title: Brain single cell 577

description: processed data column: Brain.EC4_J22


title: WG960039_A06-W30

status: Public on Dec 06 2017

type: SRA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: Processed data file: molecules_human.xlsx

library_source: transcriptomic

data_processing:
Reads flagged as invalid by the Illumina HiSeq control software were discarded. In the remaining reads, any 3′ bases with a quality score of B were removed. If any of the six UMI bases in the 5' end had a Phred score <17 the read was discarded, else the UMI was cut away and saved. The following three bases had to be G for the read to be kept. These, as well as any additional up to totally nine (presumably template-switch derived) G:s were cut away. Reads were discarded if the remaining transcript-derived sequence ended in a poly(A) sequence leaving <25 bases, or if the remaining sequence consisted of fewer than six non-A bases or a dinucleotide repeat with fewer than six other bases at either end. The reads were sorted by the well, as defined by the combined two index read barcodes.
Alignment was performed using the Bowtie aligner, allowing for up to three mismatches and up to 24 alternative mappings. Reads with no alignments were realigned against an artificial chromosome, containing all possible splice junctions arising from the exons defined by the UCSC transcript models. The coordinates of aligned splice junctions were translated back to the corresponding genomic positions.
For expression level calculation, the exons of each locus with several transcript variants were merged to a combined model representing total expression of the locus. To account for incomplete cap site knowledge, the 5′ ends of all models were extended by 100 bases, but not beyond the 3′ end of any upstream nearby exon of another gene of the same orientation.
The annotation step was performed separately for each well. For each genomic position and strand combination the number of reads in each UMI was counted. Any multiread that mapped to some repeat outside exons was assigned randomly as one of these repeats and did not contribute to the transcript corresponding to the exon. Else, if the multiread mapped to some exon, and not to any repeat outside exons, it was assigned to the exon where it was closest to the transcript model 5′ end. If it had no exon mapping, it was assigned randomly at one of the mappings. The total number of molecules at each mapping position was determined by the number of distinct UMIs observed. Any UMI represented by only a single read was excluded, in order to reduce false molecules due to PCR and sequencing errors. The raw UMI count was corrected for the UMI collision probability. For the human samples all reads mapping anywhere within the whole locus, defined as the region (including actual introns) from the start of the 100 base 5'end extension of the first exon up to the end of the last exon, were counted as exon-derived.
Genome_build: UCSC mm10 (GRCm38) and hg19 (GRCh37)
Supplementary_files_format_and_content: *xlsx: Excel tables of mRNA molecule counts with genes in rows and cells in columns.

molecule: total RNA

organism: Homo sapiens

source_name: middle temporal gyrus

growth_protocol: Male and female wild type CD-1 mice (Charles River) between postnatal days 21-37 were used. Postmortem human brain tissue was provided to the Allen Institute for Brain Science by the San Diego Medical Examiner’s (SDME) office.

extract_protocol:
Mice were anesthetized with isoflurane, perfused with ice-cold aCSF, brains collected and sectioned using a vibratome or brain matrix and the somatosensory cortex was microdissected. Single cell suspensions were generated using the Worthington Papain dissociation system. Human nuclei were isolated from a -80°C frozen tissue piece using Dounce homogenization.
50nl lysis mix (500nM STRT-P1-T31, 4.5nM dNTP, 2% Triton-X-100, 20mM DTT, 1.5U/μl TaKaRa RNase Inhibitor) was dispensed, followed by 3min lysis at 72°C. Then, 85nl reverse transcription (RT) mix (2.1X SuperScript II First-Strand Buffer, 12.6mM MgCl2, 1.79M betaine, 14.7U/μl SuperScript II, 1.58U/μl TaKaRa RNase Inhibitor, 10.5μM P1B-UMI-RNA-TSO) were dispensed and RT carried out 42°C for 90 minutes. 96 Transposome stocks were assembled (6.25μM barcoded adapter (STRT-Tn5-Idx[1-96]), 6.25μM Tn5 transposase, 40% glycerol), 37°C 1h. Tn5 reactions were assembled with 3μl transposome and 2μl amplified cDNA, in a total 20μl 1x CutSmart buffer (NEB), and incubated at 55°C 20min.

tag: cluster

value: dcc

tag: tissue

value: middle temporal gyrus


title: WG960039_A06-W27


title: Brain single cell 576

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

description: processed data column: Brain.EC4_J21

data_processing:
RNA-seq reads were mapped to the mouse reference genome (mm10) using STAR (version STAR_2.4.2a) and the count matrix shows the individual counts aligning to each gene per cell. In order to compare the gene expression counts between different cells, the total gene counts for each cell was normalized to 500,000.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized counts values for each sample

organism: Mus musculus

source_name: Brain

extract_protocol:
We used four different transgenic mouse reporter lines with fluorescent expression in different populations of vascular cells, Cldn5(BAC)eGFP mice that strongly labels brain endothelial cells, mice doubly positive for Pdgfrb(BAC)eGFP and NG2dsRed, in which brain vascular mural cells express both markers whereas each single marker are expressed also in other, non-overlapping cell types, and Pdgfra-H2BGFP that we found labeled a perivascular population of cells distinct from mural cells and astrocytes, in addition to the known labeling of cells of the oligendendrocyte lineage.   We chose to focus our efforts to adult mice 12 to 15 weeks old in order to primarily define fully differentiated and quiescent vascular cells and we chose a methodology based on fluorescence-activated cell sorting (FACS) into 384-well plates
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

