_TP18
small RNA-sequencing

source_name: Alg1A time point 18

value: Whole body

value: 18 hr


title: E10

value: Brain


title: 72 hours reprogramming, Control, rep1


title: MEF, Zfp266-KO, rep3

description:
MEF_Zfp266.mRp.clN_peaks.broadPeak
MEF_Zfp266.mRp.clN_peaks.gappedPeak
MEF_Zfp266.mRp.clN.bigWig
MEF_ZeovsMEF_Zfp266.mLb.deseq2.FDR0.05.results.bed
MEF_ZeovsMEF_Zfp266.mLb.deseq2.FDR0.05.results.txt

source_name: Zfp266 sgRNA transduced Mouse Embryonic Fibroblasts

value: Zfp266 KO

value: Mouse Embryonic Fibroblasts

value: P2 fibroblasts derived from E12.5 embryos

value: Zfp266 sgRNA


title: N2 time point 30

description:
N2_TP30
small RNA-sequencing

source_name: N2 time point 30

value: WT

value: 30 hr


title: D10

value: Nucleus accumbens


title: N2 time point 29

description:
N2_TP29
small RNA-sequencing

source_name: N2 time point 29

value: 29 hr


title: MEF, Zfp266-KO, rep2


title: N2 time point 28

description:
N2_TP28
small RNA-sequencing

source_name: N2 time point 28

value: 28 hr


title: N2 time point 27

description:
N2_TP27
small RNA-sequencing

source_name: N2 time point 27

value: 27 hr


title: MEF, Control, rep3

description:
MEF_Zeo.mRp.clN_peaks.broadPeak
MEF_Zeo.mRp.clN_peaks.gappedPeak
MEF_Zeo.mRp.clN.bigWig
MEF_ZeovsMEF_Zfp266.mLb.deseq2.FDR0.05.results.bed
MEF_ZeovsMEF_Zfp266.mLb.deseq2.FDR0.05.results.txt

source_name: control sgRNA transduced Mouse Embryonic Fibroblasts

value: wild type

value: control sgRNA


title: MEF, Zfp266-KO, rep1


title: C10

source_name: Brain

value: Cocaine

value: male


title: A10

value: White


title: G10


title: H9


title: N2 time point 26

description:
N2_TP26
small RNA-sequencing

source_name: N2 time point 26

value: Whole body

value: 26 hr


title: F10

value: Brain

value: Black


title: MEF, Control, rep2

value: Mouse Embryonic Fibroblasts

value: P2 fibroblasts derived from E12.5 embryos


title: N2 time point 25

description:
N2_TP25
small RNA-sequencing

source_name: N2 time point 25

value: WT

value: 25 hr


title: G9

value: Nucleus accumbens


title: MEF, Control, rep1


title: F9


title: N2 time point 24

description:
N2_TP24
small RNA-sequencing

source_name: N2 time point 24

value: 24 hr


title: M4RP

city: Chongqing

last: Lu

address: Shi you lu street

country: China

institute: Chongqing medical university

data_processing:
The raw data were filtered with SOAPnuke v.1.5.2.The clean reads were mapped to the reference genome using HISAT2v.2.0.4. Bowtie2 v.2.2.5 was applied to align the clean reads to the geneset, a database built by BGI-Shenzhen, and the expression levels of the genes were calculated with RSEM v.1.2.12. Differential expression analysis was performed using DESeq2(v1.4.5)
Supplementary files format and content: mm10
Supplementary files format and content: FPKM for each Sample

