title: mouse_MCM2ChEC_rep3B

description:
hybrid musculus / spretus mouse (Patski) cells with MCM2-Mnase construct
MCM2 binding sites in hybrid musculus / spretus mouse determined by MCM2-ChEC in cells grown to confluence

organism: Mus musculus x Mus spretus

tag: sample type

value: calcium-treated DNA (ChEC)


title: Sperm_methylation_infected_Rep10

status: Public on Aug 26 2021

type: SRA

city: Saarbrücken

first: Kathrin

last: Kattler-Lackes

state: non-US Resident

address: Campus A2.4 Raum 0.13

department: Epigenetics

country: Germany

institute: Saarland University

library_source: genomic

data_processing:
Raw fastq files were quality controlled with FastQC (http://www.bioinformatics.bbsrc. ac.uk/projects/fastqc/) and subsequently processed using the DEEP pipeline for RRBS.
Reads were first trimmed with the cutadapt wrapper Trim Galore! and then mapped with the bwa wrapper MethylCtools58.
Alignments were manipulated and filtered with Picardtools (“Picard Tools - By Broad Institute” 2017) and samtools.
After realignment and recalibration, methylation calls were made with Bis-SNP (bed files). Reference SNPs and InDels from dbSNP v138 (http://www.ncbi.nlm.nih.gov/SNP) were used in this process.
Genome_build: mm10
Supplementary_files_format_and_content: bed files with methylation calls and corresponding CpG coverage

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
DNA from sperm of 10 isogenic control males and 10 infected was isolated.
comprehensive HaeIII restriction based RRBS (reduced representation bisulfite sequencing)

treatment_protocol: Male mice were infected with subletal dose of C. albicans. One month after clearance of the infection, ‘resting’ (mock-infected with PBS, F0R) and the ‘trained’ (C. albicans-infected and recovered, F0T) mice were mated with healthy non-infected females.

tag: infection

value: C. albicans

tag: cell type

value: Sperm


title: D283_VC_rapamycin

city: Navi Mumbai

first: Neelam

middle: V

last: Shirsat

state: Maharashtra

address: Kharghar, Sector 21

department: Shirsat Lab

country: India

institute: Advanced Centre for Treatment, Research and Education in Cancer. Tata Memorial Centre

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2 was used for base calling
The fastq data was aligned to the Human genome GRCh37-hg19 assembly using HISAT2 aligner
HTseq algorithm was used to derive the raw count of the number of reads per transcript from the aligned sequence file in the BAM format
DESeq2 algorithm was used for normalization of the HTSeq count data using the variance stabilized transformation as well as for identifying genes differentially expressed upon miR-592 expression.
Genome_build: GRCh37-hg19
Supplementary_files_format_and_content: tab-delimited text files containing counts per gene normalized using the variance stabilized transformation

molecule: total RNA

organism: Homo sapiens

source_name: Medulloblastoma cell line

growth_protocol: D283, D425, HD-MB03 cell lines and their polyclonal populations expressing miR-592 in a doxycycline-inducible manner were grown in Dulbecco's Modified Eagle's Medium/F12  medium containing 10% fetal bovine serum at 37 °C in a CO2 incubator.

extract_protocol:
Total RNA was extracted using Qiagen RNAeasy mini kit as per manufacturer's protocol.
Libraries were prepared from Poly-A enriched fraction of total RNA using the Ilumina TruSeq RNA library preparation kit version 2.0
The libraries were sequenced in a 100 nucleotide single-end read run on the Illumina Hiseq platform

treatment_protocol: The cells were treated with 1 µg/ml doxycycline for 72 h for the induction of miR-592 expression

tag: cell line

tag: disease

value: Group 3 medulloblastoma

tag: genotype/treatment

value: vector control treated with rapamycin


title: PTCL_Sample 1

type: RNA

city: Madrid

first: Laura

middle: Jiménez

last: Tomas Roca

state: Madrid

address: Avenue Reyes Catolicos

department: Pathology Department

country: Spain

institute: Research Institute Fundacion Jimenez Diaz

hyb_protocol: Briefly, 208 genes and eight housekeeping gene probes (Supplemental Table 2) were hybridized to 400 ng of the total RNA for 16 h at 65°C, and applied to the nCounter Preparation Station for automated removal of excess probe and immobilization of probe–transcript complexes on a streptavidin-coated cartridge

scan_protocol: Non applicable

data_processing: Gene expression values were normalized through housekeeping genes. Normalized count data were log2 transformed and agglomerative hierarchical clustering of gene expression were performed

label: Non applicable

source_name: Peripheral T-cell lymphoma

label_protocol: Non applicable

extract_protocol: RNA quality and quantity were assessed with an RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA) using the TapeStation Systems (Agilent Technologies, Santa Clara, CA, USA)

treatment_protocol: Formalin-fixed, paraffin-embedded

tag: tissue

value: Peripheral T-cell lymphoma

tag: age

value: Adult


title: D283_VC

value: vector control


title: Sperm_methylation_infected_Rep9


title: mouse_MCM2ChEC_rep3A

city: Seattle

first: Eric

middle: Jan

last: Foss

state: WA

address: 1100 Fairview Ave N

department: Clinical Research Division

country: USA

institute: Fred Hutchinson Cancer Research Center

description:
hybrid musculus / spretus mouse (Patski) cells with MCM2-ChEC construct
MCM2 binding sites in hybrid musculus / spretus mouse determined by MCM2-ChEC in cells grown to confluence

data_processing:
align using bwa with -n option set to 1; reads that map to more than one location are arbitrarily assigned to one of those locations; in case of mouse, align to both the standard mm10 genome build and to mm10 genome with single nucleotide substitutions from spretus genome (provided here as a fasta file)
picard CleanSam
picard SortSam
picard FixMateInformation
picard AddOrReplaceReadGroups
picard ValidateSamFile
choose only (1) perfect matches to mm10 that do not have perfect matches to mm10musculusSNPStospretusSNPs (musculus); or (2) perfect matches to mm10musculusSNPStospretusSNPs that do not have perfect matches to mm10 (spretus); or (3) restrict fragment length (TLEN designation in sam file format) to appropriate size range, if called for
calculate per-base-pair coverage with BedTools' genomecov with -d and -split options
Genome_build: mm10 (musculus); sacCer3 (S. cerevisiae); mm10 with single nucleotide substitutions from spretus SPRET_EiJ (spretus); Schizosaccharomyces_pombe_ASM294v2 (S. pombe); hg38 (human)
Supplementary_files_format_and_content: bedgraph files or txt files with coverage for single base pairs or intervals, as indicated; 1 fasta format file with musculus genome, except with single nucleotide substitution differences replaced with spretus sequence

source_name: Antonio Bedalov

growth_protocol:
Yeast: All S. cerevisiae strains were in S288C background. S. cerevisiae experiments were carried out using standard YPD (yeast peptone dextrose) medium [2% (wt/vol) glucose, 1% yeast extract, 2% (wt/vol) peptone]. S. pombe experiments were carried out in Yeast Extract Dextrose (YES); logarithmically growing cells were arrested in early S-phase by adding 15 mM hydroxyurea and incubating for 3 hours.
Mammalian: Cells were transduced with lentiviral supernatant containing plx302-MCM2-FL-MNase, infected cells were selected out on Puromycin (2.5μg/ml) and expanded for further experiments. The expression of tagged MCM2 in HeLa and Patski cells was confirmed by Western blot using anti- MCM2 rabbit polyclonal antibody (HPA031495 Sigma) at 1:1,000 dilution.

extract_protocol: as described:  Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S. Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A. 2011;108(45):18318-23. Epub 2011/10/26. doi: 1110731108 [pii]10.1073/pnas.1110731108. PubMed PMID: 22025700; PubMed Central PMCID: PMC3215028.

treatment_protocol:
Yeast MNase-seq: Cells grown to log phase in rich medium, Yeast Peptone Agar with 2% glucose (YEPD) for S. Cerevisiae or Yeast Extract with Supplements with 3% glucose (YES), from an overnight 25 mL culture were synchronized with 3 μM alpha-factor for 1.5 hrs. at 30° C (S. cerevisiae) or with 15 mM hydroxyurea for 2 hours in S. pombe, which are the same conditions we used to prepare cells for ChEC. Arrested cells were crosslinked with 1% formaldehyde for 30 min at room temperature water bath with shaking. Formaldehyde was quenched with 125 mM glycine and cells were centrifuged at 3000 rpm for 5 min. Cells were washed twice with water and resuspended in 1.5 mL Buffer Z (1 M sorbitol, 50 mM Tris-HCl pH 7.4) with 1 mM beta-mercaptoethanol (1.1 μL of 14.3 M beta-mercaptoethanol diluted 1:10 in Buffer Z) per 25 mL culture. Cells were treated with 100 μL 20 mg/mL zymolyase at 30° C for 20–30 min depending on cell density. Spheroplasts were centrifuged at 5000 rpm for 10 min and resuspended in 5 mL NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2) supplemented with 500 μM spermidine, 1 mM beta-mercaptoethanol and 0.075% NP-40. Nuclei were aliquoted in tubes with varying concentrations of micrococcal nuclease (Worthington), mixed via tube inversion, and incubated at room temperature for 20 mins. Chromatin digested with 1.9 U– 7.5 U micrococcal nuclease per 1/5th of spheroplasts from a 25 mL culture yielded appropriate mono-, di-, tri- nucleosome protected fragments for next-generation sequencing. Digestion was stopped with freshly made 5x stop buffer (5% SDS, 50 mM EDTA) and proteinase K was added (0.2 mg/ml final concentration) for an overnight incubation at 65° C to reverse crosslinking. DNA was extracted with phenol/chloroform and precipitated with ethanol. Micrococcal nuclease digestion was analyzed via gel electrophoresis prior to proceeding to library preparation.
Yeast MCM-MNase: In budding yeast, ChEC-seq was carried out as previously described [33]. Fission yeast with MNases-tagged MCM2 were transferred from log phase to 15 mM HU for 3 hours, and then processed as in budding yeast. Two biological replicas were prepared for each genotype.
Mammalian MCM-MNase: Cells were grown in 6 well plates until >100% confluent, trypsinized and washed with a Wash Buffer (20mM HEPES, 110mM Potassium Acetate, 5mM Sodium Acetate, pH to 7.3 with NaOH). Cells were permeabilized with 0.02% digitonin in the Wash Buffer along with protease inhibitors (Roche # 04693159001) for 5 mins at RT. CaCl2 was added to a final concentration of 2.5mM for differing amounts of time, as indicated. The MNase activity was stopped by adding equal volume of a 2X Stop Buffer (400mM NaCl, 20mM EDTA, 4mM EGTA, 2% SDS). Proteinase K was added to a final concentration of 0.4mg/ml and samples incubated for 1 hr at 50° C. DNA was isolated using standard Phenol:Chloroform extraction and air dried DNA pellets resuspended in 0.1X TE (pH 8). All samples were treated with RNase A (0.3 μg/ml) before being processed for library preparation. Two biological replicas were prepared for both human and mouse cells.
Mouse replication: Patski cells were stained with propidium iodine and sorted according to DNA content into G1 and S-cells using flow cytometry. DNA was extracted from each cell fraction, fragmented by sonication and sequenced.

tag: treatment


title: HD-MB03_shCRX2

data_processing:
Illumina bcl2fastq2 was used for base calling
The fastq data was aligned to the Human genome GRCh37-hg19 assembly using HISAT2 aligner
HTseq algorithm was used to derive the raw count of the number of reads per transcript from the aligned sequence file in the BAM format
DESeq2 algorithm was used for normalization of the HTSeq count data using the variance stabilized transformation as well as for identifying genes differentially expressed upon the shRNA expression.
Genome_build: GRCh37-hg19
Supplementary_files_format_and_content: tab-delimited text files containing counts per gene normalized using the variance stabilized transformation

growth_protocol: D425, HD-MB03 and their polyclonal populations expressing shRNA targeting CRX in a doxycycline-inducible manner were grown in Dulbecco's Modified Eagle's Medium/F12  medium containing 10% fetal bovine serum at 37 °C in a CO2 incubator.