tag: strain

value: brain

tag: age

value: adult mice 12 to 15 weeks old

tag: genotype


title: Brain single cell 575

description: processed data column: Brain.EC4_J20


title: Brain single cell 582

description: processed data column: Brain.EC4_J4


title: Brain single cell 574

description: processed data column: Brain.EC4_J1


title: WG960039_A06-W21


title: WG960039_A06-W20


title: WG960039_A06-W18


title: Brain single cell 570

description: processed data column: Brain.EC4_J15


title: WG960039_A06-W17


title: WG960039_A06-W19


title: Brain single cell 573

description: processed data column: Brain.EC4_J19


title: WG960039_A06-W26


title: WG960039_A06-W14


title: WG960039_A06-W11


title: Brain single cell 569

description: processed data column: Brain.EC4_J14


title: Brain single cell 572

description: processed data column: Brain.EC4_J18


title: Brain single cell 565

description: processed data column: Brain.EC4_J10


title: WG960039_A06-W23


title: Brain single cell 567

description: processed data column: Brain.EC4_J12


title: WG960039_A06-W15


title: WG960039_A06-W10


title: Brain single cell 568

description: processed data column: Brain.EC4_J13


title: Brain single cell 563

description: processed data column: Brain.EC4_I8


title: Brain single cell 566

description: processed data column: Brain.EC4_J11


title: Brain single cell 564

description: processed data column: Brain.EC4_I9


title: Brain single cell 562

description: processed data column: Brain.EC4_I7


title: WG960039_A06-W09


title: WG960039_A06-W07


title: Brain single cell 571

description: processed data column: Brain.EC4_J16


title: WG960039_A06-W06


title: Brain single cell 561

description: processed data column: Brain.EC4_I6


title: Brain single cell 560

description: processed data column: Brain.EC4_I5


title: WG960039_A06-W04


title: WG960039_A06-W13


title: WG960039_A06-W03


title: Brain single cell 559

description: processed data column: Brain.EC4_I4


title: Brain single cell 557

description: processed data column: Brain.EC4_I2


title: Brain single cell 558

description: processed data column: Brain.EC4_I3


title: WG960039_A05-W32


title: WG960039_A06-W01


title: Brain single cell 554

description: processed data column: Brain.EC4_I22


title: Brain single cell 556

description: processed data column: Brain.EC4_I24


title: Brain single cell 553

description: processed data column: Brain.EC4_I21


title: WG960039_A05-W25


title: WG960039_A05-W30


title: WG960039_A05-W27


title: Brain single cell 555

description: processed data column: Brain.EC4_I23


title: WG960039_A05-W29


title: WG960039_A05-W24


title: Brain single cell 552

description: processed data column: Brain.EC4_I20


title: Brain single cell 551

description: processed data column: Brain.EC4_I1


title: Brain single cell 550

description: processed data column: Brain.EC4_I19


title: WG960039_A05-W23


title: Brain single cell 549

description: processed data column: Brain.EC4_I17


title: WG960039_A05-W21


title: Brain single cell 548

description: processed data column: Brain.EC4_I16


title: WG960039_A06-W02


title: Brain single cell 547

description: processed data column: Brain.EC4_I15


title: WG960039_A05-W16


title: WG960039_A05-W15


title: Brain single cell 546

description: processed data column: Brain.EC4_I14


title: Brain single cell 545

description: processed data column: Brain.EC4_I13


title: WG960039_A05-W13


title: Brain single cell 544

description: processed data column: Brain.EC4_I12


title: Brain single cell 541

description: processed data column: Brain.EC4_H9


title: WG960039_A05-W08


title: Brain single cell 542

description: processed data column: Brain.EC4_I10


title: WG960039_A05-W07


title: Brain single cell 538

description: processed data column: Brain.EC4_H6


title: WG960039_A05-W19


title: Brain single cell 540

description: processed data column: Brain.EC4_H8


title: WG960039_A05-W04


title: WG960039_A05-W03


title: WG960039_A05-W06


title: Brain single cell 537

description: processed data column: Brain.EC4_H5


title: WG960039_A05-W05


title: Brain single cell 536

description: processed data column: Brain.EC4_H4


title: Brain single cell 543

description: processed data column: Brain.EC4_I11


title: Brain single cell 535

description: processed data column: Brain.EC4_H3


title: Brain single cell 539

description: processed data column: Brain.EC4_H7


title: WG960039_A05-W01


title: WG960039_A04-W30


title: WG960039_A04-W32


title: WG960039_A05-W11


title: Brain single cell 533

description: processed data column: Brain.EC4_H24


title: WG960039_A06-W12


title: WG960039_A04-W28


title: Brain single cell 531

description: processed data column: Brain.EC4_H22


title: WG960039_A04-W29


title: Brain single cell 534

description: processed data column: Brain.EC4_H2


title: WG960039_A04-W26


title: WG960039_A04-W27


title: Brain single cell 529

description: processed data column: Brain.EC4_H20


title: WG960039_A04-W24


title: WG960039_A04-W25


title: Brain single cell 530

description: processed data column: Brain.EC4_H21


title: Brain single cell 528

description: processed data column: Brain.EC4_H1


title: Brain single cell 525

description: processed data column: Brain.EC4_H17


title: WG960039_A04-W18


title: WG960039_A04-W20


title: Brain single cell 524

description: processed data column: Brain.EC4_H16


title: Brain single cell 526

description: processed data column: Brain.EC4_H18


title: Brain single cell 527

description: processed data column: Brain.EC4_H19


title: WG960039_A04-W16


title: Brain single cell 523

description: processed data column: Brain.EC4_H15


title: WG960039_A04-W14


title: Brain single cell 522

description: processed data column: Brain.EC4_H14


title: Brain single cell 532

description: processed data column: Brain.EC4_H23


title: WG960039_A04-W12


title: Brain single cell 520

description: processed data column: Brain.EC4_H12


title: Brain single cell 519

description: processed data column: Brain.EC4_H11


title: WG960039_A04-W11


title: WG960039_A04-W10


title: WG960039_A04-W09


title: Brain single cell 518

description: processed data column: Brain.EC4_H10


title: WG960039_A04-W06


title: WG960039_A04-W19


title: Brain single cell 517

description: processed data column: Brain.EC4_G7


title: Brain single cell 516

description: processed data column: Brain.EC4_G6


title: WG960039_A04-W07


title: Brain single cell 514

description: processed data column: Brain.EC4_G3


title: WG960039_A04-W04


title: Brain single cell 513

description: processed data column: Brain.EC4_G2


title: Brain single cell 515

description: processed data column: Brain.EC4_G4


title: WG960039_A04-W05


title: Brain single cell 512

description: processed data column: Brain.EC4_G24


title: Brain single cell 511

description: processed data column: Brain.EC4_G22


title: WG960039_A03-W32


title: WG960039_A04-W23


title: WG960039_A04-W02


title: Brain single cell 510

description: processed data column: Brain.EC4_G21


title: Brain single cell 521

description: processed data column: Brain.EC4_H13


title: WG960039_A04-W17


title: WG960039_A03-W30


title: WG960039_A03-W31


title: WG960039_A03-W29


title: Brain single cell 509

description: processed data column: Brain.EC4_G20


title: Brain single cell 508

description: processed data column: Brain.EC4_G1


title: WG960039_A03-W28


title: Brain single cell 507

description: processed data column: Brain.EC4_G19


title: Brain single cell 506

description: processed data column: Brain.EC4_G18


title: WG960039_A03-W27


title: Brain single cell 505

description: processed data column: Brain.EC4_G17


title: Brain single cell 504

description: processed data column: Brain.EC4_G16


title: WG960039_A03-W24


title: WG960039_A04-W01


title: Brain single cell 501

description: processed data column: Brain.EC4_G12


title: Brain single cell 503

description: processed data column: Brain.EC4_G15


title: WG960039_A03-W21


title: WG960039_A03-W25


title: Brain single cell 500

description: processed data column: Brain.EC4_G11


title: WG960039_A03-W19


title: WG960039_A03-W22


title: Brain single cell 499

description: processed data column: Brain.EC4_F9


title: Brain single cell 502

description: processed data column: Brain.EC4_G14


title: WG960039_A03-W20


title: WG960039_A03-W17


title: WG960039_A03-W16


title: WG960039_A03-W18


title: Brain single cell 497

description: processed data column: Brain.EC4_F7


title: Brain single cell 496

description: processed data column: Brain.EC4_F6


title: WG960039_A03-W15


title: Brain single cell 495

description: processed data column: Brain.EC4_F5


title: WG960039_A03-W14


title: WG960039_A03-W13


title: Brain single cell 494

description: processed data column: Brain.EC4_F4


title: Brain single cell 493

description: processed data column: Brain.EC4_F3


title: WG960039_A03-W08


title: Brain single cell 492

description: processed data column: Brain.EC4_F2


title: WG960039_A03-W06


title: WG960039_A03-W05


title: Brain single cell 491

description: processed data column: Brain.EC4_F24


title: WG960039_A03-W04


title: Brain single cell 490

description: processed data column: Brain.EC4_F23


title: Brain single cell 498

description: processed data column: Brain.EC4_F8


title: Brain single cell 486

description: processed data column: Brain.EC4_F1


title: Brain single cell 487

description: processed data column: Brain.EC4_F20


title: Brain single cell 488

description: processed data column: Brain.EC4_F21


title: WG960039_A02-W32


title: Brain single cell 485

description: processed data column: Brain.EC4_F19


title: Brain single cell 489

description: processed data column: Brain.EC4_F22


title: WG960039_A02-W29


title: WG960039_A02-W26


title: WG960039_A02-W28


title: Brain single cell 483

description: processed data column: Brain.EC4_F15


title: Brain single cell 484

description: processed data column: Brain.EC4_F16


title: WG960039_A02-W25


title: Brain single cell 481

description: processed data column: Brain.EC4_F13


title: Brain single cell 482

description: processed data column: Brain.EC4_F14


title: Brain single cell 480

description: processed data column: Brain.EC4_F12


title: WG960039_A02-W23


title: Brain single cell 479

description: processed data column: Brain.EC4_F11


title: WG960039_A02-W22


title: WG960039_A03-W02


title: WG960039_A02-W19


title: Brain single cell 478

description: processed data column: Brain.EC4_F10


title: Brain single cell 477

description: processed data column: Brain.EC4_E9


title: WG960039_A03-W01


title: WG960039_A02-W18


title: WG960039_A02-W31


title: Brain single cell 476

description: processed data column: Brain.EC4_E8


title: WG960039_A02-W17


title: WG960039_A02-W14


title: Brain single cell 473

description: processed data column: Brain.EC4_E5


title: Brain single cell 474

description: processed data column: Brain.EC4_E6


title: WG960039_A02-W12


title: WG960039_A02-W08


title: Brain single cell 471

description: processed data column: Brain.EC4_E3


title: Brain single cell 470

description: processed data column: Brain.EC4_E2


title: Brain single cell 475

description: processed data column: Brain.EC4_E7


title: WG960039_A02-W05


title: WG960039_A02-W24


title: WG960039_A02-W07


title: Brain single cell 469

description: processed data column: Brain.EC4_E24


title: WG960039_A02-W02


title: WG960039_A02-W01


title: Brain single cell 468

description: processed data column: Brain.EC4_E23


title: WG960039_A01-W32


title: Brain single cell 467

description: processed data column: Brain.EC4_E22


title: Brain single cell 466

description: processed data column: Brain.EC4_E21


title: Brain single cell 465

description: processed data column: Brain.EC4_E20


title: WG960039_A01-W28


title: Brain single cell 464

description: processed data column: Brain.EC4_E1


title: WG960039_A01-W31


title: Brain single cell 463

description: processed data column: Brain.EC4_E19


title: WG960039_A02-W15


title: Brain single cell 462

description: processed data column: Brain.EC4_E18


title: Brain single cell 472

description: processed data column: Brain.EC4_E4


title: WG960039_A01-W27


title: WG960039_A01-W23


title: WG960039_A01-W14


title: WG960039_A01-W21


title: Brain single cell 459

description: processed data column: Brain.EC4_E14


title: Brain single cell 457

description: processed data column: Brain.EC4_E12


title: WG960039_A01-W12


title: Brain single cell 456

description: processed data column: Brain.EC4_E11


title: WG960039_A01-W11


title: Brain single cell 455

description: processed data column: Brain.EC4_E10


title: WG960039_A01-W10


title: Brain single cell 454

description: processed data column: Brain.EC4_D9


title: WG960039_A01-W02


title: Brain single cell 453

description: processed data column: Brain.EC4_D8


title: WG960039_A01-W03


title: WG960039_A01-W29


title: Mtr4-polII

city: Shanghai

first: Hong

last: Cheng

address: 320 YueYang Road

department: Shanghai Institute of Biochemistry and Cell Biology

country: China

institute: Shanghai Institutes for Biological Sciences

library_source: genomic

data_processing:
Basecalls performed using TopHat2.0,fastx_toolkit-0.0.13.2 (Q33)
All 150-bp sequence reads were uniquely mapped to the human genome NCBI build 37 (hg19) using bwa 0.6.1 with standard parameters.
All Control, hRRP40 and hMTR4 datasets were normalized to the same sequencing depth by randomly removing aligned reads.
Duplicated reads were removed before normalization.   Peak recognition for RNAPII ChIP-seq datasets was performed using MACS2 with default settings and a P-value threshold of 1E-9 using a genomic DNA as background control.
Peaks were mapped to Ensemble genes, downloaded from UCSC Genome Browser (hg19), to determine genomic location of the Pol II binding sites at promoter regions (defined as 5 kb upstream of the transcription start site and the end of the first intron of genes), intragenic, intergenic, or 25 kb away from the transcription start site of the gene.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using MICS2

molecule: genomic DNA

source_name: uterine cervix

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS (Biochrom).

extract_protocol:
Lysates were clarified from sonicated whole cells and Polymerrase II were isolated with antibody.
Libraries were generated with TruSeq ChIP-seq Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: For RNAi, siRNA transfections were carried out with Lipofectamine 2000 (Invitrogen) for 72 hr.

tag: cell line

value: HeLa cell

value: uterine cervix

tag: chip antibody


title: Brain single cell 450

description: processed data column: Brain.EC4_D5


title: Brain single cell 451

description: processed data column: Brain.EC4_D6


title: WG960039_A01-W26


title: Brain single cell 449

description: processed data column: Brain.EC4_D4


title: Brain single cell 452

description: processed data column: Brain.EC4_D7


title: Rrp40-polII


title: MW1644

city: Menlo Park

first: Christopher

middle: Dennis

last: McFarland

state: CA

address: 2647 Alpine RD

department: Cancer Systems Biology

country: USA

institute: Stanford University

data_processing:
Library strategy: Tuba-seq
Data was processed using the Tuba-seq analysis pipeline developed for the novel method detailed in this publication
See https://github.com/petrov-lab/tuba-seq
Fastq files were filtered & trimmed using preprocess.py
Barcode pileups were clustered using DADA2_clustering.R, trained via DADA2_error_training.R, and merged with postprocess.py
Bias of sizes by GC-content of barcode was corrected using a 4th-order polynomial, as described in manuscript
Tumors were called using a minimum cell size of 500 cells (unless otherwise specified in the manuscript) and a clustering proclivity of OMEGA_A = 1e-10
Genome_build: Custom Lentiviral Amplicon

source_name: Unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis

growth_protocol: Tumors were transduced in mice via Cre & Cas9-mediated genome editing via intratracheal intubation of lentivirus

extract_protocol:
Mice were humanely sacrificed, then barcodes were PCR-amplified from DNA extract derived from whole lungs harboring multiplexed tumors
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit and multiplexed by mouse sample.

value: Whole Lung Extract

tag: cell type

value: Lung Epithelium, heterogenous progression to adenocarcinoma

tag: weeks of tumor growth

value: KTC

tag: treatment

value: Tranduced with Lenti-sgTS/Pool


title: WG960039_A01-W24


title: Brain single cell 448

description: processed data column: Brain.EC4_D3


title: Brain single cell 460

description: processed data column: Brain.EC4_E16


title: Brain single cell 461

description: processed data column: Brain.EC4_E17


title: MW1642


title: Brain single cell 458

description: processed data column: Brain.EC4_E13


title: Brain single cell 447

description: processed data column: Brain.EC4_D2


title: Mtr4-input


title: Rrp40-input


title: IW2081


title: Brain single cell 445

description: processed data column: Brain.EC4_D23


title: Brain single cell 444

description: processed data column: Brain.EC4_D22


title: Brain single cell 443

description: processed data column: Brain.EC4_D21


title: Brain single cell 441

description: processed data column: Brain.EC4_D1


title: Brain single cell 442

description: processed data column: Brain.EC4_D20


title: IW2060


title: Brain single cell 446

description: processed data column: Brain.EC4_D24


title: Sample 6-Mtr4-3

data_processing:
Basecalls performed using TopHat2.0,fastx_toolkit-0.0.13.2 (Q33)
RNA-seq reads were cleaned and mapped the human genome (hg19 version) TopHat2.0. Reads mapping to multiple independent genomic locations were assigned to the most abundant biotype of the locations. Genome annotations from RefSeq and ENSEMBL were downloaded from the UCSC genome browser website, and supplemented with published datasets. Supplemented datasets contain eRNAs (FANTOM database, http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Enhancers/), PROMPTs, lnc/lincRNAs.
Spike-in control normalization: for each sample, we searched for the reads that aligned against the spike-in control genes, and obtained the number of reads for spike-in control, which was divided by the total number of reads for each samples, this ratio was named correct ratios and used to normalize the variation of different samples. For genomic sites in each sample, the value of reads was multiplied by correct ratios.
To compare the expression of individual RNAs, we calculated the corrected reads per million (RPM) of each transcript. Fold changes were computed from the average normalized read coverage per million bases for ensemble gene.
The custom Perl and SVG scripts were written to display the read alignment profiles for each expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

extract_protocol:
RNA was isolated from nuclear fraction with TRIzol (Invitrogen). 5 mg of total RNA was used for polyA RNA selection and constructed sequencing libraries.
Libraries were generated with TruSeq Stranded Total RNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.