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: mPFC

value: CUS model


title: R14RP

value: running model


title: R2RP


title: M9RP


title: N2 time point 23

description:
N2_TP23
small RNA-sequencing

source_name: N2 time point 23

value: 23 hr


title: R4RP


title: C7RP

value: control


title: B10

value: Cocaine

value: male


title: M5RP


title: N2 time point 22

description:
N2_TP22
small RNA-sequencing

source_name: N2 time point 22

value: Whole body

value: 22 hr


title: WT.2_NC

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

country: Spain

institute: Universitat de Valencia

description: IP_RNA from Non-Crosslinked untagged control cells. Replicate 2

data_processing:
Read file QC: Total reads were analysed with FastQC and visually inspected to make sure each sequenced sample met the adequate quality standards.
Adapter clipping, quality trimming and filtering: Cutadapt and Trimmomatic were used to remove Illumina adapters, filter reads shorter than 20 bases, and discard the ones with more than 30 Ns.
Genome alignment: Filtered reads were mapped to the mouse genome with HISAT2 using the Mus musculus GRCm38 (mm10) genome as reference
Read count extraction: Raw read counts were extracted with the featureCounts tool from the R package Rsubread using the mouse genome version M16 (Ensembl 91) annotation as a reference.
Filtering by expression and normalization: Genes with less than 1 count per million (CPM) in at least 4 of the samples were filtered out and remaining genes were normalised with Voom.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text file containing the filtered and Voom-normalised read count matrix

source_name: mouse brain NSC cultures

growth_protocol: Neurosphere cells derived form adult SEZ samples were cultured and mantained under non-adherent conditions and mitogenic stimulaton (EGF and FGF). Cells were passaged every 4-5 days and seeded at 1 x 10e4 cells/cm2

extract_protocol:
After IP, dynabeads were incubated with 70 µg Proteinase K in agitation for 30 min at 42 °C and then for 30 min at 60 °C. Inputs and native IP samples were also treated with Proteinase K following the previous guidelines. Total RNA was extracted with RNeasy® Plus Micro kit, following the manufacturer’s instructions.
RNA from RIP were used to construct libraries for sequencing with the TruSeq® Stranded mRNA Library Prep Kit, using the Dual index Nextera XT v2 Set A Adapters. Since RNA was already enriched due to IP, no purification and fragmentation steps were needed for library preparation, thus only random hexamers and not poly-T oligos were used during the process.

treatment_protocol: Endogenous MEX3A was immunoprecipitated in FLAG-tagged NSC cultures (Mex3aFLAG/FLAG). Wild-type cultures from the same background that did not express the knock-in FLAG sequence were used as controls for nonspecific binding.

value: brain subependymal zone

value: 10 weeks

tag: cells

value: adult NSC cultures


title: D9

value: Brain

value: White


title: E9


title: WT.2_C

description: IP_RNA from Crosslinked untagged control cells. Replicate 2


title: C9


title: WT.1_NC

description: IP_RNA from Non-Crosslinked untagged control cells. Replicate 1


title: N2 time point 21

description:
N2_TP21
small RNA-sequencing

source_name: N2 time point 21

tag: strain/background

value: WT

value: 21 hr


title: C12RP


title: N2 time point 20

description:
N2_TP20
small RNA-sequencing

source_name: N2 time point 20

tag: time point

value: 20 hr


title: WT.1_C

description: IP_RNA from Crosslinked untagged control cells. Replicate 1


title: N2 time point 19

description:
N2_TP19
small RNA-sequencing

source_name: N2 time point 19

value: 19 hr


title: B9

value: Nucleus accumbens


title: A9

value: Control

value: Black


title: Flag.3_NC

description: IP_RNA from Non-Crosslinked cells carrying a Flag-tagged Mex3a. Replicate 3


title: WT.3_NC

description: IP_RNA from Non-Crosslinked untagged control cells. Replicate 3


title: H8


title: N2 time point 18

description:
N2_TP18
small RNA-sequencing

source_name: N2 time point 18

value: 18 hr


title: Flag.2_NC

description: IP_RNA from Non-Crosslinked cells carrying a Flag-tagged Mex3a. Replicate 2


title: A549_siTILR_rep3

type: RNA

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

hyb_protocol: 300 ng of Cy5-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) and Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) were fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K v2 Microarrays (G4851B) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: SurePrint G3 Human GE 8x60K v2 Microarray with 60k distinct probes was scanned using an Agilent DNA microarray scanner (G2539A, Agilent Technologies). Images were quantified using Agilent Scan Control Software (version 10.7.1.1. or 10.10.1.1).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from ratio of processed Red signal/processed Green signal using Agilent Scan Control Software (version 10.7.1.1. or 10.10.1.1).