extract_protocol:
Total RNA was extracted using Qiagen RNAeasy mini kit as per manufacturer's protocol.
Libraries were prepared from Poly-A enriched fraction of total RNA using the Ilumina TruSeq RNA library preparation kit version 2.0

treatment_protocol: The cells were treated with 4 µg/ml doxycycline for 72 h for the induction of shRNA expression

tag: population

tag: disease state

tag: transduction

value: shCRX expressing


title: HD-MB03_shCRX1


title: Sperm_methylation_infected_Rep8


title: mouse_sonicated_G1_rep1

description:
hybrid musculus / spretus mouse (Patski) cells flow-sorted S phase cells, sonicated
genome replication in mouse assessed by copy-number analysis, G1, rep1

value: cycling cells flow-sorted based on DNA content, G1

value: sonicated DNA


title: Sperm_methylation_infected_Rep7


title: mouse_sonicated_S_rep1

description:
hybrid musculus / spretus mouse (Patski) cells flow-sorted S phase cells, sonicated
genome replication in mouse assessed by copy-number analysis, S phase, rep1

value: cycling cells flow-sorted based on DNA content, S phase


title: HD-MB03_VC

value: Vector control


title: Sperm_methylation_infected_Rep6


title: Sperm_methylation_infected_Rep5


title: HD-MB03_C

value: parental cells


title: D425_shCRX3


title: mouse_sonicated_G1_rep2


title: mouse_MCM2ChEC_rep1


title: D425_shCRX1


title: D425_VC


title: D425_shCRX2


title: Sperm_methylation_infected_Rep3


title: Sperm_methylation_infected_Rep2


title: Sperm_methylation_infected_Rep1


title: mouse_sonicated_S_rep2

description:
hybrid musculus / spretus mouse (Patski) cells flow-sorted S phase cells, sonicated
genome replication in mouse assessed by copy-number analysis, S phase, rep2


title: Sperm_methylation_infected_Rep4


title: D425_C2


title: E 3

type: genomic

city: Los Angeles

first: Darryl

last: Shibata

state: CA

address: NOR 1441 Eastlake Ave

department: Pathology

institute: USC

description: Illumina EPIC

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing: IDAT files were processed with using the noob normalization function in the minfi R package (Aryee et al., 2014)

label: Cy3, Cy5

source_name: small intestine

label_protocol: Standard Illumina Protocol

extract_protocol: Illumina Restore Protocol

tag: individual

value: E

value: crypt (small intestine)

tag: Sex

value: F


title: HPRT3 BRD4 ChIP Seq

city: Houston

first: Kapil

last: Bhalla

state: TX

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

data_processing:
The data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore.
ChIP-Seq reads were mapped to the human genome build UCSC hg19 using bowtie2 and duplicate reads were removed.
ChIP-Seq tracks were prepared using bedtools, normalized to reads per million reads mapped (rpm).
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq tracks represented normalized to reads per million mapped in TDF format

source_name: HPRT3 BRD4 ChIP Seq

growth_protocol: Human RT-DLBCL cells collected from mouse PDX models were cultured in 20% FBS containing RPMI1640 media.

extract_protocol:
RT-DLBCL cells (10 million) were treated with 1% formaldehyde for 10 minutes with rotation. The crosslinking reaction was quenched with 2.5 M Glycine for 5 minutes. Chromatin lysates were clarified from ultra-sonicated nuclei and histone-DNA complexes or BRD4-containing complexes were isolated with H3K27Ac or BRD4 antibody, respectively. Following ChIP washes, the  immunoprecipitated DNA fragments were treated with mutant Tn5 transposase for 10 minutes at 37°C to attach sequencing adapters to the DNA. Tagmented DNA was eluted and formaldehyde-induced crosslinks were reversed. Tagmented, eluted DNA was purified over a column and utilized for library preparation.
Libraries were prepared according to Illumina's instructions accompanying the Nextera DNA Library Prep Kit (Cat. No. FC-121-1030). After adapter ligation, DNA was PCR amplified with Illumina universal primer for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated utilizing AMP-XP beads. The purified DNA was captured on an Illumina NExt-Seq 500 flow cell for cluster generation. Libraries were sequenced following the manufacturer's protocols.

value: Diffuse Large B cell Lymphoma cells

tag: chip antibody

value: BRD4 rabbit monoclonal [ clone BL-149-2H5] (Bethyl Labs)  catalog #A700-004


title: M 9

description: Illumina EPIC

value: M


title: E 5

description: Illumina EPIC


title: D425_C1

value: Group 3 medulloblastoma


title: M 7

description: Illumina EPIC


title: mouse_MCM2ChEC_rep2

value: MCM2-ChEC, rep2

value: calcium-treated DNA (ChEC)


title: M 5

description: Illumina EPIC


title: HPRT2 BRD4 ChIP Seq

source_name: HPRT2 BRD4 ChIP Seq


title: M 8

description: Illumina EPIC


title: E 2

description: Illumina EPIC


title: KS 26

description: Illumina EPIC

value: KS


title: Daoy_ARID1B_shRNA

growth_protocol: Daoy and its polyclonal populations expressing ARID1B shRNA in a doxycycline-inducible manner were grown in Dulbecco's Modified Eagle's Medium/F12  medium at 37 °C in a CO2 incubator.

extract_protocol:
Total RNA was extracted using Qiagen RNAeasy mini kit as per manufacturer's protocol.
Librarieswere prepared from Poly-A enriched fraction of total RNA using the Ilumina TruSeq RNA library preparation kit version 2.0
The libraries were sequenced in a 100 nucleotide single-end read run on the Illumina Hiseq platform

treatment_protocol: The cells were treated with 1 µg/ml doxycycline for 72 h for the induction of shRNA expression

value: Daoy

value: Medulloblastoma

tag: genotype

value: shARID1B expressing


title: HPRT1 BRD4 ChIP Seq

source_name: HPRT1 BRD4 ChIP Seq


title: mouse_sonicated_S_rep3

description:
hybrid musculus / spretus mouse (Patski) cells flow-sorted S phase cells, sonicated
genome replication in mouse assessed by copy-number analysis, S phase, rep3

value: sonicated DNA


title: Daoy_WT3

value: wild-type


title: HPRT3 input DNA

source_name: HPRT3 input DNA


title: E 1

description: Illumina EPIC


title: Daoy_WT2


title: KS 25

description: Illumina EPIC


title: Daoy_WT1


title: TAMs - MK1

city: Cleveland

first: Kui

last: Zhai

state: Ohio

address: 9620 Carnegie Ave n building, Cleveland, OH 44106

department: Cancer Biology

institute: CCF

data_processing:
Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality.FASTQ format described by four lines:@HWI-ST1276:71:C1162ACXX:1:1101:1208:2458 1:N:0:CGATGTNAAGAACACGTTCGGTCACCTCAGCACACTTGTGAATGTCATGGGATCCAT+#55???BBBBB?BA@DEEFFCFFHHFFCFFHHHHHHHFAE0ECFFD/AEHHLine 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line).Line 2 is the raw sequence letters.Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again.Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.The details of Sequencing identifier of Illumina are as follows:(1) HWI-ST1276:71 HWI-ST1276,Instrument – unique identifier of the sequencer; 71,run number – Run number on instrument(2) C1162ACXX:1:1101:1208:2458 means the coordinate of read on C1162ACXX(Flowcell ID)flowcell,line 1, 1101 tile is(x=1208,y=2458)(3) 1:N:0:CGATGT the first number is 1 or 2, 1 means single reads or the first read of paired ends, 2 means the second of paired ends; the second letter means whether reads is adjusted(Y means yes, N means no); the third number represent the number of Control Bits in sequence; six bases on the fourth place is Illumina index sequence. For RNA-seq technology, sequencing error rate distribution has two features. Error rate grows with sequenced reads extension for the consumption of sequencing reagent. The phenomenon is common in the Illumina high-throughput sequencing platform (Erlich Y, Mitra PP et al.2008; Jiang L, Schlesinger F et al.2011.). The first six bases have a relatively high error rate. The reason is incomplete binding of the random hex-primers and RNA template in cDNA synthesis (Jiang et al.). In general, a single base error rate should be lower than 1%.GC-content is used to detect potential AT/GC separation.The Sequenced Reads/raw reads often contain low quality reads or reads with adaptors. In order to avoid this, it's necessary to filter the raw reads under conditions to get the clean reads. Raw reads filtering conditions are as follows:(1) Remove reads containing adaptors;(2) Remove reads containing N > 10% (N represents base that could not be determined);(3) The Qscore (Quality value) of over 50% bases of the read is <= 5.RNA-seq Adapter information:NEBNext® UltraTM RNA Library Prep KitRNA 5' Adapter(5'Adaptor)5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTRNA 3' Adapter(3'Adaptor,The underlined 6bp bases is Index)5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw counts and FPKM values for each Sample

growth_protocol: GSCs were cultured in GSC medium contaning 1% penicillin/streptomycin in a humidified chamber under 5% CO2 at 37 °C.

extract_protocol:
Total RNA samples were extracted from GSCs by using the PureLinkTM RNA Kit (ThermoFisher, 12183020)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GSCs were treated by TAM_MK-8931 or vehicle for 3 days

tag: strain

value: GBM mice

tag: tissue source

value: Xenografts

value: Sorted TAMs


title: TAMs - MK2


title: N 1

description: Illumina EPIC

value: N

value: crypt (small intestine)


title: TAMs - CTL2


title: D283_miR-592_2

growth_protocol: D283 and its polyclonal populations expressing miR-592 in a doxycycline-inducible manner were grown in Dulbecco's Modified Eagle's Medium/F12  medium at 37 °C in a CO2 incubator.

value: MiR-592 expressing


title: HPRT2 input DNA

source_name: HPRT2 input DNA

value: Diffuse Large B cell Lymphoma cells


title: HPRT3 H3K27Ac ChIP Seq

source_name: HPRT3 H3K27Ac ChIP Seq

value: H3K27Ac (Active Motif) RRID:AB_2793305


title: N 3

description: Illumina EPIC

value: F


title: HPRT2 H3K27Ac ChIP Seq

source_name: HPRT2 H3K27Ac ChIP Seq


title: TAMs - CTL1


title: D283_miR-592_1

value: Group 3 medulloblastoma


title: CT26-scr

city: Taichung

first: Yu-Ting

last: Yen

address: No.91, Hsueh-Shih Road

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: China Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: FullTable CT26.xlsx (Expected count, TPM, FPKM)

source_name: CT26-scr tumors harvested from mice

growth_protocol: culture CT26 with RPMI1640 medium and knockdown ppp2r1a or not

extract_protocol:
AllPrep DNA/RNA Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA-Seq analyses were performed on CT26-shppp2r1a and CT26-scr tumors harvested from mice when tumor volume reached around 70 mm3

value: colon cancer cell

value: BALB/c

value: ctrl

value: CT26-scr tumors harvested from mice


title: CT26-shppp2r1a 3

source_name: CT26-shppp2r1a tumors harvested from mice

value: knockdown ppp2r1a


title: CT26-shppp2r1a 2

value: CT26-shppp2r1a tumors harvested from mice


title: CT26-shppp2r1a 1


title: HPRT1 input DNA

source_name: HPRT1 input DNA


title: D283_WT2

value: wild-type


title: HPRT1 H3K27Ac ChIP Seq

source_name: HPRT1 H3K27Ac ChIP Seq


title: UQ 25

description: Illumina EPIC

source_name: uterus

value: UQ

value: gland (uterus)


title: D283_WT1


title: RR_pulp3

city: Wuhan

first: Guizhi

last: FENG

state: Hubei

address: No.1 of Shizishan street, Hongshan District

country: China

institute: Huazhong Agricultral University

data_processing:
Clean reads (high quality reads) of 18 transcriptome libraries were filtered from raw reads by removing low-quality reads with ambiguous nucleotides and adaptor sequences, and Tophat2 (Kim et al., 2013) was used to map clean reads to the reference genome C. sinensis (Xu et al., 2013) (Table S1). Gene expression levels were calculated by the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) method using the RSEM tool (Li and Dewey, 2011). Differential expression analysis was performed using the DESeq R package (1.10.1) (Anders and Huber, 2010). The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value (FDR) < 0.05 found by DESeq were assigned as differentially expressed genes.
Genome_build: Citrus sinensis Annotation Project (CAP) (http://citrus.hzau.edu.cn/).
Supplementary_files_format_and_content: xlsx files were generated by Microsoft Excel,fpkm represent the expression of genes.