title: Brain single cell 436

description: processed data column: Brain.EC4_D15


title: Brain single cell 438

description: processed data column: Brain.EC4_D17


title: Brain single cell 440

description: processed data column: Brain.EC4_D19


title: IW2046


title: IW2047


title: Sample 5-Mtr4-2


title: Brain single cell 437

description: processed data column: Brain.EC4_D16


title: Brain single cell 439

description: processed data column: Brain.EC4_D18


title: Cntr-polII


title: IW2043


title: Brain single cell 435

description: processed data column: Brain.EC4_D14


title: Sample 3-NC-3


title: IW2082


title: Sample 4-Mtr4-1


title: Brain single cell 434

description: processed data column: Brain.EC4_D13


title: IW2079


title: IW2017


title: Brain single cell 433

description: processed data column: Brain.EC4_D12


title: Brain single cell 432

description: processed data column: Brain.EC4_D11


title: Cntr-input


title: Sample 2-NC-2


title: Sample 1-NC-1


title: IW2925

value: Tranduced with Lenti-sgSetd2#2


title: Brain single cell 430

description: processed data column: Brain.EC4_C9


title: Brain single cell 429

description: processed data column: Brain.EC4_C8


title: Brain single cell 431

description: processed data column: Brain.EC4_D10


title: IW2923


title: Brain single cell 428

description: processed data column: Brain.EC4_C7


title: Sample_S13R056-Rrp40-2

extract_protocol:
RNA was isolated from nuclear fraction with TRIzol (Invitrogen). 5 mg of total RNA was depleted with rRNA and constructed sequencing libraries.
Libraries were generated with TruSeq Stranded Total RNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions. Index for NC:ATCACG, for Rrp40: CGATGT for Mtr4: TTAGGC


title: IW2829


title: IW2933

value: KPTC-Neo

value: Tranduced with Lenti-sgNeo


title: Brain single cell 427

description: processed data column: Brain.EC4_C6


title: Brain single cell 424

description: processed data column: Brain.EC4_C3


title: Brain single cell 426

description: processed data column: Brain.EC4_C5


title: Brain single cell 425

description: processed data column: Brain.EC4_C4


title: Sample_S13R056-Rrp40-1


title: Brain single cell 423

description: processed data column: Brain.EC4_C2


title: Brain single cell 421

description: processed data column: Brain.EC4_C23


title: Sample_S13R055-NC-2


title: Brain single cell 422

description: processed data column: Brain.EC4_C24


title: IW2930


title: Brain single cell 420

description: processed data column: Brain.EC4_C22


title: IW2924


title: IW2172

value: KPTC


title: Sample_S13R055-NC-1


title: Brain single cell 417

description: processed data column: Brain.EC4_C1


title: Brain single cell 416

description: processed data column: Brain.EC4_C19


title: IW2158


title: Brain single cell 415

description: processed data column: Brain.EC4_C18


title: IW2170


title: Sample_S13R057-Mtr4


title: IW2137


title: Brain single cell 413

description: processed data column: Brain.EC4_C16


title: IW2136


title: IW2034


title: IW2036


title: Brain single cell 410

description: processed data column: Brain.EC4_C13


title: Brain single cell 407

description: processed data column: Brain.EC4_C10


title: Brain single cell 409

description: processed data column: Brain.EC4_C12


title: Brain single cell 408

description: processed data column: Brain.EC4_C11


title: Brain single cell 411

description: processed data column: Brain.EC4_C14


title: Brain single cell 406

description: processed data column: Brain.EC4_B9


title: 2173


title: Brain single cell 404

description: processed data column: Brain.EC4_B7


title: Brain single cell 405

description: processed data column: Brain.EC4_B8


title: Brain single cell 419

description: processed data column: Brain.EC4_C21


title: 2135


title: Brain single cell 418

description: processed data column: Brain.EC4_C20


title: Brain single cell 402

description: processed data column: Brain.EC4_B5


title: Brain single cell 401

description: processed data column: Brain.EC4_B4


title: Brain single cell 403

description: processed data column: Brain.EC4_B6


title: 2133


title: Brain single cell 414

description: processed data column: Brain.EC4_C17


title: Brain single cell 412

description: processed data column: Brain.EC4_C15


title: Brain single cell 400

description: processed data column: Brain.EC4_B3


title: Brain single cell 398

description: processed data column: Brain.EC4_B24


title: 2050


title: Brain single cell 397

description: processed data column: Brain.EC4_B23


title: Brain single cell 399

description: processed data column: Brain.EC4_B2


title: Brain single cell 395

description: processed data column: Brain.EC4_B21


title: Brain single cell 396

description: processed data column: Brain.EC4_B22


title: 2048


title: Brain single cell 393

description: processed data column: Brain.EC4_B1


title: Brain single cell 394

description: processed data column: Brain.EC4_B20


title: ZR631


title: Brain single cell 392

description: processed data column: Brain.EC4_B19


title: ZR485


title: Brain single cell 391

description: processed data column: Brain.EC4_B18


title: ZR405


title: Brain single cell 390

description: processed data column: Brain.EC4_B17


title: Brain single cell 387

description: processed data column: Brain.EC4_B13


title: Brain single cell 388

description: processed data column: Brain.EC4_B15


title: Brain single cell 389

description: processed data column: Brain.EC4_B16


title: Brain single cell 386

description: processed data column: Brain.EC4_B12


title: ZR399


title: Brain single cell 385

description: processed data column: Brain.EC4_B11


title: ZR239


title: Brain single cell 384

description: processed data column: Brain.EC4_B10


title: Brain single cell 383

description: processed data column: Brain.EC4_A9


title: IW2593


title: Brain single cell 382

description: processed data column: Brain.EC4_A8


title: ZR479

value: KLTC-Neo


title: Brain single cell 380

description: processed data column: Brain.EC4_A6


title: ZR466


title: Brain single cell 381

description: processed data column: Brain.EC4_A7


title: ZR460


title: ZR487


title: ZR459


title: Brain single cell 376

description: processed data column: Brain.EC4_A2


title: Brain single cell 375

description: processed data column: Brain.EC4_A24


title: Brain single cell 374

description: processed data column: Brain.EC4_A23


title: Brain single cell 377

description: processed data column: Brain.EC4_A3


title: Brain single cell 373

description: processed data column: Brain.EC4_A22


title: Brain single cell 372

description: processed data column: Brain.EC4_A21


title: Brain single cell 371

description: processed data column: Brain.EC4_A20


title: ZR458


title: ZR468

value: KLTC


title: ZR464


title: Brain single cell 367

description: processed data column: Brain.EC4_A17


title: Brain single cell 369

description: processed data column: Brain.EC4_A19


title: ZR465


title: Brain single cell 370

description: processed data column: Brain.EC4_A1


title: Brain single cell 368

description: processed data column: Brain.EC4_A18


title: Brain single cell 365

description: processed data column: Brain.EC4_A14


title: Brain single cell 364

description: processed data column: Brain.EC4_A12


title: Brain single cell 363

description: processed data column: Brain.EC4_A11


title: ZR387


title: ZR462


title: Brain single cell 366

description: processed data column: Brain.EC4_A15


title: Brain single cell 361

description: processed data column: Brain.EC3_P9


title: ZR377


title: Brain single cell 379

description: processed data column: Brain.EC4_A5


title: Brain single cell 360

description: processed data column: Brain.EC3_P8


title: Brain single cell 378

description: processed data column: Brain.EC4_A4


title: Brain single cell 359

description: processed data column: Brain.EC3_P7


title: Brain single cell 358

description: processed data column: Brain.EC3_P6


title: Brain single cell 357

description: processed data column: Brain.EC3_P5


title: Brain single cell 355

description: processed data column: Brain.EC3_P3


title: IW2507


title: Brain single cell 356

description: processed data column: Brain.EC3_P4


title: IW2506


title: Brain single cell 354

description: processed data column: Brain.EC3_P2


title: IW2343


title: Brain single cell 353

description: processed data column: Brain.EC3_P24


title: Brain single cell 351

description: processed data column: Brain.EC3_P22


title: Brain single cell 352

description: processed data column: Brain.EC3_P23


title: IW2330


title: Brain single cell 350

description: processed data column: Brain.EC3_P21


title: Brain single cell 349

description: processed data column: Brain.EC3_P20


title: Brain single cell 348

description: processed data column: Brain.EC3_P19


title: IW2252


title: IW2245


title: Brain single cell 346

description: processed data column: Brain.EC3_P17


title: Brain single cell 362

description: processed data column: Brain.EC4_A10


title: Brain single cell 347

description: processed data column: Brain.EC3_P18


title: Brain single cell 345

description: processed data column: Brain.EC3_P16


title: IW2577


title: Brain single cell 342

description: processed data column: Brain.EC3_P13


title: Brain single cell 343

description: processed data column: Brain.EC3_P14


title: RNAseq_piwi_mut_rep2

city: New York

first: Felipe

last: Karam Teixeira

state: New York

address: 540 1st Avenue

department: Skirball Institute

institute: New York University Medical Center

description: Poly(A)-selected RNA-seq from piwi mutant (in Harwich background)

data_processing:
ChIP-seq analysis was performed on the Galaxy web-based platform following previously described methods (Han et al, 2015 - Bioinformatics). Illumina adaptors and other low quality sequences were removed using the ‘Trim Galore!’ package. ChIP-seq input and IP filtered data were mapped to the Drosophila genome (dm3) and transposon consensus sequences using Bowtie2, using the -k = 1 parameter.
RNA-seq: Paired-end (100-nt-long reads) RNA-seq data were mapped to the Drosophila melanogaster genome (dm3) and the FlyBase and Repbase transposon consensus database using the piPipes package (version 1.5.0; https://github.com/bowhan/piPipes), following the RNA-seq pipeline as previously described (Han et al., 2015 - Bioinformatics). Briefly, libraries were first aligned to ribosomal RNA using Bowtie2. Non-rRNA reads were then mapped to the transcriptome and transposon consensus using Bowtie2.
Genome_build: Drosophila melanogaster dm3
Supplementary_files_format_and_content: ChIP-seq: Files contain density coverage of uniquely mapped reads to dm3
Supplementary_files_format_and_content: RNA-seq: Files contain strand-specific density coverage of uniquely mapped reads to dm3

organism: Drosophila melanogaster

growth_protocol: Flies were grown at standard conditions at 29º C

extract_protocol:
Poly(A)-selected RNA-sequencing (RNA-seq) was performed on 2.5µg of RNA purified from adult ovaries using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina®.
Total RNA from adult ovaries was isolated using Trizol reagent (Invitrogen) and quantified by Qubit (Invitrogen)

treatment_protocol: no treatment

value: F1 piwi homozygous progeny:(females) [Harwich]; piwi[2]/CyO; [Harwich] vs. (males) w[1118]; piwi[1]/CyO, w+

tag: developmental stage

value: Adult

value: Ovary


title: RNAseq_piwi_mut_rep1


title: Brain single cell 341

description: processed data column: Brain.EC3_P12

value: brain


title: RNAseq_piwi_het_rep2

description: Poly(A)-selected RNA-seq from piwi heterozygous (in Harwich background)

value: F1 piwi heterozygous progeny:(females) [Harwich]; piwi[2]/CyO; [Harwich] vs. (males) w[1118]; piwi[1]/CyO, w+


title: Brain single cell 340

description: processed data column: Brain.EC3_P11

value: adult mice 12 to 15 weeks old


title: Brain single cell 339

description: processed data column: Brain.EC3_P10


title: RNAseq_piwi_het_rep1


title: RNAseq_aub_mut_rep2

description: Poly(A)-selected RNA-seq from aub mutant (in Harwich background)

value: F1 aub homozygous progeny:(females) [Harwich]; aub[HN2] cn[1] bw[1]/CyO; [Harwich] vs. (males) w[1118]; aub[QC42] cn[1] bw[1]/CyO


title: Brain single cell 335

description: processed data column: Brain.EC3_O5


title: Brain single cell 337

description: processed data column: Brain.EC3_O8


title: Brain single cell 336

description: processed data column: Brain.EC3_O6


title: Brain single cell 334

description: processed data column: Brain.EC3_O4


title: Brain single cell 333

description: processed data column: Brain.EC3_O3


title: Brain single cell 332

description: processed data column: Brain.EC3_O2


title: Brain single cell 331

description: processed data column: Brain.EC3_O24


title: RNAseq_aub_mut_rep1


title: RNAseq_aub_het_rep2

description: Poly(A)-selected RNA-seq from aub heterozygous (in Harwich background)