source_name: A549 cells were transfected with siTILR, replicate 3

label_protocol: Cy5-sample cRNA and Cy3-sample cRNA were generated and hybridized to a SurePrint G3 Human GE 8x60K v2 Microarray kit (Agilent Technologies) with 60k distinct probes.

growth_protocol: A549 cells were cultured with 10% (v/v) FBS-containing RPMI 1640 at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 100 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

treatment_protocol: A549 cells were transfected with siRNAs and incubated for 72h before harvest

value: mixture of 20 cell ines


title: Flag.1_NC

description: IP_RNA from Non-Crosslinked cells carrying a Flag-tagged Mex3a. Replicate 1


title: C24RP

value: mPFC

value: control


title: E8

value: male


title: F8


title: Flag.1_C

description: IP_RNA from Crosslinked cells carrying a Flag-tagged Mex3a. Replicate 1

value: brain subependymal zone


title: D8


title: Balb-NeuT overexpression p140Cap mouse cell line 2

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
Trimming adapters with skewer v0.2.2
Mapping with STAR (v2.5) against mm10
Gene level counts done with RSEM v0.1.1 and ENSEMBL mm10 annotation v86
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited counts file

source_name: Balb-NeuT  cell line over expressing p140Cap

growth_protocol: As described in Rovero et al J. Immunol. 165, 5133–5142 (2000)

extract_protocol:
Trizol following manufacturer indication
Ilumina Trueseq plolyA selected RNAseq, following manufacturer indications

treatment_protocol: To over-express p140Cap into TuBo cells, p140Cap cDNA was cloned into pBabe-puro. The retroviruses particles, for 4T1 cells were produced by exploiting the Lipo2000 (ThermoFisher Scientific) transfection of Platinum Retroviral Packaging Cell Lines (Cell BioLabs), in 6 mm dishes. 48 h after transfection, supernatants that contained the retrovirus particles were collected and added directly to subconfluent cells, cultured in 6-well plates. After 48 h, cells were washed and cultured with a selection medium containing puromycin (Sigmaaldrich) at a final concentration of 1 mg/ml. The efficiency of infection was controlled by western blot and immuno-fluorescence analysis. Cells were then cultured at a single cell level in four 96-well adherent multiwell plates (Corning). Individual p140Cap expressing clones were isolated 20 days after the start of the selection, by assessing the p140Cap expression through western blot and immunofluorescence.

value: breast tumor

value: Balb-NeuT

value: overexpressing p140Cap


title: B8

value: Brain


title: Balb-NeuT overexpression p140Cap mouse cell line 3


title: Balb-NeuT overexpression p140Cap mouse cell line 1


title: A549_siTILR_rep1

source_name: A549 cells were transfected with siTILR, replicate 1


title: Balb-NeuT control mouse cell line 3

source_name: Balb-NeuT wt cell line

value: wt


title: A8

value: White


title: A549_siControl_rep3

source_name: A549 cells were transfected with siControl, replicate 3


title: A549_siControl_rep2

source_name: A549 cells were transfected with siControl, replicate 2


title: Balb-NeuT control mouse cell line 2


title: G7

source_name: Brain


title: Balb-NeuT control mouse cell line 1


title: F7


title: 6H_T3_mRNA_seq

city: Shanghai

first: Huiming

address: No. 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

data_processing:
we download the genome and the annotation files from the NCBI genebank database(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/072/605/GCA_003072605.1_ASM307260v1/).
The genebank format of gene annotaion file will be convert to the .ptt file format by script gb2ppt.pl. The raw fastq data  is preprocessed by trimmomatic (version 0.36).
Then, the clean reads   will executed bacteria RNAseq data analysis by  Rockhopper(version 2.04).
Q-value which is lower than 0.01 identified as DEGs(differential expression genes).
Genome_build: YC4_R4 Bacteria genome
Supplementary_files_format_and_content: tab-delimited text files include genes expression values and DEGs