organism: Citrus sinensis

source_name: Fruit

growth_protocol: Fruit samples of the six cultivars were harvested at 220DAF. Three trees as one biological replicate. Three biological replicates (three trees per replicate) were harvested at developmental stage. experiment.

extract_protocol:
Approximate 2 to 3 g of  powdered material was subjected to each RNA extraction, including 10 mL buffer  extraction, 5 mL chloroform-isoamylalcohol extraction (twice), 5 mL isopropanol  precipitation, 5 mL 75% ethanol cleaning and RNA purification as described  by Camacho-Villasana YM et al.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: After isolating two fruit tissues (peel and pulp) by hand dissection, the samples were frozen rapidly in liquid nitrogen and kept at -80°C.

value: Pulp

tag: full name

value: Rohde Red Valencia Orange

tag: cultivar

value: SO


title: RR_pulp1


title: RR_pulp2


title: N 4

description: Illumina EPIC

value: N

value: crypt (small intestine)


title: N 2

description: Illumina EPIC


title: HPRT3 ATAC 1

data_processing:
The data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore.
ATAC-Seq reads were mapped to the human genome build UCSC hg19 using bowtie2 and duplicate reads were removed.
ATAC-Seq tracks were prepared using bedtools, normalized to reads per million reads mapped (rpm).
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-Seq tracks represented normalized to reads per million mapped in TDF format

source_name: HPRT3 ATAC 1

extract_protocol:
RT-DLBCL cells (75,000 cells) were treated with nuclear isolation buffer and centrifuged for 10 minutes. Following this, mutant Tn5 transposase was added to the nuclei preparation. Tagmentation reactions were carried out at 37°C for 30 minutes to fragment the accessible genomic DNA and simultaneously add sequencing adapter sequences. Tagmentation reactions were stopped by the addition of binding buffer from a PCR purification kit and the tagmented DNA fragments were purified over a column. The eluted DNA fragments were utilized for library preparation and amplification. PCR Amplified libraries were size selected with AMPure XP beads to remove unbound Illumina index primers. Finished libraries were pooled and paired-end sequenced on a NextSeq 500 sequencer with a 150 cycle mid-output kit.
Libraries were prepared according to Illumina's instructions accompanying the Nextera DNA Library Prep Kit (Cat. No. FC-121-1030). After adapter ligation, DNA was PCR amplified with Illumina universal primer for 12-15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated utilizing a 1X concentration of  AMPure-XP beads. The purified DNA was captured on an Illumina NExt-Seq 500 flow cell for cluster generation. Libraries were sequenced following the manufacturer's protocols.

tag: cell type

value: Diffuse Large B cell Lymphoma cells

tag: clonal relationship

value: Clonally related to CLL


title: HPRT3 ATAC 2

source_name: HPRT3 ATAC 2


title: HPRT2 ATAC 2

source_name: HPRT2 ATAC 2

value: Clonally unrelated to CLL


title: DE_pulp2

value: Delta Valencia Orange


title: KS 24

description: Illumina EPIC

source_name: small intestine

value: KS

value: F


title: DE_pulp3


title: HPRT2 ATAC 1

source_name: HPRT2 ATAC 1


title: DE_pulp1


title: KS 22

description: Illumina EPIC


title: CU_pulp3

value: Cutter Valencia Orange


title: ydhB KO rep1

city: La Jolla

first: Ye

last: Gao

address: 9500 Gilman Dr.

institute: UCSD

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from RNA-seq were mapped onto the reference genome (NC_000913.2) using bowtie with the maximum insert size of 1000 bp, and 2 maximum mismatches after trimming 3 bp at 3’ ends
SAM files generated from bowtie, then, were then used for Cufflinks (http://cufflinks.cbcb.umd.edu/) to calculate fragments per kilobase of exon per million fragments (FPKM).
DESeq2 was run with default options with the library type of dUTP RNA-seq and the default normalization method (classic TPM)
Genome_build: reference genome (NC_000913.2)
Supplementary_files_format_and_content: Tab-delimited text files containing TPM values for each sample

organism: Escherichia coli K-12

source_name: bacteria cells

growth_protocol: Glycerol stocks of E. coli strains were inoculated into M9 minimal media with the glucose M9 minimal medium for each candidate TF. The concentration of carbon sources was 0.2% (w/v). M9 minimal media was also supplemented with 1 ml trace element solution (100X). The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5)

extract_protocol:
Three milliliters of cells from mid-log phase culture were mixed with 6 ml RNAprotect Bacteria Reagent (Qiagen), mixed immediately by vortexing for 5 seconds, incubated for 5 minutes at room temperature, and then centrifuged at 5000g for 10 minutes. The supernatant was decanted and any residual supernatant was removed, then samples were frozen at -80℃. Next, RNA was harvested using RNeasy Plus Mini kit (Qiagen) in accordance with the manufacturer’s instruction. Illumina Ribo-Zero rRNA removal kit (bacteria) (MRZMB126) was used with 1 ug of total RNA for the removal of rRNA procedure. Then KAPA RNA HyperPrep kits(Cat.No.08098107702) was used with rRNA-depleted RNA samples for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To create oxidative stress, the overnight cultures were inoculated to an optical density 600 (OD600) = 0.01 into the fresh 70 ml of M9 minimal media in a 500-ml flask supplemented with 250 uM paraquat (PQ) at OD600 = 0.3 and incubated for 20 min with stirring; for regulatory condition, M9 minimal media was supplemented with 1 mL trace element solution (100X) containing 1 g EDTA, 29 mg ZnSO4.7H2O, 198 mg MnCl2.4H2O, 254 mg CoCl2.6H2O, 13.4 mg CuCl2, and 147 mg CaCl2.

tag: medium

value: glucose M9 minimal

tag: phase

value: mid-log phase

value: ydhB deletion


title: yfeC KO rep2

value: yfeC deletion


title: ydhB KO rep2


title: UQ 23

description: Illumina EPIC

value: UQ

tag: tissue

value: gland (uterus)

tag: age


title: yfeC KO rep1


title: HPRT1 ATAC 1

source_name: HPRT1 ATAC 1

value: GCB subtype


title: HPRT1 ATAC 2

source_name: HPRT1 ATAC 2


title: ynfL KO rep1

value: ynfL deletion


title: ynfL KO rep2


title: UQ 24

description: Illumina EPIC


title: CU_pulp2

value: Pulp

value: SO


title: XF_pulp3

value: Xianfeng Orange

value: CO


title: CU_pulp1


title: mov10_1

city: Durham

first: Marcos

last: Morgan

address: 111 TW Alexander Dr

institute: NIEHS

data_processing:
Base calling was done with Guppy version 5.0.10.
The alignment to the reference transcriptome was done with Minimap2 version 2.20.
The poly (A) tail length was determined with Nanopolish version 0.13.3.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: Comma separated value file wih polyA tail length, mapping transcript and replicate information for each read.

source_name: Embryonic Stem Cell_Mov10 KO

growth_protocol: Mouse ESCs (mESCs) were cultured in mouse ESC media that contains DMEM, supplemented with 15% fetal calf serum, 0.1mM b-mercaptoethanol, 2mM L-glutamine, 0.1mM NEAA, 1% of nucleoside mix , 1000 U/ml LIF/ESGRO, and 50U/ml Penicillin/Streptomycin. mESCs were cultured at 37ºC, 5% CO2.

extract_protocol:
Total RNA (DNA free) was isolated through RNeasy Mini Kit (Cat. No. 74104, Qiagen)
4 µg of total RNA from wild-type and Mov10 KO mESCs were used for each sample. Poly (A) containing mRNAs were enriched with Oligo(dT)25 Dynabead™ (61002, Thermo Fisher Scientific) and libraries were prepared using the Direct RNA Sequencing Kit (SQK-RNA002, Oxford Nanopore Technologies). All the libraries were multiplexed using the DeePlexiCon adapters, loaded to Nanopore R9 Flow Cells (FLO-MIN106D, Oxford Nanopore Technologies) and run on a MinION sequencer.

tag: genotype/variation

value: Mov10 KO

tag: strain background

value: Embryonic Stem Cell


title: mov10_2


title: yciT KO rep1

value: yciT deletion


title: yciT KO rep2


title: wt_2

source_name: Embryonic Stem Cell_WT

value: Wild-type


title: US 29

description: Illumina EPIC

value: US

value: F


title: XF_pulp2


title: wt_1


title: ybcM KO rep2

value: glucose M9 minimal

value: mid-log phase

value: ybcM deletion


title: XF_pulp1


title: ybcM KO rep1


title: E14P0_NFI_overexpression_rep2_scRNAseq

city: Baltimore

first: Seth

last: Blackshaw

state: Maryland

address: 733 N. Broadway Avenue

institute: Johns Hopkins University

description:
E14P0_NFI_overexpression_scRNAseq_cell_annotation.txt
E14P0_NFI_overexpression_scRNAseq_gene_annotation.txt
E14P0_NFI_overexpression_scRNAseq_raw_matrix.mtx

data_processing:
We processed raw scRNA-seq data with the Cell Ranger software for formatting reads, demultiplexing samples, genomic alignment, and generating the cell-by-gene count matrix. The ‘cellranger mkfastq’ function was used to convert BCL files to fastq files. The ‘cellranger count’ function was used to process fastq files for each sample with the mm10 mouse reference index provided by 10x Genomics. The cell-by-gene count matrix is the final output from the Cell Ranger pipeline. We used the cell-by-gene count matrix for all downstream analysis.
We applied the Seurat (Stuart et al., 2019) package to create Seurat objects for each sample with the cell-by-gene count matrix with the function ‘CreateSeuratObject’. After visual checking the violin plot of the total counts for each cell, we filtered out cells with nCount_RNA. We further filtered out the cells with a mitochondrial fraction > 10%. Next, we used Scrublet (Wolock et al., 2019) to identify and remove doublets with default parameters.  After  performing dimensional reduction and clustering analysis through the standard Seurat pipeline, we annotated the cell types for each cluster according to the well-known markers. We filtered out non-neuroretinal cells, such as microglia and astrocytes for each sample. The cleaned data were used for downstream integration and DEG analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell annotation, gene annotation and raw data matrix files
The Cell Ranger (Zheng et al., 2017) ATAC pipeline was used to process the raw sequencing data for mapping, de-duplication and identification of Tn5 cut sites.
We generated the cell-by-peaks matrix for each sample using the same method as described in Satpathy, A. T. et al .First, we constructed 2.5-kb tiled windows across the mm10 genome using the local script. Next, a cell-by-window sparse matrix was computed by counting the Tn5 insertion overlaps for each cell, and this matrix was then binarized and inputted to Signac package (0.2.5) to create a Seurat object using ‘CreateSeuratObject.’ Second, we normalized the cell-by-window matrix by TF-IDF methods using ‘RunTFIDF’ and ran a singular value decomposition (SVD) on the TF-IDF normalized matrix with ‘RunSVD.' We retained the 2nd to 30th dimensions, and identified clusters using SNN graph clustering with 'FindClusters' with a resolution of 0.3. Third, to identify high-quality peaks for each cluster in each sample, we called peaks for each cluster by MACS2 with the command: '-shift -75 --extsize 150 --nomodel --callsummits --nolambda --keep-dup all -q 0.05'. The peak summits were then extended to 250 bp on either side to a final width of 500 bp and then filtered by the mm10 v2 blacklist regions (https://github.com/Boyle-Lab/Blacklist/blob/master/lists/mm10blacklist.v2.bed.gz). The top 50,000 peaks for each cluster in each sample were kept, converted to Granges, and merged into a union peak set with the function ‘reduce’ in the GenomicRanges package.
The ArchR package(Granja et al., 2020) was used to process the fragment files.  We calculated the TSS enrichment, unique fragments and nucleosome banding for each cell with the function ‘createArrowFiles’’. Then we kept the high-quality cells with the following criteria: 1) The number of unique nuclear fragments > 1000.  2) TSS enrichment score > 10.  3) nucleosome banding score < 4. We next identified potential doublets with the function ‘addDoubletScores’, and removed doublets using ‘filterDoublets’’ with the following parameters: cutEnrich = 2, cutScore = -Inf, and filterRatio =2. Finally, we filtered the fragment files according to the cells we retained. These cleaned fragment files were used for all downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell annotation, peak annotation and raw data matrix files