value: F1 aub heterozygous progeny:(females) [Harwich]; aub[HN2] cn[1] bw[1]/CyO; [Harwich] vs. (males) w[1118]; aub[QC42] cn[1] bw[1]/CyO


title: Brain single cell 344

description: processed data column: Brain.EC3_P15


title: Brain single cell 328

description: processed data column: Brain.EC3_O21


title: Brain single cell 327

description: processed data column: Brain.EC3_O20


title: Brain single cell 329

description: processed data column: Brain.EC3_O22


title: RNAseq_dysgenic_rep2

description: Poly(A)-selected RNA-seq from dysgenic F1 progeny

source_name: dysgenic

growth_protocol: Flies were grown at standard conditions at 18º C

value: F1 dysgenic progeny:(females) w[1118] vs. (males) Harwich


title: RNAseq_aub_het_rep1


title: Brain single cell 330

description: processed data column: Brain.EC3_O23


title: RNAseq_dysgenic_rep1


title: Brain single cell 323

description: processed data column: Brain.EC3_O17


title: Brain single cell 325

description: processed data column: Brain.EC3_O19


title: Brain single cell 338

description: processed data column: Brain.EC3_O9


title: Brain single cell 326

description: processed data column: Brain.EC3_O1


title: Brain single cell 324

description: processed data column: Brain.EC3_O18


title: RNAseq_non_dysgenic_rep2

description: Poly(A)-selected RNA-seq from non-dysgenic F1 progeny

value: F1 non-dysgenic progeny:(females) Harwich vs. (males) w[1118]


title: RNAseq_non_dysgenic_rep1


title: Brain single cell 322

description: processed data column: Brain.EC3_O16


title: Brain single cell 321

description: processed data column: Brain.EC3_O15


title: ChIPseq_antiH3K9me3_dysgenic_rep2

description: anti-H3K9me3 ChIP-seq from dysgenic F1 progeny

extract_protocol:
IP and input libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®
ChIP on formaldehyde-crosslinked ovaries was performed as previously described (Rozhkiv et al, 2013 - Genes Dev), using 100-200 dissected adult ovaries as starting material and the anti-H3K9me3 (Abcam, ab8898).

value: anti-H3K9me3 (Abcam, catalog# ab8898, lot# GR271507-1)


title: Brain single cell 320

description: processed data column: Brain.EC3_O14


title: ChIPseq_antiH3K9me3_dysgenic_rep1


title: Brain single cell 319

description: processed data column: Brain.EC3_O13


title: Brain single cell 317

description: processed data column: Brain.EC3_O10


title: Brain single cell 315

description: processed data column: Brain.EC3_N8


title: ChIPseq_antiH3K9me3_non_dysgenic_rep2

description: anti-H3K9me3 ChIP-seq from non-dysgenic F1 progeny


title: Brain single cell 314

description: processed data column: Brain.EC3_N7


title: ChIPseq_antiH3K9me3_non_dysgenic_rep1


title: Brain single cell 313

description: processed data column: Brain.EC3_N6


title: Brain single cell 318

description: processed data column: Brain.EC3_O12


title: ChIPseq_input_dysgenic_rep2

description: Input of H3K9me3 ChIP-seq from dysgenic F1 progeny


title: ChIPseq_input_dysgenic_rep1


title: Brain single cell 312

description: processed data column: Brain.EC3_N5


title: Brain single cell 311

description: processed data column: Brain.EC3_N4


title: Brain single cell 316

description: processed data column: Brain.EC3_N9


title: Brain single cell 310

description: processed data column: Brain.EC3_N3


title: Brain single cell 309

description: processed data column: Brain.EC3_N2


title: ChIPseq_input_non_dysgenic_rep2

description: Input of H3K9me3 ChIP-seq from non-dysgenic F1 progeny


title: Brain single cell 307

description: processed data column: Brain.EC3_N23


title: DZ PTBP1 cKO female replicate 3

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: Total RNA was extracted from GC B cells. mRNAseq was carried out from polyadenylated transcripts using the SMART-Seq v4 Ultra low input RNA kit from Clontech

data_processing:
Raw sequence reads were trimmed with Trimgalore (v0.4.2, (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters.
Trimmed reads  were mapped to the mouse Mus_musculus.GRCm38 genome with Hisat2 using  --no-mixed --no-discordant  parameters and providing a known splice sites file generated from the Mus_musculus.GRCm38.70.gtf annotation
Counting of reads mapping to all exons of a particular gene was done with HTSeq using the Mus_musculus.GRCm38.84.gtf annotation and default parameters
HTSeq Count File, read counts mapping to all annotated exons of a gene. First colum is Ensembl ID gene identifier, second colum is the number of reads
Genome_build: GRCm38

source_name: Dark zone germinal centre B cells

extract_protocol:
RNA was extracted using the RNeasy Micro Kit from Qiagen (Cat. #74004)
2 ng of total RNA was used to generate cDNA from polyadenylated transcripts using the SMART-Seq v4 Ultra low input RNA kit from Clontech (Cat. #634888). 0.5 ng cDNA were used to prepare the mRNAseq libraries with 8 cycles of PCR using the Ultra Low library preparation kit v2 from Clontech (Cat. #634899).

tag: Sex

value: Female

tag: day of sort

value: Day 3

value: Dark zone germinal centre B cells


title: Brain single cell 306

description: processed data column: Brain.EC3_N22


title: ChIPseq_input_non_dysgenic_rep1


title: DZ PTBP1 cKO male replicate 2

value: Male

value: Day 2


title: Brain single cell 304

description: processed data column: Brain.EC3_N20


title: Brain single cell 305

description: processed data column: Brain.EC3_N21


title: Brain single cell 308

description: processed data column: Brain.EC3_N24


title: Brain single cell 303

description: processed data column: Brain.EC3_N1


title: DZ PTBP1 cKO male replicate 1

value: Day 1


title: Brain single cell 302

description: processed data column: Brain.EC3_N19


title: Brain single cell 301

description: processed data column: Brain.EC3_N18


title: Brain single cell 300

description: processed data column: Brain.EC3_N17


title: Brain single cell 299

description: processed data column: Brain.EC3_N16


title: DZ control female replicate 3


title: DZ PTBP1 cKO female replicate 4

value: Day 4


title: DZ control male replicate 2


title: Brain single cell 296

description: processed data column: Brain.EC3_N13


title: Brain single cell 297

description: processed data column: Brain.EC3_N14


title: DZ control male replicate 1


title: Brain single cell 292

description: processed data column: Brain.EC3_M9


title: Brain single cell 294

description: processed data column: Brain.EC3_N11


title: LZ PTBP1 cKO female replicate 4

source_name: Light zone germinal centre B cells

value: Light zone germinal centre B cells


title: Brain single cell 295

description: processed data column: Brain.EC3_N12


title: Brain single cell 291

description: processed data column: Brain.EC3_M8


title: LZ PTBP1 cKO female replicate 3


title: Brain single cell 293

description: processed data column: Brain.EC3_N10


title: Brain single cell 290

description: processed data column: Brain.EC3_M7


title: Brain single cell 288

description: processed data column: Brain.EC3_M5


title: LZ PTBP1 cKO male replicate 1


title: Brain single cell 287

description: processed data column: Brain.EC3_M4


title: LZ control female replicate 4


title: LZ PTBP1 cKO male replicate 2


title: DZ control female replicate 4


title: Brain single cell 286

description: processed data column: Brain.EC3_M3


title: LZ control female replicate 3


title: Brain single cell 284

description: processed data column: Brain.EC3_M24


title: Brain single cell 298

description: processed data column: Brain.EC3_N15


title: Brain single cell 283

description: processed data column: Brain.EC3_M23


title: Brain single cell 282

description: processed data column: Brain.EC3_M22


title: LZ control male replicate 2


title: Brain single cell 281

description: processed data column: Brain.EC3_M21


title: Brain single cell 280

description: processed data column: Brain.EC3_M1


title: LZ control male replicate 1


title: Brain single cell 276

description: processed data column: Brain.EC3_M16


title: Brain single cell 277

description: processed data column: Brain.EC3_M17


title: Brain single cell 278

description: processed data column: Brain.EC3_M18


title: Brain single cell 275

description: processed data column: Brain.EC3_M15


title: Brain single cell 289

description: processed data column: Brain.EC3_M6


title: Brain single cell 274

description: processed data column: Brain.EC3_M14


title: prl1prl2_2

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

data_processing:
The data analysis was performed the PIHSDA pipeline (https://github.com/grubbybio/PIHSDA).
The raw reads were aligned to the TAIR10 genome using HISAT2.
Exonic and intronic reads were classified and quantified as follows. Reads with five or more nucleotides overlapping with intronic regions (including splicing donor/acceptor sites) were counted as intronic reads, and reads that mapped exclusively to exonic regions were counted as exonic reads. Transcript levels were measured in reads per million total read counts.
Differentially expressed genes were identified using DEseq2 with fold change of 1.5 and p ≤ 0.01 as the parameters.
To identify genes that exhibited significantly higher levels of intron retention compared to Col-0, the intron/exon ratio was calculated as (I1 + I2)/2 over (E1+E2)/2 (I: Intronic reads, E: Exonic reads, 1: biological replicate 1, 2: biological replicate 2) while applying an abundance cutoff (raw intronic read number ≥ 2 and exonic read number ≥ 5). We only considered intron/exon (I/E) ratios between 0 to 1. The genes with intron retention were identified using DEseq2 based on values of Imutant, Emutant, ICol-0 and ECol-0 and fold changes ≥ 2 and FDR < 0.01 as parameters
Genome_build: TAIR10
Supplementary_files_format_and_content: exonic and intronic read counts of each gene in txt file

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: prl1prl2, 12-day-old seedlings

growth_protocol: 12-day-old seedlings grown on ½ Murashige and Skoog (MS) plates under 16h light/8h dark cycle

extract_protocol:
RNA was extracted with TRIzol reagent (Life Technologies, USA, 15596018)
Polyadenylated RNA was isolated from total RNA extracted from 12-day-old seedlings using the Magnetic mRNA Isolation Kit (New England Biolabs). RNA-seq libraries were prepared using NEBNext® mRNA Library Prep Reagent Set for Illumina (New England Biolabs).