organism: Priestia megaterium

source_name: 6-hours-growth bacteria in LB

growth_protocol: Bacteria cells were growth from OD 600nm=0.1 in flask filled upt to 50 mL of LB during 6 h with continuous agitation (150 rpm) at 30ºC

extract_protocol:
Bacteria RNA samples were extracted by using RNeasy Protect Bacteria Mini Kit (Qiagen).
An aliquot with 1 μg of total RNA per sample was used for library preparation with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7420L) following the manufacturer’s instructions. All library preparation and subsequent sequencing processes were performed at the Core Facility of Genomics at Shanghai Center for Plant Stress Biology.

treatment_protocol: Bacteria were growth in LB (mock) or LB supplemented with 5 mM myo-inositol (treated) from a pre-inoculum prepared in just LB broth

value: Treated with myo-inositol

value: wild type

value: full cell


title: E7

value: Nucleus accumbens

value: Control


title: Flag.2_C

description: IP_RNA from Crosslinked cells carrying a Flag-tagged Mex3a. Replicate 2

value: 10 weeks

value: adult NSC cultures


title: D7


title: 6H_T2_mRNA_seq


title: C7


title: 6H_T1_mRNA_seq


title: A549_siControl_rep1

source_name: A549 cells were transfected with siControl, replicate 1

value: mixture of 20 cell ines


title: C8


title: 6H_C3_mRNA_seq

value: Regular


title: B7

value: male


title: Postnatal OPC rep 4

city: Edmonton

first: Anastassia

last: Voronova

state: Alberta

address: 8-43A Medical Sciences Building

department: Medical Genetics

country: Canada

institute: University of Alberta

description: 20 millions reads

data_processing:
Quality assessment was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
We then used STAR (https://github.com/alexdobin/STAR) to generate a Genome Index to align the sequenced reads to the reference genome (M25 release, GRCm38).
Aligned reads were sorted by coordinate as .BAM files, and raw counts were extracted using featureCounts version 1.22.2 from the Rsubread software package (https://www.rdocumentation.org/packages/Rsubread/versions/1.22.2/topics/featureCounts)
Column names were adjusted to match convention used in manuscript (aNSC, pNSC, pOPC) and raw counts matrix was exported as a .txt file
Assembly: M25 release, GRCm38
Supplementary files format and content: tab delimited file, rows are raw counts for each Ensembl gene ID, columns each biological replicate

source_name: Brain subventricular zone

growth_protocol: Neural stem cells were cultured as neurospheres for 6-7 days in serum-free media supplemented with 2% B27, 10 ng/mL FGF, 20 ng/mL EGF, and 2 ug/mL heparin. Oligodendrocyte precursor cells were generated from primary neurospheres by dissociating and plating primary neurosphere cells as monolayer in serum-free media, 2% B27, 10 ng/mL FGF, and 10 ng/mL PDGF-AA for 2 days. See associated publication for detailed description of culture protocol

extract_protocol:
RNA extraction was performed using the OMEGA Biotek EZNA Total RNA or MicroElute RNA kit according to manufacturer’s instructions.
RNA was assessed by Fragment Analyzer, and high quality total RNA (RIN > 9.9) was subjected to library preparation using the Illumina TruSeq Stranded mRNA Library Preparation Kit (Cat# 20020594) according to the manufacturer’s instructions. Library fragment size was checked using an Agilent Fragment, and then quantified with qPCR using Collibri™ Library Quantification Kit (A38524500, ThermoFisher) on a BioRad CFX96 Touch Real-Time PCR Detection System. Real-time base call (.bcl) files were converted to FASTQ files using Illumina bcl2fastq2 conversion software