source_name: retina

extract_protocol:
Dissociated cells were resuspended in ice-cold PBS containing 0.04% bovine serum albumin (BSA). Cell count and viability were assessed by Trypan blue staining.Trypan blue staining.
ScRNA-seq analysis was performed on dissociated retinal cells using 10x Genomics. Briefly, dissociated retinal cells (~10,000 cells per sample) were loaded into a 10x Genomics Chromium Single Cell system using Chromium Single Cell 3’ Reagents Kits v3.1 (10X Genomics, Pleasanton, CA). scRNA libraries were generated by following the manufacturer’s instructions. Libraries were pooled and sequenced on Illumina NextSeq 500 or NovaSeq 6000. Sequencing reads were processed through the Cell Ranger 3.1 pipeline (10x Genomics) using default parameters.
single cell RNAseq
Dissociated cells were resuspended in ice-cold PBS containing 0.04% bovine serum albumin (BSA). Cell count and viability were assessed by Trypan blue staining.Trypan blue staining.
scATAC-seq was performed using the 10x Genomic single cell ATAC reagent v1.1 kit following the manufacturer’s instruction. Briefly, dissociated cells were centrifuged at 300xg for 5 min at 4oC. Cell pellet was resuspended in 100 μl of Lysis buffer, mixed 10x by pipetting and incubated on ice for 3 min. Wash buffer (1 ml) was added to the lysed cells, and cell nuclei were centrifuged at 500xg for 5 min at 40C. Nuclei pellet was re-suspended in 250 μl of 1x Nuclei buffer. Cell nuclei were then counted using Trypan blue. Re-suspended cell nuclei (10-15k) were used for transposition and loaded into the 10x Genomics Chromium Single Cell system. Libraries were amplified with 10 PCR cycles and were sequenced on Illumina NextSeq or NovaSeq with ~200 million reads per library. Sequencing data was processed through the Cell Ranger ATAC 1.1.0 pipeline (10x Genomics) using default parameters.
single cell ATACseq

treatment_protocol:
Chx10-Cre-EGFP;Nfiafl/fl;Nfibfl/fl;Nfixfl/fl mice were generated as described previously (Clark et al., 2019). Mice were euthanized, and eyes were removed and incubated in ice-cold PBS. Retinas were dissected, and cells were dissociated using Papain Dissociation System as described previously (Hoang et al., 2020). Each sample contains a minimum of 4 retinas from 4 animals, regardless of sex. Dissociated cells were resuspended in ice-cold PBS containing 0.04% bovine serum albumin (BSA). Cell count and viability were assessed by Trypan blue staining.
Chx10-Cre-EGFP;Nfiafl/fl;Nfibfl/fl;Nfixfl/fl mice were generated as described previously (Clark et al., 2019). Mice were euthanized, and eyes were removed and incubated in ice-cold PBS. Retinas were dissected, and cells were dissociated using Papain Dissociation System as described previously (Hoang et al., 2020). Each sample contains a minimum of 4 retinas from 4 animals, regardless of sex. Dissociated cells were resuspended in ice-cold PBS containing 0.04% bovine serum albumin (BSA). Cell count and viability were assessed by Trypan blue staining.

value: retina

value: Nfi overexpression

tag: replicate


title: TY_pulp3

value: Taoye Orange


title: yidZ KO rep2

value: yidZ deletion


title: TY_pulp2

value: Pulp


title: yidZ KO rep1


title: E14P0_NFI_overexpression_rep1_scRNAseq


title: WT rep2

value: wild type


title: TY_pulp1


title: E14P0_NFI_eGFP_rep2_scRNAseq

value: NFI eGFP (Ctrl)


title: JC_pulp3

value: Jincheng Orange

value: CO


title: WT rep1


title: US 17

description: Illumina EPIC

tag: individual

value: gland (uterus)


title: JC_pulp2


title: E14P0_NFI_eGFP_rep1_scRNAseq


title: E14E16_NFI_overexpression_scRNAseq

description:
E14E16_NFI_overexpression_scRNAseq_cell_annotation.txt
E14E16_NFI_overexpression_scRNAseq_gene_annotation.txt
E14E16_NFI_overexpression_scRNAseq_raw_matrix.mtx


title: UR 28

description: Illumina EPIC

value: UR

tag: Sex


title: NSL3RNAi_ovary_RNAseq

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
RiboZero-RNA-seq
NSL3_RNAi_rep1

data_processing:
Quality control, mapping and quantificaion were performed using piPipes (Han et al, "piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing" Bioinformatics (2015) doi: 10.1093/bioinformatics/btu647 )
Genome_build: dm3
Supplementary_files_format_and_content: bigwig files and DEseq2 counts output

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: Standard fly food

extract_protocol: Ovary was dissected in PBS. Then crushed in Trizol. RNA was extracted using the Zymo RNA extraction kit.

treatment_protocol: KD was achieved by crossing the flies carrying the haripin against gene of interestn with flies expressing GAL4 under the nanos promoter. Flies were grown on standard fly food. F1 flies of the correct genotype were fed standard fly food supplemented with yeast for 3-5 days before dissecting the ovary

tag: fly strain

value: Vienna Stock Center 108002

tag: treatment

value: NSL3 knockdown

value: ovary


title: E14E16_eGFP_scRNAseq

tag: genotype

value: eGFP (Ctrl)


title: UQ 22

description: Illumina EPIC

value: UQ

value: F


title: UT 21

description: Illumina EPIC

value: UT


title: UT L 22

description: Illumina EPIC


title: US 16

description: Illumina EPIC

value: US


title: UF 11

description: Illumina EPIC

value: UF


title: P2_Nfi_Het_rep2_scRNAseq

description:
P2_Nfi_KO_scRNAseq_cell_annotation.txt
P2_Nfi_KO_scRNAseq_gene_annotation.txt
P2_Nfi_KO_scRNAseq_raw_matrix.mtx

value: retina

value: Nfi Het (Ctrl)


title: RR_peel3

value: Peel

value: Rohde Red Valencia Orange

value: SO


title: NSL2RNAi_ovary_RNAseq

description:
RiboZero-RNA-seq
NSL2_RNAi_rep1

value: Bloomington stock number 58162

value: NSL2 knockdown


title: UT L 23

description: Illumina EPIC

value: gland (uterus)


title: UF 14

description: Illumina EPIC


title: US 20

description: Illumina EPIC


title: JC_pulp1

value: Pulp

value: Jincheng Orange

value: CO


title: UR 1

description: Illumina EPIC

value: UR


title: P2_Nfi_Het_rep1_scRNAseq


title: UF 15

description: Illumina EPIC


title: UF 13

description: Illumina EPIC


title: RR_peel1


title: UH 15

description: Illumina EPIC

value: UH


title: UR 4

description: Illumina EPIC

value: F


title: whiteRNAi_VirginOvary_RNAseq

description:
RiboZero-RNA-seq
whiteRNAi_virgins_rep1

value: Bloomington stock number 35573

value: white knockdown

value: ovary


title: P2_Nfi_Input_ChIPseq

data_processing:
After removing adaptors with Trimmomatic (Bolger et al., 2014), we mapped the cleaned fastq files to mm10 genome using bowtie2 (Langmead and Salzberg, 2012). We next filtered low quality reads with SAMtools (Li et al., 2009)(MAPQ < 10), and removed PCR duplicates using Picard tools (http://broadinstitute.github.io/picard/) .
For NFI ChIP-seq data, we used IgG and Input samples as control, and used MACS2 (Zhang et al., 2008) to call peaks with the default parameters except: -q 0.01. Finally, we identified 13,680 NFI binding peaks and used them in the downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: P2_Nfi_peaks.txt
The Cell Ranger (Zheng et al., 2017) ATAC pipeline was used to process the raw sequencing data for mapping, de-duplication and identification of Tn5 cut sites.
We generated the cell-by-peaks matrix for each sample using the same method as described in Satpathy, A. T. et al .First, we constructed 2.5-kb tiled windows across the mm10 genome using the local script. Next, a cell-by-window sparse matrix was computed by counting the Tn5 insertion overlaps for each cell, and this matrix was then binarized and inputted to Signac package (0.2.5) to create a Seurat object using ‘CreateSeuratObject.’ Second, we normalized the cell-by-window matrix by TF-IDF methods using ‘RunTFIDF’ and ran a singular value decomposition (SVD) on the TF-IDF normalized matrix with ‘RunSVD.' We retained the 2nd to 30th dimensions, and identified clusters using SNN graph clustering with 'FindClusters' with a resolution of 0.3. Third, to identify high-quality peaks for each cluster in each sample, we called peaks for each cluster by MACS2 with the command: '-shift -75 --extsize 150 --nomodel --callsummits --nolambda --keep-dup all -q 0.05'. The peak summits were then extended to 250 bp on either side to a final width of 500 bp and then filtered by the mm10 v2 blacklist regions (https://github.com/Boyle-Lab/Blacklist/blob/master/lists/mm10blacklist.v2.bed.gz). The top 50,000 peaks for each cluster in each sample were kept, converted to Granges, and merged into a union peak set with the function ‘reduce’ in the GenomicRanges package.
The ArchR package(Granja et al., 2020) was used to process the fragment files.  We calculated the TSS enrichment, unique fragments and nucleosome banding for each cell with the function ‘createArrowFiles’’. Then we kept the high-quality cells with the following criteria: 1) The number of unique nuclear fragments > 1000.  2) TSS enrichment score > 10.  3) nucleosome banding score < 4. We next identified potential doublets with the function ‘addDoubletScores’, and removed doublets using ‘filterDoublets’’ with the following parameters: cutEnrich = 2, cutScore = -Inf, and filterRatio =2. Finally, we filtered the fragment files according to the cells we retained. These cleaned fragment files were used for all downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell annotation, peak annotation and raw data matrix files

growth_protocol: CD1 mice were purchased from Charles River Laboratories. All experimental procedures were pre-approved by the Institutional Animal Care and Use Committee (IACUC) of the Johns Hopkins University School of Medicine. Mouse embryos or pups at different timepoints of retinal development P2 were used for this study.