tag: genotype/variation

value: seedlings


title: prl1prl2_1


title: Brain single cell 272

description: processed data column: Brain.EC3_M12

value: brain


title: Brain single cell 273

description: processed data column: Brain.EC3_M13


title: Brain single cell 271

description: processed data column: Brain.EC3_M11


title: Brain single cell 285

description: processed data column: Brain.EC3_M2


title: Brain single cell 270

description: processed data column: Brain.EC3_L9


title: mac3amac3b_1

source_name: mac3amac3b, 12-day-old seedlings


title: mac7-1_2

source_name: mac7-1, 12-day-old seedlings


title: Brain single cell 268

description: processed data column: Brain.EC3_L7


title: mac7-1_1


title: Brain single cell 266

description: processed data column: Brain.EC3_L4


title: Brain single cell 263

description: processed data column: Brain.EC3_L24


title: Col-0_1

source_name: Col-0, 12-day-old seedlings


title: Brain single cell 279

description: processed data column: Brain.EC3_M19


title: Col-0_2


title: mac3amac3b_2


title: Brain single cell 261

description: processed data column: Brain.EC3_L22


title: Brain single cell 260

description: processed data column: Brain.EC3_L21


title: Brain single cell 262

description: processed data column: Brain.EC3_L23


title: Brain single cell 259

description: processed data column: Brain.EC3_L20


title: Brain single cell 258

description: processed data column: Brain.EC3_L1


title: Brain single cell 257

description: processed data column: Brain.EC3_L19


title: ChIP:Input_Cell_hESC:WT_rep2

city: Palo Alto

first: Nian

last: Liu

address: 265 Campus Drive, Rm. G3145

department: Chemical and Systems Biology

data_processing:
The base calling was done using bcl2fastq v2.17.1.14 (Illumina).
CasTLE analysis for the CRISPR screen was performed as previously described (Morgens et al, 2016)
Genome_build: human (hg38)
Supplementary_files_format_and_content: txt files including the name, location and function of identified genes, as well as their effect size and CasTLE scores

growth_protocol: K562 cells (ATCC) were grown in Roswell Park Memorial Institute (RPMI) 1640 Medium (11875093, Life Technologies) supplemented with 10% Fetal Bovine Serum (Fisher, Cat# SH30910), 2 mM L-glutamine (Fisher, Cat# SH3003401) and 1% penicillin-streptomycin (Fisher, Cat#SV30010), and cultured at 37 C with 5% CO2. HeLa cells (ATCC) were grown in Dulbecco’s Modified Eagle’s Medium (Life Technologies, Cat# 11995073) supplemented with 10% FBS (Fisher, Cat# SH30910), 2 mM L-glutamine (Fisher, Cat# SH3003401), and 1% penicillin-streptomycin (Fisher, Cat# SV30010), and cultured at 37 C with 5% CO2. Human ES cells (H9 line) were expanded in feeder-free, serum-free medium mTeSR-1 from StemCell technologies. Cells were passaged 1:6 every 5–6 days by incubation with accutase (Invitrogen) and the resulting small cell clusters (50–200 cells) were subsequently re-plated on tissue culture dishes coated overnight with growth-factor-reduced matrigel (BD Biosciences). Cell cultures were routinely tested and found negative for mycoplasma infection (MycoAlert, Lonza).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Total RNA was isolated from K562 cells using the RNAeasy kit (Qiagen # 74104) and treated with RNase-Free DNase Set (Qiagen # 79254) to remove genomic DNA, according to the manufacturer’s instructions.
ChIP DNA, input DNA or cDNA were subject to end repair, A-tailing, adaptor ligation and cleavage with USER enzyme, followed by size selection to 250-500 bp and amplification with NEBNext sequencing primers. Libraries were purified, quantified, multiplexed and sequenced with 1x75bp single-end reads on an Illumina NEXT-seq (Stanford Functional Genomics Facility).

value: hESC

value: Human embryonic stem cell lines

value: wild type


title: Brain single cell 256

description: processed data column: Brain.EC3_L18

value: adult mice 12 to 15 weeks old


title: Brain single cell 255

description: processed data column: Brain.EC3_L17


title: Brain single cell 254

description: processed data column: Brain.EC3_L16


title: ChIP:MORC2_Cell_hESC:WT_rep1

value: MORC2 (A300-149A, Bethyl Laboratories)


title: Brain single cell 253

description: processed data column: Brain.EC3_L15


title: Brain single cell 269

description: processed data column: Brain.EC3_L8


title: Brain single cell 252

description: processed data column: Brain.EC3_L13


title: ChIP:MPP8_Cell_hESC:WT_rep2

value: MPP8 (16796-1-AP, Protein Technologies Inc)


title: Brain single cell 251

description: processed data column: Brain.EC3_L12


title: Brain single cell 265

description: processed data column: Brain.EC3_L3


title: Brain single cell 267

description: processed data column: Brain.EC3_L6


title: Brain single cell 250

description: processed data column: Brain.EC3_L11


title: ChIP:MPP8_Cell_hESC:WT_rep1


title: Brain single cell 264

description: processed data column: Brain.EC3_L2


title: ChIP:Input_Cell_K562:WT_rep2

value: Chronic myelogenous leukemia


title: Brain single cell 248

description: processed data column: Brain.EC3_K9


title: ChIP:Input_Cell_K562:WT_rep1


title: Brain single cell 247

description: processed data column: Brain.EC3_K8


title: ChIP:Input_Cell_hESC:WT_rep1


title: Brain single cell 246

description: processed data column: Brain.EC3_K7


title: ChIP:MORC2_Cell_hESC:WT_rep2


title: Brain single cell 244

description: processed data column: Brain.EC3_K5


title: ChIP:PolII_Cell_K562:TASOR-KO_rep1

value: TASOR KO

value: RNA Pol II (Santa Cruz Biotechnology, N-20 sc-899)


title: Brain single cell 243

description: processed data column: Brain.EC3_K4


title: ChIP:PolII_Cell_K562:TASOR-KO_rep2


title: Brain single cell 242

description: processed data column: Brain.EC3_K3


title: Brain single cell 239

description: processed data column: Brain.EC3_K23


title: ChIP:PolII_Cell_K562:MPP8-KO_rep1

value: MPP8 KO


title: Brain single cell 240

description: processed data column: Brain.EC3_K24


title: Brain single cell 238

description: processed data column: Brain.EC3_K22


title: Brain single cell 237

description: processed data column: Brain.EC3_K21


title: Brain single cell 236

description: processed data column: Brain.EC3_K20


title: ChIP:PolII_Cell_K562:MORC2-KO_rep2

value: MORC2 KO


title: Brain single cell 235

description: processed data column: Brain.EC3_K1


title: ChIP:PolII_Cell_K562:WT_rep2


title: Brain single cell 249

description: processed data column: Brain.EC3_L10


title: ChIP:PolII_Cell_K562:MORC2-KO_rep1


title: Brain single cell 234

description: processed data column: Brain.EC3_K19


title: Brain single cell 231

description: processed data column: Brain.EC3_K16


title: ChIP:PolII_Cell_K562:WT_rep1


title: Brain single cell 233

description: processed data column: Brain.EC3_K18


title: prl1prl2_2_sRNA

data_processing:
Bases are called using Illumina CASAVA
The raw reads were processed using an automated script pRNASeqTools (https://github.com/grubbybio/pRNASeqTools)
Normalization was performed by calculating the RPMR (reads per million of 45S rRNA fragments) value.
Genome_build: TAIR10
Supplementary_files_format_and_content: Sequences of mapped reads and read counts

extract_protocol:
To isolate small RNAs from total RNA (Total RNA was extracted with TRIzol reagent, Life Technologies, USA, 15596018), 50 µg of total RNA from each sample was resolved on 15% urea-PAGE gel, and the 18–30-nt region was excised from the gel. Small RNAs were recovered by soaking the smashed gel in 0.3M NaCl overnight, followed by ethanol precipitation.
Small RNA libraries were constructed following instructions from the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (E7300).

tag: ecotype background

value: 12-day-old seedlings


title: Brain single cell 232

description: processed data column: Brain.EC3_K17


title: prl1prl2_1_sRNA


title: Brain single cell 230

description: processed data column: Brain.EC3_K15


title: Brain single cell 245

description: processed data column: Brain.EC3_K6


title: mac7-1_2_sRNA


title: ChIP:PolII_Cell_K562:MPP8-KO_rep2


title: mac7-1_1_sRNA


title: Brain single cell 241

description: processed data column: Brain.EC3_K2


title: K562_Batch-screen_G418_rep1_(opt)-L1-G418

description: processed data file: K562_(opt)-L1-G418_secondary_screen.txt

data_processing:
library strategy: CRISPR screen
The base calling was done using bcl2fastq v2.17.1.14 (Illumina).
CasTLE analysis for the CRISPR screen was performed as previously described (Morgens et al, 2016)
Genome_build: human (hg38)
Supplementary_files_format_and_content: txt files including the name, location and function of identified genes, as well as their effect size and CasTLE scores

value: N/D


title: Brain single cell 228

description: processed data column: Brain.EC3_K13


title: Brain single cell 229

description: processed data column: Brain.EC3_K14


title: K562_Batch-screen_G418_rep2_(opt)-L1-G418


title: Brain single cell 226

description: processed data column: Brain.EC3_K11


title: Col-0_1_sRNA

source_name: wild type_seedling


title: K562_Batch-screen_untreated_rep2_(opt)-L1-G418


title: Brain single cell 225

description: processed data column: Brain.EC3_K10


title: Brain single cell 227

description: processed data column: Brain.EC3_K12


title: Brain single cell 224

description: processed data column: Brain.EC3_J9


title: RNA MG1655 csrA::kan 5

city: Gainesville

first: Anastasia

middle: Haley

last: Potts

state: FL

address: 1355 Museum Drive, Bldg. 981

department: Department of Microbiology and Cell Science

institute: University of Florida

data_processing:
Basecalls were made with Casava…
Reads were trimmed to remove adaptor sequences and reads shorter than 12 bases were discarded. Reads were aligned to the E. coli rRNA sequences with bowtie with default parameters and unaligned reads were retained
Reads were aligned to the E. coli genome with bowtie using default parameters.
Read counts per gene were calculated with Htseq Count
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Raw count matrix

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacterial cells

growth_protocol: Strains were grown in LB media to mid-exponential phase (OD600 = 0.5)

extract_protocol:
Cell pellets were thawed and lysed with bead beating. Total RNA was extracted with miRNeasy RNA Extraction Kit (Qiagen). rRNA was subtracted with the Ribozero Gram Negative Kit (Illumina). RNA was then fragmented with heat and alkalinity and size selected between 20 and 40 bases with denaturing PAGE.
RNA samples were ligated to a 3' adaptor and reverse transcribed. The cDNA was circularized to add a 5' adaptor then PCR amplified to add sample specific barcodes.

treatment_protocol: Samples were treated with 100ug/ml choramphenicol for 2 minutes, quick chilled on ice, washed, and frozen with liquid nitrogen

value: csrA::kan (Tn10-mini transposon inserted after codon 51)


title: RNA MG1655 csrA::kan 4


title: K562_Batch-screen_untreated_rep1_(opt)-L1-G418


title: Brain single cell 223

description: processed data column: Brain.EC3_J8


title: Brain single cell 222

description: processed data column: Brain.EC3_J7


title: HeLa_Batch-screen_G418_rep2

description: processed data file: HeLa_secondary_screen.txt

value: HeLa

value: Cervical cancer cells


title: Brain single cell 221

description: processed data column: Brain.EC3_J6

value: brain


title: Brain single cell 220

description: processed data column: Brain.EC3_J5


title: Brain single cell 219

description: processed data column: Brain.EC3_J4


title: HeLa_Batch-screen_G418_rep1


title: RNA MG1655 csrA::kan 3


title: HeLa_Batch-screen_untreated_rep2


title: Brain single cell 217

description: processed data column: Brain.EC3_J2


title: RNA MG1655 csrA::kan 1


title: Brain single cell 215

description: processed data column: Brain.EC3_J23


title: Brain single cell 214

description: processed data column: Brain.EC3_J22


title: HeLa_Genome-wide-screen_G418_rep2

description: processed data file: HeLa_Genome_wide_screen.txt


title: Brain single cell 216

description: processed data column: Brain.EC3_J24


title: RNA MG1655 5


title: Brain single cell 213

description: processed data column: Brain.EC3_J21


title: Brain single cell 212

description: processed data column: Brain.EC3_J1


title: Brain single cell 211

description: processed data column: Brain.EC3_J19


title: RNA MG1655 3


title: Brain single cell 210

description: processed data column: Brain.EC3_J18


title: HeLa_Genome-wide-screen_untreated_rep2


title: RNA MG1655 2


title: Brain single cell 209

description: processed data column: Brain.EC3_J17


title: Brain single cell 208

description: processed data column: Brain.EC3_J15


title: HeLa_Genome-wide-screen_untreated_rep1


title: RNA MG1655 csrA::kan 2


title: RNA MG1655 1


title: Brain single cell 218

description: processed data column: Brain.EC3_J3


title: Brain single cell 207

description: processed data column: Brain.EC3_J14


title: Brain single cell 205

description: processed data column: Brain.EC3_J12


title: hiPSC_primed_cloneB6

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description:
RNA isolated for cDNA synthesis
FigS4.xlsx

data_processing:
NextSeq 500 run was performed as paired-end seuencing (75 nt + 75 nt) with single index. Illumina NextSeq Real-Time Analysis (RTA) v2 generated base calling (BCL) files, which was converted into fastq files with index information by Illumina BaseSpace.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR. The STAR genome reference was constructed for 75 nt, and run parameters included --sjdbOverhang 74.
Reads mapped on genes were counted using Bioconductor package 'Rsubread," and the counts were subjected to normalization and differentially expressged gene detection using Bioconductor package 'edgeR.'
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft Excel xlsx spreadsheets including edgeR-normalized counts for each sample and gene.