treatment_protocol: None (see published associated article for more details)

value: Brain subventricular zone

value: Primary

value: Oligodendrocyte precursor cell


title: Postnatal OPC rep 3

description: 20 millions reads


title: A7

value: Black


title: A549_siTILR_rep2

source_name: A549 cells were transfected with siTILR, replicate 2


title: 6H_C2_mRNA_seq


title: Postnatal OPC rep 2

description: 20 millions reads


title: 6H_C1_mRNA_seq


title: rdd_T3_mRNA_seq

data_processing:
the raw data is preprocessed by trimmomatic (version 0.36).
The clean reads were aligned to the TAIR 10 reference genome using hisat2 (version 2.1.0) with parameters "--rna-strandness RF -p 30 --dta”.
Reads_count matrix was produced by htseq-count (version 0.9.1).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each Sample

organism: Arabidopsis thaliana

source_name: 2-week-old plants grown in soil

extract_protocol:
Plant RNA samples were extracted by using the RNeasy RNA extraction Plant Mini Kit (Qiagen).
An aliquot with 1 μg of total RNA per sample was used for library preparation with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7420L) following the manufacturer’s instructions. All library preparation and subsequent sequencing processes were performed at the Core Facility of Genomics at Shanghai Center for Plant Stress Biology.

value: Treated with YC4-R4 in soil

value: rdd triple mutant in Col-0 background

value: full plants


title: Postnatal OPC rep 1

description: 20 millions reads


title: G6

value: Brain


title: F6

value: White


title: Adult NSC rep 4

description: 20 millions reads

value: Neural stem cell

value: 2 months


title: rdd_T2_mRNA_seq


title: rdd_T1_mRNA_seq


title: Adult NSC rep 3

description: 20 millions reads


title: E6

value: Caudate nucleus

value: Cocaine


title: G8

value: Nucleus accumbens

value: Control


title: H6


title: Adult NSC rep 2

description: 20 millions reads


title: CHP212, Nutlin, replicate 2

description: sgRNA cassette amplicon

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the HiSeq 2500 Real-Time Analysis (RTA) software (Illumina)
Conversion to FASTQ format was carried out using bcl2fastq (v1.8.4, Illumina)
Samples were demultiplexed using fastx_barcode_splitter from the fastx_toolkit (v0.0.13.2), allowing 2 mismatches
FASTQC v0.11.2 was used to assess sequence data quality
Sequences were trimmed using fastx_trimmer from the fastx_toolkit (v0.0.13.2), with the following options: -Q33 -f 43 -l 62. This keeps only the section of each read corresponding to the unique sgRNA sequences (positions 43-62 inclusive)
Bases with qual ≥10 were removed with fastx_quality_filter from the fastx_toolkit (v0.0.13.2), with the following options: -Q33 -q 10 -p 94.
Trimmed and filtered sequences were mapped with Bowtie2 v2.2.3 using the following options (--phred33 --end-to-end --very-sensitive)
Genome_build: A reference index was generated for Bowtie2 using only the unique sgRNA sequences from the Human GeCKOv2 library annotation available from https://media.addgene.org/cms/filer_public/7d/87/7d87eaa7-e940-41bf-bf2f-47b43c7ab905/zhang_human_geckov2_grna_sequences.zip (PMID: 24336571; PMID: 25075903)
Supplementary_files_format_and_content: Tab delimited text files containing raw sgRNA counts for each sample

source_name: CHP212 cells

growth_protocol: CHP212 cells were cultured in DMEM:F12 supplemented with 10% fetal bovine serum and 1x antibiotic/antimycotic and were maintained at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Cells were transduced with the GeCKOv2 Library A and Library B, selected with puromycin, and allowed to recover for 10 days to exclude cells with CRISPR-mediated edits in essential genes
In triplicate, cells were treated with either 0.2% DMSO or 10 uM Nutlin-3a for 48 hours. DMSO treated cells were collected for DNA extraction, while Nutlin-treated cells were allowed to recover. Next, Nutlin-treated cells underwent another round of Nutlin treatment and recovery followed by sample collection for DNA extraction.
Genomic DNA was extracted using a DNeasy Blood and Tissue kit (Qiagen)
Custom