extract_protocol:
Chromatin immunoprecipitation was then performed on the sheared DNA using the iDeal ChIP-seq kit for transcription factors (Diagenode Cat# C01010170). One percent of chromatin was kept aside to be used as an input control. Antibodies against targets used for chromatin immunoprecipitation are NFI (NFIA, NFIB, NFIX), and IgG. Briefly, equal volume of sheared chromatin was incubated overnight with 3 μg of antibody in iC1b buffer with protease inhibitors and BSA and washed DiaMag Protein A-coated magnetic beads (Diagenode Cat# C03010020-220) on a tube rotator at 4°C overnight. The magnetic beads were then washed sequentially with wash buffers iW1, iW2, iW3 and iW4. DNA was then de-crosslinked and eluted for 4 hours at 65C before being purified using IPure beads (Diagenode Cat# C03010014). The purified DNA was then subjected to sequencing library preparation or qPCR analysis.
Libraries were prepared from 5ng of DNA using the Ovation Ultralow System V2 (Tecan Genomics Cat# 0344NB-32) and sequenced on the Illumina NextSeq500.
Dissociated cells were resuspended in ice-cold PBS containing 0.04% bovine serum albumin (BSA). Cell count and viability were assessed by Trypan blue staining.Trypan blue staining.
scATAC-seq was performed using the 10x Genomic single cell ATAC reagent v1.1 kit following the manufacturer’s instruction. Briefly, dissociated cells were centrifuged at 300xg for 5 min at 4oC. Cell pellet was resuspended in 100 μl of Lysis buffer, mixed 10x by pipetting and incubated on ice for 3 min. Wash buffer (1 ml) was added to the lysed cells, and cell nuclei were centrifuged at 500xg for 5 min at 40C. Nuclei pellet was re-suspended in 250 μl of 1x Nuclei buffer. Cell nuclei were then counted using Trypan blue. Re-suspended cell nuclei (10-15k) were used for transposition and loaded into the 10x Genomics Chromium Single Cell system. Libraries were amplified with 10 PCR cycles and were sequenced on Illumina NextSeq or NovaSeq with ~200 million reads per library. Sequencing data was processed through the Cell Ranger ATAC 1.1.0 pipeline (10x Genomics) using default parameters.
single cell ATACseq

treatment_protocol:
Freshly dissected P2 retinas were homogenized and cross-linked for 10 minutes using 1% formaldehyde (ThermoFisher Scientific Cat# 28906) on a tube rotator at room temperature. Glycine was added to a final concentration of 0.125 M to quench the cross-linking reaction and washed three times with ice-cold PBS with cOmplete protease inhibitors (Millipore Sigma Cat# 11836170001). The cells were then prepared for sonication using the truChIP chromatin shearing kit (Covaris Cat# 520154). Briefly, cells were lysed at 4C on a tube rotator for 10 minutes using the 1X lysis buffer B. Intact nuclei were then collected by centrifugation at 1700xg for 5 minutes and washed with 1X wash buffer C before being resuspended in 1ml of 1X shearing buffer D3. Nuclei were then transferred to 1mL milliTUBE with AFA fiber (Covaris Cat# 520130) and sonicated using the E220 focused-ultrasonicator (Covaris Cat# 500239).
Chx10-Cre-EGFP;Nfiafl/fl;Nfibfl/fl;Nfixfl/fl mice were generated as described previously (Clark et al., 2019). Mice were euthanized, and eyes were removed and incubated in ice-cold PBS. Retinas were dissected, and cells were dissociated using Papain Dissociation System as described previously (Hoang et al., 2020). Each sample contains a minimum of 4 retinas from 4 animals, regardless of sex. Dissociated cells were resuspended in ice-cold PBS containing 0.04% bovine serum albumin (BSA). Cell count and viability were assessed by Trypan blue staining.

value: retina

value: Nfia/b/x cKO

tag: chip antibody


title: UH 16

description: Illumina EPIC


title: whiteRNAi_ovary_RNAseq

description:
RiboZero-RNA-seq
whiteRNAi_rep1


title: UT 19

description: Illumina EPIC

value: UT


title: NSL2RNAi_ovary_smallRNAseq

description:
small-RNA seq
NSL2RNAi_1

extract_protocol: Ovary was dissected in PBS. Then crushed in Trizol. RNA was extracted using the Zymo RNA extraction kit. 15 µg of RNA was run on a 15% Urea denaturing gel and 18-30 nt long RNAs were gel cut.


title: UR 3

description: Illumina EPIC


title: DE_peel3

value: Peel

tag: full name

value: Delta Valencia Orange


title: UAH B 20

description: Illumina EPIC

value: UAH


title: UAH B 16

description: Illumina EPIC


title: whiteRNAi_ovary_smallRNAseq

description:
small-RNA seq
white_RNAi_1


title: UH L 13

description: Illumina EPIC


title: RR_peel2

value: Rohde Red Valencia Orange

tag: cultivar

value: SO


title: P2_Nfi_lgG_ChIPseq

value: IgG


title: DE_peel1


title: P2_Nfi_ChIP_rep2_ChIPseq

value: NFI (NFIA, NFIB, NFIX)


title: NSL2RNAi_H3K4me3_IP_CHIPseq_ovary

extract_protocol: Ovary was dissected in PBS. Then crushed in 1.8% formaldehyde for 15 mins. Sonication was performed in the Covaris E220. ChIP was performed by incubating the sheared chromatin overnight with the antibody at 4C. Decrosslinking was performed overnight at 65C. DNA was isolated using the Zymo ChIP DNA kit.

value: Bloomington stock number 58162

value: NSL2 knockdown

tag: antibody


title: UAH B 17

description: Illumina EPIC

value: gland (uterus)


title: P2_Nfi_ChIP_rep1_ChIPseq


title: CU_peel3

value: Cutter Valencia Orange


title: P14_Nfi_KO_rep2_scATACseq

description:
P14_KO_scATACseq_cell_annotation.txt
P14_KO_scATACseq_raw_matrix.mtx
P14_KO_scATACseq_peak_annotation.txt

data_processing:
The Cell Ranger (Zheng et al., 2017) ATAC pipeline was used to process the raw sequencing data for mapping, de-duplication and identification of Tn5 cut sites.
We generated the cell-by-peaks matrix for each sample using the same method as described in Satpathy, A. T. et al .First, we constructed 2.5-kb tiled windows across the mm10 genome using the local script. Next, a cell-by-window sparse matrix was computed by counting the Tn5 insertion overlaps for each cell, and this matrix was then binarized and inputted to Signac package (0.2.5) to create a Seurat object using ‘CreateSeuratObject.’ Second, we normalized the cell-by-window matrix by TF-IDF methods using ‘RunTFIDF’ and ran a singular value decomposition (SVD) on the TF-IDF normalized matrix with ‘RunSVD.' We retained the 2nd to 30th dimensions, and identified clusters using SNN graph clustering with 'FindClusters' with a resolution of 0.3. Third, to identify high-quality peaks for each cluster in each sample, we called peaks for each cluster by MACS2 with the command: '-shift -75 --extsize 150 --nomodel --callsummits --nolambda --keep-dup all -q 0.05'. The peak summits were then extended to 250 bp on either side to a final width of 500 bp and then filtered by the mm10 v2 blacklist regions (https://github.com/Boyle-Lab/Blacklist/blob/master/lists/mm10blacklist.v2.bed.gz). The top 50,000 peaks for each cluster in each sample were kept, converted to Granges, and merged into a union peak set with the function ‘reduce’ in the GenomicRanges package.
The ArchR package(Granja et al., 2020) was used to process the fragment files.  We calculated the TSS enrichment, unique fragments and nucleosome banding for each cell with the function ‘createArrowFiles’’. Then we kept the high-quality cells with the following criteria: 1) The number of unique nuclear fragments > 1000.  2) TSS enrichment score > 10.  3) nucleosome banding score < 4. We next identified potential doublets with the function ‘addDoubletScores’, and removed doublets using ‘filterDoublets’’ with the following parameters: cutEnrich = 2, cutScore = -Inf, and filterRatio =2. Finally, we filtered the fragment files according to the cells we retained. These cleaned fragment files were used for all downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell annotation, peak annotation and raw data matrix files
The Cell Ranger (Zheng et al., 2017) ATAC pipeline was used to process the raw sequencing data for mapping, de-duplication and identification of Tn5 cut sites.
We generated the cell-by-peaks matrix for each sample using the same method as described in Satpathy, A. T. et al .First, we constructed 2.5-kb tiled windows across the mm10 genome using the local script. Next, a cell-by-window sparse matrix was computed by counting the Tn5 insertion overlaps for each cell, and this matrix was then binarized and inputted to Signac package (0.2.5) to create a Seurat object using ‘CreateSeuratObject.’ Second, we normalized the cell-by-window matrix by TF-IDF methods using ‘RunTFIDF’ and ran a singular value decomposition (SVD) on the TF-IDF normalized matrix with ‘RunSVD.' We retained the 2nd to 30th dimensions, and identified clusters using SNN graph clustering with 'FindClusters' with a resolution of 0.3. Third, to identify high-quality peaks for each cluster in each sample, we called peaks for each cluster by MACS2 with the command: '-shift -75 --extsize 150 --nomodel --callsummits --nolambda --keep-dup all -q 0.05'. The peak summits were then extended to 250 bp on either side to a final width of 500 bp and then filtered by the mm10 v2 blacklist regions (https://github.com/Boyle-Lab/Blacklist/blob/master/lists/mm10blacklist.v2.bed.gz). The top 50,000 peaks for each cluster in each sample were kept, converted to Granges, and merged into a union peak set with the function ‘reduce’ in the GenomicRanges package.
The ArchR package(Granja et al., 2020) was used to process the fragment files.  We calculated the TSS enrichment, unique fragments and nucleosome banding for each cell with the function ‘createArrowFiles’’. Then we kept the high-quality cells with the following criteria: 1) The number of unique nuclear fragments > 1000.  2) TSS enrichment score > 10.  3) nucleosome banding score < 4. We next identified potential doublets with the function ‘addDoubletScores’, and removed doublets using ‘filterDoublets’’ with the following parameters: cutEnrich = 2, cutScore = -Inf, and filterRatio =2. Finally, we filtered the fragment files according to the cells we retained. These cleaned fragment files were used for all downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell annotation, peak annotation and raw data matrix files

extract_protocol:
Dissociated cells were resuspended in ice-cold PBS containing 0.04% bovine serum albumin (BSA). Cell count and viability were assessed by Trypan blue staining.Trypan blue staining.
scATAC-seq was performed using the 10x Genomic single cell ATAC reagent v1.1 kit following the manufacturer’s instruction. Briefly, dissociated cells were centrifuged at 300xg for 5 min at 4oC. Cell pellet was resuspended in 100 μl of Lysis buffer, mixed 10x by pipetting and incubated on ice for 3 min. Wash buffer (1 ml) was added to the lysed cells, and cell nuclei were centrifuged at 500xg for 5 min at 40C. Nuclei pellet was re-suspended in 250 μl of 1x Nuclei buffer. Cell nuclei were then counted using Trypan blue. Re-suspended cell nuclei (10-15k) were used for transposition and loaded into the 10x Genomics Chromium Single Cell system. Libraries were amplified with 10 PCR cycles and were sequenced on Illumina NextSeq or NovaSeq with ~200 million reads per library. Sequencing data was processed through the Cell Ranger ATAC 1.1.0 pipeline (10x Genomics) using default parameters.
single cell ATACseq
Dissociated cells were resuspended in ice-cold PBS containing 0.04% bovine serum albumin (BSA). Cell count and viability were assessed by Trypan blue staining.Trypan blue staining.
scATAC-seq was performed using the 10x Genomic single cell ATAC reagent v1.1 kit following the manufacturer’s instruction. Briefly, dissociated cells were centrifuged at 300xg for 5 min at 4oC. Cell pellet was resuspended in 100 μl of Lysis buffer, mixed 10x by pipetting and incubated on ice for 3 min. Wash buffer (1 ml) was added to the lysed cells, and cell nuclei were centrifuged at 500xg for 5 min at 40C. Nuclei pellet was re-suspended in 250 μl of 1x Nuclei buffer. Cell nuclei were then counted using Trypan blue. Re-suspended cell nuclei (10-15k) were used for transposition and loaded into the 10x Genomics Chromium Single Cell system. Libraries were amplified with 10 PCR cycles and were sequenced on Illumina NextSeq or NovaSeq with ~200 million reads per library. Sequencing data was processed through the Cell Ranger ATAC 1.1.0 pipeline (10x Genomics) using default parameters.
single cell ATACseq

value: Nfi KO

tag: cell type

value: retinal progenitor cells (RPCs)