source_name: Primed iPSC

growth_protocol: Human iPS cells were maintained in the mTeSR1 medium and converted to naïve pluripotency in the 4i/LIF medium for 72 hours. During the last 24 hours in the 4i/LIF culture, cells were casted into microwells to form embryoid bodies.

extract_protocol:
Embryoid bodies were digested using Miltenyi Biotec embryoid body dissociation kit to prepeare single cell suspensions, which were stained for APC-conjugated anti-CD38 antibody and subjected to FACS. Total RNA was isolated from the FACS-enriched cell populations using QIAGEN AllPrep Mini or Micro kits.
Total RNA was subjected to cDNA synthesis using TAKARA Bio SMARTer Ultra Low Input RNA kit. Alternatively, cells were subjected to direct lysis for cDNA synthesis without intermediate preparation of total RNA.
Single-index Illumina deep sequencing libraries were prepared using TAKARA Bio Low Input DNA Library Prep Kit.

treatment_protocol: Embryoid bodies were cultured for up to 8 days in the PGCLC production medium. Where appropriate, ROCKi was removed from the PGCLC production medium from the fifth day of embryoid body culture with or without SDF1 or AMD3100.

value: male

tag: ethnicity

value: Caucassian

value: primed pluripotent stem cells


title: Brain single cell 204

description: processed data column: Brain.EC3_J11

value: adult mice 12 to 15 weeks old


title: Brain single cell 206

description: processed data column: Brain.EC3_J13


title: HeLa_Batch-screen_untreated_rep1

value: wild type


title: RPF MG1655 csrA::kan 5

description:
Ribosome protected fragments (RPF)
EC_10

data_processing:
Library strategy: Ribosome profiling
Basecalls were made with Casava…
Reads were trimmed to remove adaptor sequences and reads shorter than 12 bases were discarded. Reads were aligned to the E. coli rRNA sequences with bowtie with default parameters and unaligned reads were retained
Reads were aligned to the E. coli genome with bowtie using default parameters.
Read counts per gene were calculated with Htseq Count
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Raw count matrix

extract_protocol:
Cell pellets were thawed, lysed with bead beating, and treated with micrococcal nuclease to release single monosomes. Ribosomes were isolated by ultracentrifuging lysate over a sucrose cushion. Ribosome protected fragments  (RPF) were extracted from the pelleted ribosomes with miRNeasy RNA Extraction Kit (Qiagen) and size selected between 20 and 35 bases with denaturing PAGE.
RNA samples were ligated to a 3' adaptor and reverse transcribed. The cDNA was circularized to add a 5' adaptor then PCR amplified to add sample specific barcodes.


title: hiPSC_primed_cloneA5


title: Brain single cell 203

description: processed data column: Brain.EC3_J10


title: Brain single cell 202

description: processed data column: Brain.EC3_I9


title: hiPSC_primed_cloneA4


title: RNA MG1655 4


title: RPF MG1655 csrA::kan 4

description:
Ribosome protected fragments (RPF)
EC_9


title: Brain single cell 201

description: processed data column: Brain.EC3_I7


title: HeLa_Genome-wide-screen_G418_rep1


title: RPF MG1655 csrA::kan 3

description:
Ribosome protected fragments (RPF)
EC_8


title: Brain single cell 200

description: processed data column: Brain.EC3_I6


title: hiPSC_naive_cloneA5

source_name: Naïve iPSC

value: naive pluripotent stem cells


title: Brain single cell 198

description: processed data column: Brain.EC3_I4


title: hiPSC_naive_cloneB6


title: RPF MG1655 csrA::kan 2

description:
Ribosome protected fragments (RPF)
EC_7


title: RPF MG1655 csrA::kan 1

description:
Ribosome protected fragments (RPF)
EC_6


title: Brain single cell 197

description: processed data column: Brain.EC3_I3


title: RPF MG1655 5

description:
Ribosome protected fragments (RPF)
EC_5


title: Brain single cell 196

description: processed data column: Brain.EC3_I2


title: Brain single cell 195

description: processed data column: Brain.EC3_I24


title: EBday7CD38plus_cloneB6

source_name: Day 7 embryoid body

value: CD38-positive PGC-like cells


title: Brain single cell 194

description: processed data column: Brain.EC3_I23


title: Brain single cell 193

description: processed data column: Brain.EC3_I22


title: hiPSC_naive_cloneA4


title: EBday7CD38plus_cloneA5


title: RPF MG1655 4

description:
Ribosome protected fragments (RPF)
EC_4


title: RPF MG1655 3

description:
Ribosome protected fragments (RPF)
EC_3


title: EBday7CD38plus_cloneA4


title: Brain single cell 190

description: processed data column: Brain.EC3_I1


title: Brain single cell 191

description: processed data column: Brain.EC3_I20


title: Brain single cell 192

description: processed data column: Brain.EC3_I21


title: RPF MG1655 2

description:
Ribosome protected fragments (RPF)
EC_2


title: Brain single cell 189

description: processed data column: Brain.EC3_I18


title: EBday7CD38minus_cloneB6

value: CD38-negative embryoid body cells


title: Brain single cell 199

description: processed data column: Brain.EC3_I5


title: Brain single cell 186

description: processed data column: Brain.EC3_I15


title: RPF MG1655 1

description:
Ribosome protected fragments (RPF)
EC_1


title: Brain single cell 187

description: processed data column: Brain.EC3_I16


title: Brain single cell 188

description: processed data column: Brain.EC3_I17


title: EBday7CD38minus_cloneA5


title: Brain single cell 185

description: processed data column: Brain.EC3_I14


title: csrA::kan 2 T15

data_processing:
Basecalls were made with Casava.
Reads were aligned to the E. coli genome and ERCC spike-in sequences with bowtie using default parameters.
Read counts per gene/spike-in were determined with Htseq Count
Reads within each time series were normalized to each other using the relative abundance of RNA spike-ins in each library
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Normalized count matrix

extract_protocol:
Samples were extracted with RNeasy kit (Qiagen) treated with Turbo Dnase (Ambion), and cleaned with the Rneasy kit (Qiagen). RNA was normalized using fluorometric methods then an ERCC RNA spike-in was added to all samples (Ambion) to represent 5% of the total sample.
Standard Illumina protocols

treatment_protocol: Samples were treated with 200ug/ml rifampicin and aliquoted collected at the indicated time points and added directly to RNA Protect Bacteria Reagent (Qiagen). Samples were centrifuged and the stabilized RNA samples frozen at -80C until extraction.

tag: time point

value: 15 min post-rifampicin addition


title: Brain single cell 184

description: processed data column: Brain.EC3_I13


title: csrA::kan 2 T10

value: 10 min post-rifampicin addition


title: EBday7CD38minus_cloneA4


title: EBday0_cloneB6

source_name: Day 0 embryoid body


title: Brain single cell 181

description: processed data column: Brain.EC3_I10


title: csrA::kan 2 T5

value: 5 min post-rifampicin addition


title: EBday0_cloneA5


title: Brain single cell 179

description: processed data column: Brain.EC3_H8


title: Brain single cell 180

description: processed data column: Brain.EC3_H9


title: EBday0_cloneA4


title: Brain single cell 178

description: processed data column: Brain.EC3_H7


title: csrA::kan 2 T2.5

value: 2.5 min post-rifampicin addition


title: Brain single cell 176

description: processed data column: Brain.EC3_H5


title: Brain single cell 177

description: processed data column: Brain.EC3_H6


title: csrA::kan 2 T0

value: 0 min post-rifampicin addition


title: EBday8CD38plus_2

description:
Direct cell lysis for cDNA synthesis
FigS3.xlsx

source_name: Day 8 embryoid body


title: MG1655 2 T15


title: Brain single cell 175

description: processed data column: Brain.EC3_H3

source_name: Brain


title: Brain single cell 174

description: processed data column: Brain.EC3_H2


title: EBday8CD38plus_1


title: Brain single cell 172

description: processed data column: Brain.EC3_H23


title: Brain single cell 171

description: processed data column: Brain.EC3_H22


title: EBday8CD38minus_2


title: Brain single cell 183

description: processed data column: Brain.EC3_I12


title: Brain single cell 182

description: processed data column: Brain.EC3_I11


title: EBday8CD38minus_1


title: MG1655 2 T10


title: Brain single cell 170

description: processed data column: Brain.EC3_H21


title: Brain single cell 167

description: processed data column: Brain.EC3_H19


title: MG1655 2 T2.5


title: MG1655 2 T0


title: Brain single cell 169

description: processed data column: Brain.EC3_H20


title: Brain single cell 166

description: processed data column: Brain.EC3_H18


title: EBday5CD38plus_2 fig3

source_name: Day 5 embryoid body


title: Brain single cell 164

description: processed data column: Brain.EC3_H16


title: EBday5CD38plus_1 fig3


title: csrA::kan 1 T10

value: csrA::kan (Tn10-mini transposon inserted after codon 51)


title: Brain single cell 165

description: processed data column: Brain.EC3_H17


title: Brain single cell 163

description: processed data column: Brain.EC3_H15


title: Brain single cell 162

description: processed data column: Brain.EC3_H14


title: EBday5CD38minus_1 fig3


title: EBday5CD38minus_2 fig3


title: Brain single cell 173

description: processed data column: Brain.EC3_H24


title: Brain single cell 161

description: processed data column: Brain.EC3_H13


title: csrA::kan 1 T5


title: Brain single cell 160

description: processed data column: Brain.EC3_H12


title: RockIremoved_SDF1_CD38plus_3

description:
RNA isolated for cDNA synthesis
Fig6.xlsx


title: MG1655 2 T5


title: csrA::kan 1 T2.5


title: Brain single cell 159

description: processed data column: Brain.EC3_H11


title: RockIremoved_SDF1_CD38plus_2


title: Brain single cell 158

description: processed data column: Brain.EC3_H10


title: csrA::kan 1 T0


title: Brain single cell 156

description: processed data column: Brain.EC3_G8


title: RockIremoved_SDF1_CD38plus_1


title: MG1655 1 T15


title: Brain single cell 154

description: processed data column: Brain.EC3_G6


title: RockIremoved_SDF1_CD38minus_3


title: Brain single cell 153

description: processed data column: Brain.EC3_G5


title: Brain single cell 152

description: processed data column: Brain.EC3_G4


title: MG1655 1 T10


title: MG1655 1 T5


title: Brain single cell 150

description: processed data column: Brain.EC3_G2


title: RockIremoved_SDF1_CD38minus_2


title: Brain single cell 151

description: processed data column: Brain.EC3_G3


title: Brain single cell 148

description: processed data column: Brain.EC3_G23


title: RockIremoved_SDF1_CD38minus_1


title: RockIremoved_CD38plus_3


title: Brain single cell 147

description: processed data column: Brain.EC3_G22


title: Brain single cell 146

description: processed data column: Brain.EC3_G21


title: Brain single cell 149

description: processed data column: Brain.EC3_G24


title: MG1655 1 T0


title: MG1655 1 T2.5


title: RockIremoved_CD38plus_2


title: Brain single cell 157

description: processed data column: Brain.EC3_G9


title: Brain single cell 155

description: processed data column: Brain.EC3_G7


title: Brain single cell 168

description: processed data column: Brain.EC3_H1


title: Brain single cell 145

description: processed data column: Brain.EC3_G20


title: Brain single cell 144

description: processed data column: Brain.EC3_G1


title: Brain single cell 143

description: processed data column: Brain.EC3_G19


title: RockIremoved_CD38plus_1


title: untagged control 5

data_processing:
Basecalls were made with Casava.
Reads were trimmed to remove adaptor sequences and reads shorter than 12 bases were discarded. Reads were aligned to the E. coli rRNA sequences with bowtie with default parameters and unaligned reads were retained
Reads were aligned to the E. coli genome with bowtie using default parameters. PCR duplicates were removed using Picard MarkDuplicates
All 3xFLAG-CsrA samples were merged into a single sam file and used as input into PIPE-CLIP to identify CLIP-seq peaks. HTSeq Count was used to count reads per peak in each individual sample bam file using the identified peaks
DESeq2 was used to identify peaks significantly enriched over the untagged control samples using the individual sample count data
Genome_build: NC_000913.3
Supplementary_files_format_and_content: csv file with peaks and sample counts

extract_protocol:
Samples were thawed, lysed with sonication over ice, and cleared with centrifugation. CsrA-RNA complexes were immunoprecipated with M2 anti-FLAG mouse antibody conjugated paramagnetic particles (Sigma) for 4 hours at 4C. Complexes were washed, 5'-end labeled with 32P, and eluted from the particles by heating in non-reducing PAGE sample buffer. Protein-RNA complexes were seperated with SDS-PAGE and transferred to nitrocellulose. RNA was extracted from the nitrocellulose by treatment with proteinase K,  phenol chloroform extraction, and ethanol precipitation.
NEB small RNA library prep kit (Catalog #: E7300S)

treatment_protocol: Samples were treated with 400mJ of UV light at 254nM. They were then quickly cooled, washed, and flash frozen in liquid nitrogen.