value: Neuroblastoma

tag: gecko library

value: HGLibA and HGLibB

tag: culture condition

value: 48h 10 uM Nutlin-3a, recovery, 48h 10 uM Nutlin-3a


title: Adult NSC rep 1

description: 20 millions reads

value: Brain subventricular zone

value: Primary


title: D6

tag: brain region

value: male


title: rdd_C2_mRNA_seq

value: Regular


title: rdd_C3_mRNA_seq

value: rdd triple mutant in Col-0 background


title: CHP212, Nutlin, replicate 1

description: sgRNA cassette amplicon


title: Postnatal NSC rep 3

description: 37 million reads


title: C6

tag: group

value: Black


title: rdd_C1_mRNA_seq

value: full plants


title: Col-0_T3_mRNA_seq

value: Treated with YC4-R4 in soil

value: wild type Col-0


title: Postnatal NSC rep 4

description: 37 million reads

value: Neural stem cell


title: CHP212, Nutlin, replicate 3

description: sgRNA cassette amplicon


title: CHP212, DMSO, replicate 2

description: sgRNA cassette amplicon


title: Postnatal NSC rep 2

description: 37 million reads


title: H5

value: Brain

value: Caudate nucleus

tag: race


title: Col-0_T2_mRNA_seq


title: B6

value: Cocaine

value: White

tag: Sex


title: CHP212, DMSO, replicate 1

description: sgRNA cassette amplicon

value: Neuroblastoma


title: CHP212, DMSO, replicate 3

description: sgRNA cassette amplicon

value: HGLibA and HGLibB


title: G5

tag: age


title: Col-0_T1_mRNA_seq


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 325 AG019_NS500289

first: Annemieke

last: de Jong

email: ad2952@cumc.columbia.edu, mongaisha4@gmail.com, im2569@cumc.columbia.edu, gwennaelle.monnot@gmail.com

address: 1150 st. Nicholas Avenue

department: Department of Dermatology

institute: Columbia University Irving Medical Center

description:
CD1a-lysylPG tetramer+ CD4+ T cells from donor 325
all_plates_umi_counts_325.csv
Single-cell RNAseq-Donor_325

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
In Bulk RNA-seq files, the trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.BAM files were generated as a result of this step.  In the case of single-cell RNA sequencing, during alignment, reads with more than one mapping were recorded as unmapped using the arguments ‘--outFilterMultimapNmax 1’ and ‘--outSAMunmapped Within’. Alignment counts were generated using Subread’s featureCounts (version 1.6) with default parameters. Reads were assigned to cell and unique molecular indicator (UMI) barcodes using UMI-tools. Rest single-cell data was analyzed using Seuratv4.
For bulk RNAseq, unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. These hit counts were used to perform downstream differential gene expression, and pathway analyses. The differential gene expression analysis was performed by using the  DESeq2 package in Bioconductor. Differential gene expression analysis was performed on the batch corrected data set based on the negative binomial distribution using a significance of FDR<0.05 comparing  Normal control cohort to the each kind of PCA subtype. For single-cell analysis, genes expressed in <3 cells were removed from the analysis, as well as cells that had <200 genes expressed. Moreover, cells that had a total UMI count of less than 200 or more than 5000 or a percentage of mitochondrial reads higher than 11% were removed from the analysis. Contaminating APCs forming a separate cluster and overexpressing DCs markers were also removed from the analysis. The datasets from two donors were merged using Seurat V4 methods of anchoring, and clusters were computed using the “FindClusters” Seurat function. Data was normalized using the Normalizedata function and scaled using the ScaleData function. Logistic regression differential expression test was used via the "FindMarkers" function in Seurat. For data representation, RunPCA and RunUMAP functions were used, as well as DoHeatmap
Gene count files obtained as txt files, UMI counts as csv and DEseq2 in csv format.
Genome_build: GRCh38