title: CU_peel2


title: NSL1RNAi_ovary_RNAseq

description:
RiboZero-RNA-seq
NSL1_RNAi_rep1

value: Bloomington stock number 58328

value: NSL1 knockdown

value: ovary


title: whiteRNAi_H3K4me3_input_CHIPseq_ovary

value: Bloomington stock number 35573

value: white knockdown


title: whiteRNAi_H3K4me3_IP_CHIPseq_ovary


title: UAG W 15

description: Illumina EPIC

value: UAG

value: F


title: P14_Nfi_KO_rep1_scATACseq

value: retina


title: CU_peel1

value: Peel

value: SO


title: NSL2RNAi_input_fpr Rhino_and H3K4me3_CHIPseq_ovary


title: UH L 14

description: Illumina EPIC

value: UH


title: XF_peel3

value: Xianfeng Orange

value: CO


title: NSL2RNAi_Rhino_IP_CHIPseq_ovary

value: Bloomington stock number 58162

value: NSL2 knockdown

value: Rhino (guinea-pig, gift from William Theurkauf)


title: whiteRNAi_Rhino_input_CHIPseq_ovary


title: UAG W 14

description: Illumina EPIC

value: gland (uterus)


title: XF_peel2


title: P2_Nfi_KO_rep1_scRNAseq

value: Nfi KO


title: whiteRNAi_Rhino_IP_CHIPseq_ovary


title: P2_Nfi_KO_rep1_scATACseq

description:
P2_KO_scATACseq_cell_annotation.txt
P2_KO_scATACseq_raw_matrix.mtx
P2_KO_scATACseq_peak_annotation.txt

value: retinal progenitor cells (RPCs)


title: XF_peel1


title: P2_Nfi_KO_rep2_scATACseq


title: E14E16_NFI_overexpression_scATACseq

description:
E14E16_overexpression_scATACseq_cell_annotation.txt
E14E16_overexpression_scATACseq_raw_matrix.mtx
E14E16_overexpression_scATACseq_peak_annotation.txt

value: Nfi overexpression


title: UAH B 18

description: Illumina EPIC

value: UAH


title: UAG M 13

description: Illumina EPIC


title: E14E16_eGFP_scATACseq

value: eGFP (Ctrl)


title: NSL2RNAi_HP1a_input_CHIPseq_ovary

value: ovary


title: TY_peel3

value: Taoye Orange


title: TY_peel2


title: DE_peel2

value: Delta Valencia Orange


title: NSL2RNAi_HP1a_IP_CHIPseq_ovary

value: C1A9 (DSHB)


title: TY_peel1

value: Peel


title: VMB-Mutant 4 (D3)

city: Be'er Sheva

first: Daniel

last: Halperin

address: Ben Gurion 1 st

country: Israel

institute: Ben-Gurion University of the Negev

data_processing:
Reads were trimmed using cutadapt (v1.8.3)
After trimming the reads were mapped to the human genome using TopHat v2.0.10
Counting proceeded over genes annotated in Ensembl release 83, using htseq-count v0.6.1p1
Normalization and differential expression was performed using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file includes the normalized counts and the differential expression analysis

source_name: Ventral mid-brain tissue extract

extract_protocol:
Total RNA was extracted from the micro-dissected tissues using GENzolTM Tri RNA Pure Kit (Geneaid Biotech Ltd.) according to the manufacturer’s instructions
Inhouse poly A based RNA seq

value: Cdh2 mutant

value: 13 weeks

tag: strain

value: Ventral mid-brain tissue extract


title: VMB-WT4 (E3)

value: Wildtype


title: VMB-Mutant 2 (C4)


title: JC_peel1

value: Jincheng Orange

value: CO


title: JC_peel3


title: NSL2RNAi_H3K9me3_IP_CHIPseq_ovary

value: Bloomington stock number 58162

value: NSL2 knockdown


title: whiteRNAi_HP1a_IP_CHIPseq_ovary

value: Bloomington stock number 35573

value: white knockdown


title: whiteRNAi_HP1a_input_CHIPseq_ovary


title: NSL2RNAi_H3K9me3_input_CHIPseq_ovary


title: VMB-Mutant 1 (A2)


title: VMB-Mutant 3 (D1)


title: CD 17

description: Illumina EPIC

source_name: colon

value: CD

value: crypt (colon)

value: F


title: VMB-WT3 (E1)


title: JC_peel2


title: CD 16

description: Illumina EPIC


title: UAG B 11

description: Illumina EPIC

value: UAG

value: gland (uterus)


title: whiteRNAi_H3K9me3_input_CHIPseq_ovary

value: ovary


title: VMB-WT2 (C2)


title: whiteRNAi_H3K9me3_IP_CHIPseq_ovary


title: VMB-WT1 (B1)


title: CD 5

description: Illumina EPIC


title: Male placenta - LPS_rep2

city: Seoul

first: Da Som

last: Jeong

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

department: Embryology

country: South Korea

institute: Yonsei University

data_processing:
Total RNA Seq reads were mapped using TopHat software (Cole Trapnell et al., 2009.) tool in order  to obtain bam file (alignment file). The alignment files also were used for assembling transcripts,  estimating their abundances and detecting differential expression of genes, isoforms, lncRNAs using  cufflinks. We used the FPKM (fragments per kilobase of exon per million fragments) as the method  of determining the expression level of the gene regions. The FPKM data were normalized based on  Quantile normalization method  using EdgeR within R (R development Core Team, 2016).
10X Genomics Next GEM technology labraries are processed by ExDaga developed by ebiogen incorporation.
Fragments per kilobase of transcript per million (FPKM) was used for criteria when identify placental gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and fold change comparing the PBS group and LPS group

source_name: whole placental tissues

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed by Agilent 2100  bioanaly z er using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands),  and RNA quantification was performed using ND 2000 Spectrophotometer (Thermo Inc., DE, USA).
Libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA  Seq Kit ( NEW  ENGLAND BioLabs, Inc., UK). rRNA was removed using RIBO COP rRNA depletion kit (LEXOGEN, Inc.,  Austria). The rRNA depleted RNA s were used for the cDNA synthesis and shearing, following  manufacture’s instruction. Indexing was performed using the Illumina indexe s 1 12. The enrichment  step was carried out using of PCR. Subsequently, libraries were checked using the Agilent 2100  b ioanalyzer (DNA High Sensitivity Kit) to evaluate the mean fragment size. Quantification was  performed using the library quantification k it using a StepOne Real Time PCR System (Life  Technologies, Inc., USA). High throughput sequencing was performed as paired end 100 sequencing  using Hi seq X10 (Illumina, Inc., USA).

treatment_protocol: treasted with PBS or LPS (400 mg/kg) for 48 hrs

value: whole placental cells

value: ICR

value: treated with LPS


title: CE 20

description: Illumina EPIC

extract_protocol: Illumina Restore Protocol

value: CE


title: NSL1ovaryWORinput_CHIPseq

value: w1118 flies

value: WT


title: NSL1ovaryWOR_IP_CHIPseq

value: NSL1 (Rabbit, homemade)


title: PFC-Mutant 3 (D3)

source_name: Prefrontal cortex tissue extract

value: Cdh2 mutant

value: 13 weeks

value: Prefrontal cortex tissue extract


title: Female placenta - LPS_rep2


title: PFC-Mutant 2 (A2)


title: Female placenta - LPS_rep1


title: Male placenta - LPS_rep1


title: CE 18

description: Illumina EPIC


title: Male placenta - LPS_rep3


title: PFC-Mutant 1 (A1)


title: CE 21

description: Illumina EPIC


title: Male placenta - PBS_rep2

value: treated with PBS


title: NA 11

description: Illumina EPIC


title: Male placenta - PBS_rep1


title: PFC-WT3 (E2)

value: Wildtype


title: PFC-WT4 (E4)


title: Female placenta - PBS_rep2


title: hrt-Ler-br2

city: Lancaster

first: Pablo

middle: D

last: Jenik

state: PA

address: PO Box 3003

department: Department of Biology

institute: Franklin and Marshall College

data_processing:
Libraries were sequenced on Illumina HiSeq 4000 sequencer.
Each lane of sequencing for each sample is attached as an individual compressed file.  The sequence data are in the fastq format.
Sequenced reads were quality-filtered, reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to Arabidopsis thalian primary transcripts (TAIR10) using bowtie v0.12.7 with parameters -v 2 -5 10 -3 40 -m 1 --best --strata
Read counts for each gene models were computed using a custom script. TMM-normalized counts are obtained using the EdgeR package v3.0.8 (Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including the raw counts for each sample.

organism: Arabidopsis thaliana

source_name: late heart stage Arabidopsis embryos

growth_protocol: Plants were grown at 22°C with 16 hours of light in a growth chamber (Conviron). Seeds were planted directly in soil (Fafard-2, SunGro Horticulture) supplemented with Osmocote Plus 15-9-12 fertilizer.

extract_protocol:
Total RNA was purified using PureLink RNA reagent (Thermo Fisher Scientific), according to the manufacturer’s instructions.
Libraries were generated from 70-90 ng of total RNA using Nugen Ovation RNA-Seq Systems for Model Organisms, as per manufacturer's instructions.

treatment_protocol: Hand-dissected late heart embryos were collected in ice-cold 5% sucrose, twice washed and concentrated on a 9:1 5%sucrose:Percoll gradient for 10 minutes at 1000g, then finally rinsed in 5% sucrose before flash-freezing in liquid nitrogen.

value: embryos

tag: ecotype

value: Landsberg erecta

value: wild type


title: hrt-Ler-br1

tag: tissue


title: PFC-Mutant 4 (D4)

tag: age


title: Female placenta - LPS_rep3


title: CD 4

description: Illumina EPIC

value: CD

value: crypt (colon)

value: F


title: CE 19

description: Illumina EPIC


title: hrt-Col-br3


title: hrt-Col-br2


title: hrt-Ler-br3


title: PFC-WT2 (C2)


title: PFC-WT1 (B1)


title: hrt-asil2-2-br3


title: HA-NSL2_input_CHIPseq_Ovary

value: CRISPR N-tagged NSL2

value: ovary


title: Female placenta - PBS_rep1

value: whole placental cells

value: ICR


title: hrt-Col-br1


title: NA 10

description: Illumina EPIC


title: HA-NSL2_IP_CHIPseq_Ovary

value: w1118 flies

value: HA (Covance, MMS-101R)


title: hrt-asil2-2-br2


title: NA 5

description: Illumina EPIC


title: KO

city: Dallas

first: Peter

middle: M

last: Douglas

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
10x Genomics’ cellranger mkfastq version 5.0.0 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 5.0.0 was used to generate mapped bam files using default settings
Genome_build: mm10
Supplementary_files_format_and_content: R object containing both the samples

source_name: Single nuclei

extract_protocol:
Nuclei were loaded with Single Cell 3’ Gel Beads into a Next GEM Chip G and run on the Chromium™ Controller. GEM emulsions were incubated and then broken. Silane magnetic beads were used to clean up GEM reaction mixture. Read one primer sequence was added during incubation and full-length, barcoded cDNA was then amplified by PCR after cleanup. Sample size was checked on the Agilent Tapestation 4200 using the DNAHS 5000 tape and concentration was determined by the Qubit® 4.0 Fluorimeter (ThermoFisher) using the DNA HS assay. Samples were enzymatically fragmented and underwent size selection before proceeding to library construction.
During library preparation, Read 2 primer sequence, sample index, and both Illumina adapter sequences were added. Subsequently, samples were cleaned up using Ampure XP beads and post library preparation quality control was performed using the DNA 1000 tape on the Agilent Tapestation 4200. Final concentration was ascertained using the Qubit DNA HS assay. Samples were loaded at 1.6 pM and run on the Illumina NextSeq500 High Output Flowcell using V2.5 chemistry. Run configuration was 28x98x8.