title: untagged control 4


title: Brain single cell 142

description: processed data column: Brain.EC3_G18


title: RockIremoved_CD38minus_3


title: Brain single cell 141

description: processed data column: Brain.EC3_G17


title: untagged control 3


title: Brain single cell 140

description: processed data column: Brain.EC3_G16


title: RockIremoved_CD38minus_2


title: untagged control 2


title: Brain single cell 139

description: processed data column: Brain.EC3_G15


title: RockIremoved_CD38minus_1


title: untagged control 1


title: Brain single cell 138

description: processed data column: Brain.EC3_G14


title: Brain single cell 136

description: processed data column: Brain.EC3_G11


title: Control_CD38plus_3


title: Brain single cell 135

description: processed data column: Brain.EC3_G10


title: 3xFLAG-CsrA 5


title: Brain single cell 134

description: processed data column: Brain.EC3_F9


title: Brain single cell 133

description: processed data column: Brain.EC3_F8


title: 3xFLAG-CsrA 4


title: Control_CD38plus_2


title: Brain single cell 132

description: processed data column: Brain.EC3_F7


title: Control_CD38plus_1


title: 3xFLAG-CsrA 3


title: Brain single cell 131

description: processed data column: Brain.EC3_F6


title: csrA::kan 1 T15


title: Brain single cell 130

description: processed data column: Brain.EC3_F5


title: Brain single cell 129

description: processed data column: Brain.EC3_F4


title: Control_CD38minus_3


title: Brain single cell 128

description: processed data column: Brain.EC3_F2


title: Control_CD38minus_2


title: Brain single cell 127

description: processed data column: Brain.EC3_F24


title: 3xFLAG-CsrA 1


title: Brain single cell 137

description: processed data column: Brain.EC3_G12


title: Brain single cell 126

description: processed data column: Brain.EC3_F23


title: Brain single cell 125

description: processed data column: Brain.EC3_F22


title: DMSO_GM15851_Rep4

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

data_processing:
Base-calling and demultiplexing were performed using Casava (v1.8.2).
Sequences were filtered and trimmed to remove low quality reads, adapters, and other sequencing artifacts.
The remaining reads were aligned to 19084 Refseq genes extracted from the Illumina iGenomes reference, selecting only those with ‘NM_’ annotations. The reference also included 13 mitochondrial mRNAs taken from ENSEMBL build GRCh37.75.
Bowtie (v0.12.9) was used for alignment, allowing two mismatches in a 28 bp seed. Reads with more than 200 alignments were excluded from further analysis.
RSEM (v1.2.3) was used to estimate isoform and relative gene expression levels (expected counts or “EC”).
EBseq was used to determine differential expression.
Genome_build: GRCh37.75
Supplementary_files_format_and_content: ec.tab.txt files containing expected counts for mitochondrial and nuclear protein coding transcripts

source_name: GM15851 LCLs (FRDA)

growth_protocol: RPMI 1640 Medium with 2 mM L-glutamine and 15% FBS

extract_protocol:
After treatment, cells were harvested and total RNA was purified with the RNeasy Mini Kit (Qiagen, Valencia, California), and DNA was removed by on-column DNase I treatment (ZYMO Research) or Ambion TURBO DNA-free Kit, according to manufacturer’s directions.
Final indexed cDNA libraries were pooled with 36 uniquely indexed LM-Seq cDNA libraries per lane and sequenced on an Illumina HiSeq 2500 with a single 64 base pair (bp) read and a 10 bp index read.

treatment_protocol: GM15850 cells were treated with the indicated molecules for 24 h

value: GM15851 LCLs (FRDA)

value: 0.1% DMSO

tag: treatment time


title: Control_CD38minus_1


title: Brain single cell 123

description: processed data column: Brain.EC3_F20

extract_protocol:
We used four different transgenic mouse reporter lines with fluorescent expression in different populations of vascular cells, Cldn5(BAC)eGFP mice that strongly labels brain endothelial cells, mice doubly positive for Pdgfrb(BAC)eGFP and NG2dsRed, in which brain vascular mural cells express both markers whereas each single marker are expressed also in other, non-overlapping cell types, and Pdgfra-H2BGFP that we found labeled a perivascular population of cells distinct from mural cells and astrocytes, in addition to the known labeling of cells of the oligendendrocyte lineage.   We chose to focus our efforts to adult mice 12 to 15 weeks old in order to primarily define fully differentiated and quiescent vascular cells and we chose a methodology based on fluorescence-activated cell sorting (FACS) into 384-well plates
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

tag: tissue

value: brain


title: Brain single cell 122

description: processed data column: Brain.EC3_F1

tag: strain


title: DMSO_GM15851_Rep2


title: Brain single cell 120

description: processed data column: Brain.EC3_F18

tag: age


title: DMSO_GM15851_Rep3


title: Brain single cell 121

description: processed data column: Brain.EC3_F19

tag: genotype


title: hiPSC_primed_2

description:
RNA isolated for cDNA synthesis
Fig2.xlsx

value: male


title: Brain single cell 119

description: processed data column: Brain.EC3_F17


title: 3xFLAG-CsrA 2


title: Brain single cell 118

description: processed data column: Brain.EC3_F16


title: hiPSC_naive_3

value: Caucassian


title: Brain single cell 117

description: processed data column: Brain.EC3_F15


title: DMSO_GM15850_Rep4

source_name: GM15850 LCLs (FRDA)

tag: cell line

value: GM15850 LCLs (FRDA)


title: hiPSC_primed_1

value: primed pluripotent stem cells


title: DMSO_GM15850_Rep3


title: Brain single cell 115

description: processed data column: Brain.EC3_F13

value: adult mice 12 to 15 weeks old


title: DMSO_GM15851_Rep1


title: Brain single cell 114

description: processed data column: Brain.EC3_F12


title: hiPSC_naive_1

value: naive pluripotent stem cells


title: Brain single cell 124

description: processed data column: Brain.EC3_F21


title: DMSO_GM15850_Rep2


title: Brain single cell 112

description: processed data column: Brain.EC3_F10


title: hiPSC_naive_2


title: Brain single cell 111

description: processed data column: Brain.EC3_E8


title: Brain single cell 113

description: processed data column: Brain.EC3_F11


title: Brain single cell 110

description: processed data column: Brain.EC3_E7


title: hiPSC_primed_3


title: Brain single cell 109

description: processed data column: Brain.EC3_E6


title: EBday5CD38plus_1 fig2

value: CD38-positive PGC-like cells


title: EBday5CD38plus_2 fig2


title: Brain single cell 108

description: processed data column: Brain.EC3_E5


title: Brain single cell 116

description: processed data column: Brain.EC3_F14


title: Brain single cell 106

description: processed data column: Brain.EC3_E3


title: 1000nM_Syn-TEF1_GM15851_Rep3

value: 1000nM Syn-TEF1


title: Brain single cell 105

description: processed data column: Brain.EC3_E2


title: 1000nM_Syn-TEF1_GM15851_Rep2


title: Brain single cell 104

description: processed data column: Brain.EC3_E24


title: 1000nM_Syn-TEF1_GM15851_Rep1


title: EBday5CD38minus_1 fig2

value: CD38-negative embryoid body cells


title: EBday5CD38minus_2 fig2


title: 1000nM_Syn-TEF1_GM15850_Rep4


title: EBday0_3


title: DMSO_GM15850_Rep1


title: EBday5CD38plus_3


title: Brain single cell 101

description: processed data column: Brain.EC3_E21


title: 1000nM_Syn-TEF1_GM15850_Rep3


title: EBday0_2


title: 1000nM_Syn-TEF1_GM15850_Rep2


title: EBday0_1


title: 1000nM_Syn-TEF1_GM15850_Rep1


title: pSer2_IP_DMSO

data_processing:
n/a
Genome_build: Human: GRCh37 (hg19)  Mouse: mm9

extract_protocol:
Cells were chemically crosslinked by the addition of 4 mL of 1.5% formaldehyde in PBS per 10 cm2 dish for 15 min at room temperature. Cells were resusupended in Lysis Buffer 1 (50 mM HEPES , pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL, 0.25% Triton X-100, 1X HALT protease inhibitor) and 3T3 mouse embryonic fibroblast cells (formaldehyde fixed as above) equivalent to 10% GM15850 cells were added to each sample for downstream ChIP-RX analysis.
NGS libraries were generated with Thruplex DNAseq Single Index Kit (Rubicon) and sequenced (single end, 150 bp reads) via NextSeq 500.

tag: antibody


title: Brain single cell 99

description: processed data column: Brain.EC3_E1

data_processing:
RNA-seq reads were mapped to the mouse reference genome (mm10) using STAR (version STAR_2.4.2a) and the count matrix shows the individual counts aligning to each gene per cell. In order to compare the gene expression counts between different cells, the total gene counts for each cell was normalized to 500,000.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized counts values for each sample


title: 1000nM_PA1+JQ1_GM15851_Rep4


title: Brain single cell 97

description: processed data column: Brain.EC3_E18


title: Brain single cell 103

description: processed data column: Brain.EC3_E23


title: MethylCseq_IPSC_GFP+

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

data_processing:
CASAVA v1.8.2
For methylC-seq, adapters were trimmed with BBduk with the options mink=3, qtrim=r, trimq=10 minlength=20, before alignment to mm10 with Bowtie and BSseeker2 with the option -n 1. PCR duplicates were removed using Sambamba v.0.5.9 before methylation quantification with BSseeker2. For ATAC-seq, Paired-end ATAC-seq reads were adapter trimmed using the BBduk algorithm, with the option mink=3 and aligned to UCSC mm10 using bowtie227 with the option -X 2000. PCR duplicates were removed using Sambamba v.0.6.3. To call ATAC-seq peaks, we first merged time point replicate BAM files and removed reads aligning to blacklisted genomic regions before calling peaks with MACS2 using the options callpeak --nomodel --keep-dup all --gsize mm. We then created a union peak set by merging all peaks within 100 bp at each time point and removed any peaks with a pileup count in the upper 0.001% quantile being removed as these were typically located in highly repetitive regions. Peak sets from all time points were then merged to generate a consensus union peak set. For ChIP-seq, single-end reads were adapter trimmed using the BBduk algorithm with the options mink=3 qtrim=r minlength=20 and aligned to UCSC mm10 using bowtie2 with the options -m 1 -v 1 -q -S. To call ChIP-seq peaks, reads aligning to blacklisted genomic regions were removed before calling peaks with MACS2 using the options callpeak --call-summits --bdg --gsize mm -q 0.01. For RNA-seq, reads were adapter trimmed using the BBduk algorithm with the options ktrim=r, mink=3, qtrim=rl, minlength=20, forcetrimleft=1. Trimmed reads were aligned to UCSC mm10 reference genome with HISAT2 with the option --rna-strandness FR and with known splice sites from mm10 UCSC gene models. Gene level expression quantification was performed by first counting reads overlapping genes using the summarizeOverlaps function in GenomicRanges with the options mode = "IntersectionNotEmpty", ignore.strand = FALSE, singleEnd=FALSE, fragments=TRUE. Read counts were gene-length normalized by calculating gene level transcripts per million (TPM).
Genome_build: UCSC mm10
Supplementary_files_format_and_content: all_chip_peak_calls.xlsx file contains all ChIP-seq peak calls, with one tab for each time point and antibody. atac_all_peaks_union.bed file contains the union of all ATAC-seq peaks. polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt file contains gene expression data for each sample expressed as TPM. Bigwig files for Bisulfite-Seq data contain CG methylation levels on a 0-1 scale.