source_name: PBMCs

growth_protocol: For both bulk and single-cell sequencing,PBMCs were isolated using Ficoll-paque (GE lifesciences - 17-5442-02) and following manufacturer’s instruction. PBMCs were cryopreserved in FBS supplemented with 10% dimethyl sulfoxide (DMSO) and stored in liquid nitrogen.

extract_protocol:
Reverse transcription was performed by adding 7.5 μl of RT mix to each well [containing: 40U Maxima H- (Thermo Fisher Scientific), 2X Maxima H- Buffer (Thermo Fisher Scientific), 4U SUPERaseIN (Thermo Fisher Scientific), 15% polyethylene glycol, 2µM Template Switching Oligo (Integrated DNA Technologies)]. Further sample processing and library preparation was performed by the Single Cell Analysis Core of Columbia University according to published protocol.
For bulk RNAseq, RNA sequencing library preparation used the NEBNext Ultra RNA Library Prep Kit for Illumina by following manufacturer’s recommendations (NEB, Ipswich, MA, USA). The samples were sequenced using a Illumina HiSeq 2x150 Paired End (PE) configuration. The single-cell RNA libraries were prepared for sequencing using Illumina NextSeq 500 using the 75-cycle High Outpit Kit [read lengths 26(R1) × 8(i) × 58(R2)].

treatment_protocol: For single-cell RNAseq, PBMCs were thawed and rested overnight at 37°C. The next day, cell stimulation cocktail (eBioscience 00497003) was added to the cells for 2.5 hours before staining as described in tetramer staining. The gating strategy included: lymphocyte gate, gating out of doublets, dead cells, CD14+, CD19+ cells, and positive selection for CD3+ CD4+. Individual tetramer+ and tetramer- CD4+ T cells were sorted with a BD Influx analyzer into the wells of a 96-well plate, each containing 7.5 µl of lysis buffer [0.2% Triton X-100 (Sigma), SUPERaseIN (1 U/μl) (Thermo Fisher Scientific), 2 mM deoxyribonucleotides (dNTPs) (Thermo Fisher Scientific), and 2 μM reverse transcriptase (RT) primer (Integrated DNA Technologies)]. Primer annealing was performed at 72°C for 3 min.  For bulk RNA sequencing, T cell lines were either untreated (unstim) or treated for 6 hrs with anti-CD3/CD28 before RNA was extracted using RNAeasy

value: PBMC-derived CD4+ T cells


title: adult_int_rna_eedko_rep2

city: Toronto

first: Tae-Hee

last: Kim

state: Ontario

address: 686 Bay St.

department: Development and Stem Cell Biology

institute: The Hospital for Sick Children

data_processing:
read trimming with trimmomatic v0.32: PE ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:15:true HEADCROP:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:5:20 MINLEN:36
alignment with STAR v2.5.1b: --runThreadN 16 --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 8000000000 --twopassMode Basic --outWigType bedGraph --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3
counting with featureCounts v1.5.0: -a gencode.vM4.annotation.SIRVome_isoforms_ERCCs_C_170612a.gtf -g gene_name -p -s 0 -C --donotsort
Assembly: mm10 / GENCODE.vM4 with ERCCs_C_170612a
Supplementary files format and content: featureCounts outputs for gene level counts

source_name: intestinal mesenchyme

extract_protocol:
RNeasy Plus micro kit (74034, QIAGEN)
NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® NEB #E6420