treatment_protocol: Single nuclei isolation methods were adapted from 10x Genomics protocols CG000212 Rev B and CG000124 Rev D. Surf1 +/+ and -/- brains were harvested under cold sterile 1x Dulbecco’s PBS (without Ca2+ and Mg2+). Immediately after harvesting, the cortex, olfactory bulbs and cerebellum were removed on an ice block and discarded. Brains were then triturated and lysed using the Nuclei PURE Prep Isolation Kit (Cat. No. NUC-201, Sigma). Briefly, brains were homogenized under cold Nuclei PURE Lysis Buffer and mechanically triturated with sterile pipettes and pipette tips of decreasing sizes until creating a uniform suspension. Suspensions were then filtered through 70 μm, 40 μm and 30 μm cell strainers to remove cell debris. Myelin removal proceeded using the Debris Removal Solution (Cat. No. 130-109-398, Miltenyi) according to manufacturer’s instructions. Single nuclei were isolated and purified via density gradient centrifugation with the Nuclei PURE sucrose cushion solution (Cat. No. NUC-201, Sigma) at a centrifugation speed of 13,000 rcf. Nuclei was resuspended in 1x Dulbecco’s PBS supplemented with 1% bovine serum albumin and 20 U/μl RNase inhibitor (Cat. No. AM2694, Invitrogen).

value: brain

value: 10 weeks old


title: WT


title: PL15M3

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

data_processing:
The raw sequence files were first chekced for quality by FASTQC.
The quality control was performed using cutadpat
Read mapping was performed by Subread aligener using the full indexed reference followed by seed-and-vote mapping strategy implemented in Subread.
The mapped reads to miRNAs were counted using featureCounts tooL with Ensembl  annotation
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Tab-delimited text file with raw read counts for each miRNA.

source_name: Placenta

growth_protocol: Gestation day 15 of wildtype mice. The vaginal plug was observed was considered day 0.5 of gestation to detemine gestational age.

extract_protocol:
Freshly collected day 15 placenta and fetal brain from  wildtype mice were snap frozen in liquid nitrogen. Total RNA was isolated from frozen speciment using a standard TRIzol-based protocol (Catalog 15596026, Thermo Fisher). To eliminate genomic DNA contamination, extracted RNA was treated with DNase I and purified using a RNeasy MinElute Cleanup Kit (Qiagen). The quality and concentration of RNA were determined using a Fragment Analyzer (Advanced Analytical Technologies).
Libraries were prepared by the University of Missouri DNA core using an TruSeq Small RNA Library Prep Kit (Illumina Inc.)
The miRNA-seq strategy of TruSeq small RNA libraries was used.

value: Placenta

tag: gender

value: Male


title: PL15M2

value: Wildtype


title: PL15M1


title: hrt-asil2-1-br3

value: embryos


title: hrt-asil2-1-br2


title: hrt-asil2-2-br1

value: Landsberg erecta


title: NA 6

description: Illumina EPIC

data_processing: IDAT files were processed with using the noob normalization function in the minfi R package (Aryee et al., 2014)


title: EAN 10

description: Illumina EPIC

value: EAN

value: M


title: hrt-asil2-1-br1


title: PL15F3

value: Female


title: Study2_SmallRNA_IntmiS1_2

city: Philadelphia

first: Paul

middle: T

last: Ranum

address: 3501 Civic Center Blvd.

department: Center for Cellular and Molecular Therapy

institute: The Children's Hospital of Philadelphia

description: small RNA

data_processing:
Read Alignment with STAR_2.6.0c to the rhesus macaque genome (mmul10 from ensembl).
Feature counts values generated by STAR were used as the basis for differential expression analysis using DESeq2
Genome_build: mmul10
Supplementary_files_format_and_content: STAR generated tab delimited splice junction counts files "_SJ_out.tab"

organism: Macaca mulatta

source_name: Intermediate Deep

extract_protocol:
For RNA-Seq, total RNA (1 µg) was extracted from tissue using TRIzol (Ambion by Life Technologies) and treated to remove contaminating DNA using RNAeasy Plus Miniprep kit (QIAgen). For small RNA-Seq Small RNAs were extracted from tissue using miRNeasy Kit (QIAgen).
For RNA-Seq, RIN values were acquired using RNA Nano Chips (Agilent Technologies) in Agilent 2100 BioAnalyzer as per manufacturer’s protocol. Sequencing libraries were prepared using, NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). As no Rhesus specific ribosomal RNA (rRNA) depletion kit was available rRNA depletion was performed using combined Human, Mouse, and Rat species specific QIAseq FastSelect RNA Removal Kit (QIAgen). SPRIselect Beads (Beckman Coulter) were used for the purification steps. cDNA libraries were then indexed using the NEBNext Dual Index Kit (New England Biolabs).  Samples were analyzed on High Sensitivity DNA Chips (Agilent Technologies) with Agilent 2100 BioAnalyzer as per manufacturer’s protocol to determine library size, concentration and purity. For small RNA-Seq, RIN values were acquired using RNA Nano Chips (Agilent Technologies) in Agilent 2100 BioAnalyzer as per manufacturer’s protocol. Sequencing libraries were prepared using TruSeq Small RNA Library Prep Kit (Illumina) with the QIAquick Gel Extraction Kit DNA extraction supplement (QIAgen).  SPRIselect Beads (Beckman Coulter) were used for the purification steps. cDNA libraries were then indexed using the TruSeq Small RNA Library Prep Kit-Set A Indices (Illumina). Samples were analyzed on High Sensitivity DNA Chips (Agilent Technologies) with Agilent 2100 BioAnalyzer as per manufacturer’s protocol to determine library size, concentration and purity

treatment_protocol: The indicated treatments for each sample were administered by clearpoint MRI guided injection into the deep cerebellar nuclei of the the indicated Rhesus macaque.  A detailed protocol can be found in our publication Keiser et al., 2021 Nat Med.

tag: ID

value: cerebellum


title: Study2_SmallRNA_EmptyCapsid_1

description: small RNA


title: Study2_SmallRNA_IntmiS1_3

description: small RNA


title: Study2_SmallRNA_IntmiS1_1

description: small RNA


title: PL15F1


title: PL15F2


title: Study1_SmallRNA_Vehicle_3

description: small RNA

value: Vehicle


title: Study2_SmallRNA_EmptyCapsid_3

description: small RNA


title: Study2_SmallRNA_EmptyCapsid_2

description: small RNA


title: hrt-asil1-1-br2


title: hrt-asil1-1-br3


title: EAN 11

description: Illumina EPIC

value: crypt (colon)


title: hrt-asil1-1-br1


title: Study1_SmallRNA_Vehicle_2

description: small RNA


title: hrt-asil1-1-2-2-br3

value: Columbia-0/Landsberg erecta

value: asil1-1 asil2-2


title: BR15M2

source_name: Fetal brain

value: Fetal brain


title: Contusion injury cord + AAV5-dYFP, 28DPI, biological rep4

city: Auckland

first: Connor

middle: Andrew

last: Clemett

state: Auckland

address: 85 Park Rd

department: Anatomy and Medical Imaging

country: New Zealand

institute: University of Auckland

description:
SD_Rat_Injury_dYFP_28DPI_04
Rattus norvegicus domestica

hyb_protocol: Rat Clariom S arrays were incubated in the Affymetrix® GeneChip® Hybridization Oven 645 at 45° C / 60 RPM for 16-18 hours.

scan_protocol: GeneChips were scanned with the GeneChip™ Scanner 3000 (Applied Biosystems, #00-0186) according to manufacturer's instructions.

data_processing: Raw intensity CEL files were imported into Transcriptome Analysis Console (TAC software v4.0.2.15. Applied Biosystems), and gene level expression analysis was performed using the default ANOVA settings.

label: Biotin

organism: Rattus norvegicus

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA.

extract_protocol: Total RNA was extracted by mechanical tissue dissociation, TRIzol / chloroform extraction and phase separation. RNA extract quantified by Implen NP80 nanophotometer and quality assed by Agilent Bioanalyzer (RIN >8.80).

treatment_protocol: Adult female Sprague-Dawley rats (220-250 g) underwent surgical T10 laminectomy and moderate contusive injury (175 kDyn) by an Infinite Horizons impactor. Treatment groups were acutely administered the AAV5-GfaABC1D-dYFP reporter vector at the time of surgery by stereotaxic microinjection. Following recovery, at 7- and 28-days post-injury animals were euthanised, perfused with ice-cold saline and a 5 mm region centered on the spinal lesion excised to be snap frozen.

value: Sprague Dawley

value: Adult

value: Spinal cord tissue

tag: injury

value: 175 kDyn, T10 contusion

value: 4 x 10^9 vg AAV5-GfaABC1D-dYFP, 4 uL

tag: time post-injury

value: 28 days


title: Contusion injury cord + AAV5-dYFP, 28DPI, biological rep3

description:
SD_Rat_Injury_dYFP_28DPI_03
Rattus norvegicus domestica

tag: Sex


title: EAN 12

description: Illumina EPIC

tag: individual


title: Study1_SmallRNA_Vehicle_1

description: small RNA

tag: treatment


title: BR15M3

value: Male

tag: genotype

value: Wildtype


title: Contusion injury cord + AAV5-dYFP, 28DPI, biological rep5

description:
SD_Rat_Injury_dYFP_28DPI_05
Rattus norvegicus domestica


title: hrt-asil1-1-2-2-br2

value: embryos


title: hrt-asil1-1-2-2-br1


title: Study1_SmallRNA_Dosed_3

description: small RNA


title: KN 4

description: Illumina EPIC

value: KN

value: M


title: EAN 9

description: Illumina EPIC

value: EAN


title: BR15F3

value: Female


title: Study1_SmallRNA_Dosed_2

description: small RNA

value: cerebellum


title: BR15M1


title: Contusion injury cord + AAV5-dYFP, 28DPI, biological rep1

description:
SD_Rat_Injury_dYFP_28DPI_01
Rattus norvegicus domestica


title: Study1_SmallRNA_Dosed_1

description: small RNA


title: BR15F2


title: Contusion injury cord + AAV5-dYFP, 7DPI, biological rep5

description:
SD_Rat_Injury_dYFP_7DPI_05
Rattus norvegicus domestica

source_name: Contusion injury cord + AAV5-dYFP, 7DPI

value: 7 days


title: Contusion injury cord + AAV5-dYFP, 7DPI, biological rep4

description:
SD_Rat_Injury_dYFP_7DPI_04
Rattus norvegicus domestica


title: hrt-asil1-1-2-1-br1

value: asil1-1 asil2-1


title: BR15F1

value: Fetal brain


title: Contusion injury cord + AAV5-dYFP, 7DPI, biological rep3

description:
SD_Rat_Injury_dYFP_7DPI_03
Rattus norvegicus domestica

value: Sprague Dawley


title: Study2_StufferOnly_2_DCN

source_name: Deep Cerebellar Nuclei

value: StufferOnly


title: Contusion injury cord + AAV5-dYFP, 28DPI, biological rep2

description:
SD_Rat_Injury_dYFP_28DPI_02
Rattus norvegicus domestica

value: Adult

value: Spinal cord tissue


title: Study2_StufferOnly_3_DCN


title: Contusion injury cord + AAV5-dYFP, 7DPI, biological rep2

description:
SD_Rat_Injury_dYFP_7DPI_02
Rattus norvegicus domestica

value: 175 kDyn, T10 contusion

value: 4 x 10^9 vg AAV5-GfaABC1D-dYFP, 4 uL


title: AM KO Rep. 3

city: Pittsburgh

first: Rachel

middle: A.