growth_protocol: Reprogrammable mouse embryonic fibroblasts (MEF) were extracted from day 13.5 embryos (rtTA3-OKSM-Oct4GFP) and reprogrammed into induced pluripotent stem cells (iPSC). MEF, day3, day6, day9 and day12 reprogramming cultures and iPSC were further processed for analysis.

extract_protocol:
DNA methylation analysis was performed using approximately 1 x 10^6 FACS isolated cells. Genomic DNA was isolated with the Qiagen Blood and Tissue Kit according to manufacturer's instructions. 0.5% (w/w) of unmethylated lambda phage DNA (Promega) was added to the sample genomic DNA for the purpose of an unmethylated control to measure the bisulfite non-conversion frequency in each sample.
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, and subjected to 4 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).

value: het-het-het

tag: cell type

value: MEF derived induced pluripotent stem cells


title: pSer2_IP_1000nM_Syn-TEF1


title: Brain single cell 102

description: processed data column: Brain.EC3_E22


title: Brain single cell 98

description: processed data column: Brain.EC3_E19


title: pSer2_IP_1000nM_PA1+JQ1


title: 1000nM_PA1+JQ1_GM15851_Rep2


title: Brain single cell 96

description: processed data column: Brain.EC3_E17


title: MethylCseq_day9_SSEA1+

value: day9 MEF reprogramming intermediates


title: Brain single cell 100

description: processed data column: Brain.EC3_E20


title: MethylCseq_day3_SSEA1+

value: day3 MEF reprogramming intermediates


title: 1000nM_Syn-TEF1_GM15851_Rep4


title: Brain single cell 107

description: processed data column: Brain.EC3_E4


title: Brain single cell 94

description: processed data column: Brain.EC3_E15


title: 1000nM_PA1+JQ1_GM15851_Rep1


title: Brain single cell 95

description: processed data column: Brain.EC3_E16


title: MethylCseq_day12_SSEA1+

value: day12 MEF reprogramming intermediates


title: pSer2_Input_DMSO

value: none, input


title: EBday5CD38minus_3


title: pSer2_Input_1000nM_Syn-TEF1


title: 1000nM_PA1+JQ1_GM15850_Rep4


title: Brain single cell 93

description: processed data column: Brain.EC3_E14


title: 1000nM_PA1+JQ1_GM15850_Rep3


title: 1000nM_PA1+JQ1_GM15851_Rep3

value: GM15851 LCLs (FRDA)


title: ATACseq_day6_Thy1+_e4e5

description:
atac_all_peaks_union.bed
atac_d6_combined_replicates_peaks.xls
16-04497

extract_protocol:
DNA was tagnemted with Illumina Tagment DNA Buffer (Cat. No. 15027866) and 2.5 µl of Tagment DNA Enzyme 1 (Cat. No. 15027865).
Transposed DNA libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, Cat. No. A63880).

value: day6 cells refractory to MEF reprogramming


title: 1000nM_PA1+JQ1_GM15850_Rep2


title: Brain single cell 92

description: processed data column: Brain.EC3_E13

value: brain


title: Pol2_IP_DMSO

value: 0.1% DMSO


title: ATACseq_day3_Thy1+_e4e5

description:
atac_all_peaks_union.bed
atac_d3_combined_replicates_peaks.xls
16-04496

value: day3 cells refractory to MEF reprogramming


title: Pol2_IP_1000nM_Syn-TEF1

value: GM15850 LCLs (FRDA)


title: 1000nM_PA1+JQ1_GM15850_Rep1


title: MethylCseq_day6_SSEA1+

value: day6 MEF reprogramming intermediates


title: ATACseq_day6_SSEA1+_e4e5

description:
atac_all_peaks_union.bed
atac_d6_combined_replicates_peaks.xls
16-04500


title: Brain single cell 90

description: processed data column: Brain.EC3_E11

value: adult mice 12 to 15 weeks old


title: Pol2_IP_1000nM_PA1+JQ1


title: 1000nM_PA1_GM15851_Rep4


title: Pol2_Input_DMSO


title: ATACseq_day3_SSEA1+_e4e5

description:
atac_all_peaks_union.bed
atac_d3_combined_replicates_peaks.xls
16-04499


title: Pol2_Input_1000nM_Syn-TEF1


title: 1000nM_PA1_GM15851_Rep2


title: 1000nM_PA1_GM15851_Rep3


title: Brain single cell 88

description: processed data column: Brain.EC3_D8


title: ATACseq_IPSC_GFP+_rep2

description:
atac_all_peaks_union.bed
atac_iPSC_combined_replicates_peaks.xls
RL118


title: Brain single cell 89

description: processed data column: Brain.EC3_D9


title: ATACseq_MEF_e4e5

description:
atac_all_peaks_union.bed
atac_MEF_combined_replicates_peaks.xls
16-04498

value: MEF


title: Pol2_Input_1000nM_PA1+JQ1


title: 1000nM_PA1_GM15851_Rep1


title: pSer2_Input_1000nM_PA1+JQ1


title: Brain single cell 87

description: processed data column: Brain.EC3_D7


title: BRD4_IP_DMSO


title: Brain single cell 91

description: processed data column: Brain.EC3_E12


title: ATACseq_day9_SSEA1+_cKIT+_rep2

description:
atac_all_peaks_union.bed
atac_d9_combined_replicates_peaks.xls
RL116


title: Brain single cell 86

description: processed data column: Brain.EC3_D6


title: ATACseq_day6_SSEA1+_rep2

description:
atac_all_peaks_union.bed
atac_d6_combined_replicates_peaks.xls
RL115


title: BRD4_IP_1000nM_Syn-TEF1

value: 1000nM Syn-TEF1


title: 1000nM_PA1_GM15850_Rep3


title: Brain single cell 85

description: processed data column: Brain.EC3_D5


title: BRD4_IP_1000nM_PA1+JQ1


title: 1000nM_PA1_GM15850_Rep4


title: Brain single cell 84

description: processed data column: Brain.EC3_D4


title: ATACseq_day12_SSEA1+_cKIT+_rep2

description:
atac_all_peaks_union.bed
atac_d12_combined_replicates_peaks.xls
RL117


title: ATACseq_day3_SSEA1+_rep2

description:
atac_all_peaks_union.bed
atac_d3_combined_replicates_peaks.xls
RL114


title: BRD4_Input_DMSO


title: Brain single cell 83

description: processed data column: Brain.EC3_D3


title: ATACseq_MEF_rep2

description:
atac_all_peaks_union.bed
atac_MEF_combined_replicates_peaks.xls
RL113


title: 1000nM_PA1_GM15850_Rep1


title: BRD4_Input_1000nM_Syn-TEF1


title: Brain single cell 82

description: processed data column: Brain.EC3_D2


title: 1000nM_JQ1_GM15851_Rep4


title: BRD4_Input_1000nM_PA1+JQ1


title: Brain single cell 81

description: processed data column: Brain.EC3_D23


title: ATACseq_day9_SSEA1+_cKIT+_rep1

description:
atac_all_peaks_union.bed
atac_d9_combined_replicates_peaks.xls
RL110


title: 1000nM_JQ1_GM15851_Rep2


title: ATACseq_day6_SSEA1+_rep1

description:
atac_all_peaks_union.bed
atac_d6_combined_replicates_peaks.xls
RL109


title: Brain single cell 79

description: processed data column: Brain.EC3_D21


title: Brain single cell 78

description: processed data column: Brain.EC3_D20


title: ATACseq_day3_SSEA1+_rep1

description:
atac_all_peaks_union.bed
atac_d3_combined_replicates_peaks.xls
RL108


title: RNA-seq_MPP8-KO_rep2

data_processing:
The base calling was done using bcl2fastq v2.17.1.14 (Illumina).
CasTLE analysis for the CRISPR screen was performed as previously described (Morgens et al, 2016)
bigWig files were generated with bedtools genomecov and bedGraphToBigWig
Genome_build: human (hg38)
Supplementary_files_format_and_content: txt files including the name, location and function of identified genes, as well as their effect size and CasTLE scores; wig files for ChIP-Seq and RNA-seq

growth_protocol: K562 cells were grown in Roswell Park Memorial Institute (RPMI) 1640 Medium supplemented with 10% Fetal Bovine Serum and 1% penicillin- streptomycin and cultured at 37 ºC with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Total RNA was isolated from K562 cells using the RNAeasy kit (Qiagen # 74104) and treated with RNase-Free DNase Set (Qiagen # 79254) to remove genomic DNA, according to the manufacturer’s instructions.
ChIP DNA, input DNA or cDNA were subject to end repair, A-tailing, adaptor ligation and cleavage with USER enzyme, followed by size selection to 250-500 bp and amplification with NEBNext sequencing primers. Libraries were purified, quantified, multiplexed and sequenced with 1x75bp single-end reads on an Illumina NEXT-seq (Stanford Functional Genomics Facility).
library strategy: CRISPR screen, ChIP-seq and RNA-seq

value: Chronic myelogenous leukemia

value: MPP8 KO


title: 1000nM_PA1_GM15850_Rep2


title: RNA-seq_TASOR-KO_rep2

value: TASOR KO


title: 1000nM_JQ1_GM15850_Rep4


title: RNA-seq_TASOR-KO_rep1


title: ATACseq_MEF_rep1

description:
atac_all_peaks_union.bed
atac_MEF_combined_replicates_peaks.xls
RL107

value: het-het-het


title: Brain single cell 77

description: processed data column: Brain.EC3_D1


title: Brain single cell 76

description: processed data column: Brain.EC3_D19


title: 1000nM_JQ1_GM15851_Rep1


title: RNA-seq_MORC2-KO_rep2

value: MORC2 KO


title: RNA-seq_MPP8-KO_rep1


title: RNAseq_day6_Thy1+

description:
polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt
16-04336

extract_protocol:
RNA was extracted from approximately 500,000 FACS isolated cells using an RNeasy Micro Kit (Qiagen, Cat. No. 74004) according to the manufacturer’s instructions.
Illumina TruSeq Stranded Total RNA protocol with Ribo-zero.


title: 1000nM_JQ1_GM15850_Rep1


title: 1000nM_JQ1_GM15851_Rep3


title: ATACseq_IPSC_GFP+_rep1

description:
atac_all_peaks_union.bed
atac_iPSC_combined_replicates_peaks.xls
RL112

value: MEF derived induced pluripotent stem cells


title: 1000nM_JQ1_GM15850_Rep2


title: RNA-seq_MORC2-KO_rep1


title: Brain single cell 80

description: processed data column: Brain.EC3_D22


title: Brain single cell 75

description: processed data column: Brain.EC3_D18


title: RNAseq_day3_Thy1+

description:
polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt
16‐04334


title: Brain single cell 74

description: processed data column: Brain.EC3_D17


title: RNAseq_Oct4_IPSC_GFP+_rep2

description:
polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt
14-13103