value: intestinal mesenchyme

value: EED-KO


title: F5

institute: Icahn School of Medicine at Mount Sinai

value: male

tag: pmi


title: Col-0_C3_mRNA_seq

last: Zhang

value: Regular

tag: genotype


title: E5


title: adult_int_rna_eedko_rep1


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 325 AG019_NB551203

tag: cell type


title: Col-0_C2_mRNA_seq


title: adult_int_rna_wt_rep2

value: WT


title: A6

value: Black


title: D5


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 325 AG018_NS500289


title: Col-0_C1_mRNA_seq

value: full plants


title: adult_int_rna_wt_rep1


title: rdd_T_BS

data_processing:
For the WGBS libraries, the sequence reads were mapped to the naturally unmethylated chloroplast genome of Arabidopsis using BSMAP to evaluate the bisulfite non-conversion rate. The libraries with non-conversion rates < 1% were retained for further analysis.
Adapters and low-quality bases in the WGBS reads were trimmed by cutadapt and SolexaQA.
Subsequently,the trimmed reads were unique mapped to each corrected pseudo-reference genome by BSMAP. After filtering the duplicate reads, the methylation information for each cytosine site was extracted and only sites that covered more than four mapped reads were considered. In the binomial test, the non-conversion rate was used as the expected probability.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig file

growth_protocol: Col-0 and rdd triple mutant were grown in half MS medium for 5-6 days and transferred to soil for treatment in a growth room (22°C, 16h light/8h dark).

extract_protocol:
Genomic DNA samples from Col-0 and rdd plants with and without bacterial treatment of YCR-R4 inoculation were extracted by using the DNeasy DNA extraction Plant Mini Kit (Qiagen).
An aliquot with 1 μg of DNA per sample was used for library preparation with NEBNext Ultra II DNA Library Prep Kit for Illumina® (New England BioLabs, E7645L) and Epitect Plus DNA Bisulfite Kit (Qiagen, Cat. No. 59124). All library preparation and subsequent sequencing processes were performed at the Core Facility of Genomics at Shanghai Center for Plant Stress Biology.

treatment_protocol: Seedlings were transferred to soil for 24 hr, and then inoculated with 50 mL of 107–108 CFU/mL bacterial inoculum per soil pot. Bacteria-free 0.45% NaCl saline solution was used for the mock control.

value: Treated with YC4-R4 in soil

value: rdd triple mutant in Col-0 background


title: C5


title: Postnatal NSC rep 1

description: 37 million reads

tag: strain

value: Brain subventricular zone

value: Primary

value: Neural stem cell


title: Lyz2Cre+/+Ctnnb1exon3del/wtYFP+/- Alveloar Macrophages 3

city: Buffalo

first: Elliot

middle: David

last: Kramer

address: 665 Elm St

department: Immunology

institute: Roswell Park Comprehensive Cancer Center

description: Triple 3

data_processing:
First pass base pairs quality control (QC) was performed using fastqc (v0.10.1)
Spliced alignment was done using Bowtie (v1.0.1) and TopHat (v2.0.13), allowing a maximum of 1 mismatch per read
Read counts were extracted with HTSeq (v0.9.1) using intersection-strict option.
Differential expression analyses were performed using DESeq2 (v1.32.0)
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes raw counts for all samples

source_name: Lung

growth_protocol: Live singlet CD45+Ly6G-SSChiCD11c+Lyz2-YFPhi alveolar macrophages were isolated by fluorescence-activated cell sorting from the whole dissociated lungs of Lyz2Cre+/+YFP+/- (YFPCtr) and Lyz2Cre+/+Ctnnb1exon3del/wtYFP+/- (Triple) mice in biological triplicate

extract_protocol:
Total RNA was extracted using the miRNeasy mini kit (Qiagen). 5 ng of total RNA was used for the construction of sequencing libraries.
Illumina compatible NGS libraries were generated using the SMARTer Stranded v2 Ultra Pico Input Total RNA Seq kit (Clonetech) following manufacturer's protocols.

value: Lung

value: Alveolar macrophage


title: B5

city: New York

value: Brain

value: Caudate nucleus

value: Cocaine

value: White