last: Gottschalk

state: Pennsylvania

address: 200 Lothrop St., W1047 BST

department: Immunology

institute: University of Pittsburgh

data_processing:
Illumina software RTA 2.0 was used for base calling
Rsubread was used for index building, alignment to mm10 and read counting. Default settings were used.
DESeq2 was used for data normalization and differential gene expression significance calculations
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for all protein coding genes and samples

source_name: Alveolar macrophages

extract_protocol:
Alveolar macrophages were sorted into TRIzol LS and RNA was extracted using the Zymo Directzol RNA MiniPrep kit
Libraries were prepared with the Nextera XT DNA Library Preparation Kit (Illunmina)

value: Cish KO, C57BL/6

value: 4 months

value: Cish KO


title: Study2_StufferOnly_1_DCN


title: AM KO Rep. 2


title: sdlg-Ler-br2

source_name: Arabidopsis 14d seedlings

growth_protocol: Plants were germinated and grown on MS medium without sucrose, at 22°C with 16 hours of light in a Percival Scientic incubator for 14 days.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Minikit (QIAGEN), per the manufacturer’s directions.
Illumina-complatible libraries were made starting with 5 ug of total RNA, using Kumar et al. (Kumar R, Ichihashi Y, Kimura S, Chitwood DH, Headland LR, Peng J, Maloof JN and Sinha NR (2012) A high-throughput method for Illumina RNA-Seq library preparation. Front. Plant Sci. 3:202. doi: 10.3389/fpls.2012.00202) Supplemetary Methods 1 library preparation protocol, at the exception of the RNA and mRNA isolation: the polyA isolation from total RNA described in Supplementary Methods 2 was used and the NEXTflex ChIP-Seq Barcodes (BiooScientific) were used for Illumina-compatible adapters. Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument.  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

treatment_protocol: Seedlings were collected 14d after germination and  flash-frozen in liquid nitrogen.

value: 14d seedlings

value: Landsberg erecta

value: wild type


title: AM KO Rep. 1


title: hrt-asil1-1-2-1-br3

value: embryos


title: CB 2

city: Los Angeles

first: Darryl

last: Shibata

address: NOR 1441 Eastlake Ave

institute: USC

description: Illumina EPIC

value: CB

value: crypt (colon)

value: M


title: sdlg-Ler-br1


title: KN 1

description: Illumina EPIC

value: KN


title: Study2_miSCA7Stuffer_3_DCN

value: cerebellum


title: Study2_miSCA7Stuffer_2_DCN


title: KN 5

description: Illumina EPIC


title: KN 6

description: Illumina EPIC


title: Contusion injury cord + AAV5-dYFP, 7DPI, biological rep1

description:
SD_Rat_Injury_dYFP_7DPI_01
Rattus norvegicus domestica

value: Sprague Dawley

value: Female

value: 7 days


title: O 6

description: Illumina EPIC

value: O


title: AM WT Rep. 3

value: WT, C57BL/6

value: WT


title: Contusion injury cord, 28DPI, biological rep3

description:
SD_Rat_Injury_28DPI_03
Rattus norvegicus domestica

source_name: Contusion injury cord, 28DPI

value: Adult

value: Spinal cord tissue

value: 175 kDyn, T10 contusion

value: 28 days


title: Study2_miSCA7Stuffer_1_DCN


title: Contusion injury cord, 28DPI, biological rep5

description:
SD_Rat_Injury_28DPI_05
Rattus norvegicus domestica


title: O 5

description: Illumina EPIC


title: sdlg-Col-br2

value: 14d seedlings

value: wild type


title: AM WT Rep. 2

value: 4 months


title: AM WT Rep. 4


title: sdlg-Col-br3


title: Study2_intmiS1_3_DCN


title: Contusion injury cord, 28DPI, biological rep4

description:
SD_Rat_Injury_28DPI_04
Rattus norvegicus domestica


title: KC 30

description: Illumina EPIC

value: KC

value: crypt (colon)

value: F


title: sdlg-Col-br1


title: Study2_intmiS1_2_DCN

value: cerebellum


title: Contusion injury cord, 28DPI, biological rep1

description:
SD_Rat_Injury_28DPI_01
Rattus norvegicus domestica

value: Sprague Dawley


title: CB 5

description: Illumina EPIC

value: CB

value: M


title: Contusion injury cord, 7DPI, biological rep5

description:
SD_Rat_Injury_7DPI_05
Rattus norvegicus domestica

source_name: Contusion injury cord, 7DPI

value: Female

value: 7 days


title: sdlg-asil2-2-br3

value: Landsberg erecta


title: AM WT Rep. 1

value: WT, C57BL/6

value: WT


title: Study2_intmiS1_1_DCN


title: hrt-asil1-1-2-1-br2

value: embryos

value: asil1-1 asil2-1


title: sdlg-asil2-2-br2

value: 14d seedlings


title: H1_PP_D14_R2

city: University park

first: Yuqian

last: Jiang

address: W345 millennium science complex

institute: PSU

data_processing:
Data were collected with Nextseq High Output 75nt single read sequencing. Original output files are Fastq files.
Raw reads was checked on quality control with FastQC.
Reads was mapped and counted in Kallisto with defaulted parameters. Use human hg38 genome assembly for reference.
Genome_build: hg38
Supplementary_files_format_and_content: tsv files include counts number and tpm values for each transcript.

source_name: H1 Oct4-GFP cells_treated with the protocol of pancreatic progenitor differentiation for 14 days

growth_protocol: H1 Oct4-GFP cells were cultured in mTeSR1 medium on imatrix-coated plates.

extract_protocol:
Cells were lysed with TRI-reagent for 1min and RNA was extracted with Direct-zol RNA MiniPrep Plus kit (Zymo research), followed by RNA purification with RNA clean & concentrator kit (Zymo Research).
Samples were analyzed with Agilent Bioanalyer for quality control. mRNA libraries were generated with the TruSeq Stranded mRNA library construction kit. Data were collected with Nextseq High Output 75nt single read sequencing.

treatment_protocol: H1 Oct4-GFP cells were induced into definitive endoderm (DE) cells with our reported GiBi protocol, followed by pancreatic progenitor induction protocols.

value: human ESCs (H1)

tag: genotype/variation

tag: differentiation time

tag: replicate number


title: O 7

description: Illumina EPIC

value: O


title: CB 4

description: Illumina EPIC


title: H1_PP_D14_R1


title: sdlg-asil2-2-br1


title: Study2_EmptyCapsid_3_DCN


title: H1_PP_D12_R2

source_name: H1 Oct4-GFP cells_treated with the protocol of pancreatic progenitor differentiation for 12 days


title: Study2_EmptyCapsid_2_DCN


title: sdlg-asil2-1-br3


title: CB 1

description: Illumina EPIC


title: H1_PP_D12_R1


title: KC 28

description: Illumina EPIC

value: KC


title: KC 27

description: Illumina EPIC

value: crypt (colon)


title: Contusion injury cord, 7DPI, biological rep4

description:
SD_Rat_Injury_7DPI_04
Rattus norvegicus domestica

value: Adult

value: Spinal cord tissue

value: 175 kDyn, T10 contusion


title: Study2_EmptyCapsid_1_DCN

value: cerebellum


title: sdlg-asil2-1-br2


title: O 8

description: Illumina EPIC

value: M


title: H1_PP_D8_R2

source_name: H1 Oct4-GFP cells_treated with the protocol of pancreatic progenitor differentiation for 8 days


title: Contusion injury cord, 7DPI, biological rep3

description:
SD_Rat_Injury_7DPI_03
Rattus norvegicus domestica

value: Sprague Dawley

value: Female


title: H1_PP_D8_R1


title: Contusion injury cord, 7DPI, biological rep1

description:
SD_Rat_Injury_7DPI_01
Rattus norvegicus domestica

value: 7 days


title: Uninjured cord, biological rep5

description:
SD_Rat_Control_05
Rattus norvegicus domestica

source_name: Uninjured cord

value: No Injury


title: sdlg-asil2-1-br1


title: Contusion injury cord, 7DPI, biological rep2

description:
SD_Rat_Injury_7DPI_02
Rattus norvegicus domestica


title: H1_PP_D6_R1

source_name: H1 Oct4-GFP cells_treated with the protocol of pancreatic progenitor differentiation for 6 days


title: H1_PP_D6_R2


title: Study1_DCN08


title: sdlg-asil1-1-br2


title: Study1_DCN09


title: Study1_DCN07


title: KC 29

description: Illumina EPIC

source_name: colon

value: F


title: H1_PP_D4_R2

source_name: H1 Oct4-GFP cells_treated with the protocol of pancreatic progenitor differentiation for 4 days


title: Study1_DCN06

value: Vehicle


title: sdlg-asil1-1-br1


title: Uninjured cord, biological rep4

description:
SD_Rat_Control_04
Rattus norvegicus domestica


title: sdlg-asil1-1-2-2-br3

value: Columbia-0/Landsberg erecta

value: asil1-1 asil2-2


title: H1_PP_D4_R1

value: human ESCs (H1)


title: Uninjured cord, biological rep3

description:
SD_Rat_Control_03
Rattus norvegicus domestica


title: Uninjured cord, biological rep2

description:
SD_Rat_Control_02
Rattus norvegicus domestica


title: sdlg-asil1-1-br3

value: 14d seedlings


title: Study1_DCN05


title: Contusion injury cord, 28DPI, biological rep2

description:
SD_Rat_Injury_28DPI_02
Rattus norvegicus domestica

value: 28 days


title: sdlg-asil1-1-2-2-br2


title: IN2

city: Kolkata

first: Manikuntala

last: Kundu

state: West Bengal

address: 93/1, Acharya Prafulla Chandra Road

institute: Bose Institute

data_processing:
The quality check of raw reads was performed using the Genotypic FastQC tool.
The reads were aligned to the reference M. tuberculosis H37Rv genome using the Bowtie alignment tool
Peak detection was carried out using the Hypergeometric Optimization of Motif EnRichment (Homer) tool.
Genome_build: H37Rv

organism: Mycobacterium tuberculosis

source_name: Mtb phosphate  limited, input rep2

growth_protocol: Mtb was  grown to log phase in Middle Brook 7H9 medium  containing 10% ADC

extract_protocol:
Mtb  grown in phosphate depleted medium  was crosslinked using 1% formaldehyde followed by quenching with 250mM glycine. The cells were  lysed and the DNA was sheared on Bioruptor plus (Diagenode) with 25 cycles of 30 sec/ 90 sec on/off, respectively, so as to generate fragment sizes of ~250 bp. Immune complexes were precipitated with  RegX3 antibody or control  IgG, and washed. DNA from total lysates (input) and immunoprecipitates (IP) were purified after decrosslinking with Proteinase K and samples were used immediately for next-generation sequencing (NGS).
ChIP-Seq libraries for sequencing were constructed at Genotypic Technology’s Genomics facility according to the NEXTflex ChIP-Seq library protocol outlined in the NEXTflex ChIP-Seq kit (cat nos102–1001)
The libraries were enriched using PCR followed by purification using Agencourt AMPURE XP beads (Beckman Coulter #A63881) and quality was checked on a High Sensitivity Bioanalyzer Chip (Agilent).Sequencing was performed at Genotypic Technology’s Genomics facility following certified protocols from Illumina on an Illumina Hi-seq platform using single-end 75 bp chemistry.

treatment_protocol: Log phase cells were harvested and resuspended in  phosphate limited medium and grown  for 72 hours under shaking at 37◦C

tag: media

value: phosphate limited

tag: chip antibody

value: none (input)

tag: molecule subtype

value: INPUT DNA


title: IN1

source_name: Mtb phosphate  limited, input rep1


title: Study1_DCN04


title: H1_PP_D2_R2

source_name: H1 Oct4-GFP cells_treated with the protocol of pancreatic progenitor differentiation for 2 days

tag: cell type


title: H1_PP_D2_R1


title: Study1_DCN03

tag: tissue


title: sdlg-asil1-1-2-2-br1

tag: ecotype


title: C3B

source_name: Mtb phosphate  limited (IgG-IP) rep2

value: anti-IgG

value: IP DNA


title: sdlg-asil1-1-2-1-br2

value: asil1-1 asil2-1


title: C3A

source_name: Mtb phosphate limited (IgG-IP) rep1


title: H1_PP_D0_R1

source_name: H1 Oct4-GFP cells


title: C1B

source_name: Mtb phosphate  limited (RegX3-IP) rep2

value: anti-RegX3 (custom-made antibody of RegX3 was raised by Thermo Fisher Scientific, USA)


title: Study1_DCN01

source_name: Deep Cerebellar Nuclei

value: cerebellum


title: H1_PP_D0_R2