title: PN 414-414

description:
PN 414
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 440-440

status: Public on Dec 12 2019

type: protein

city: Guangzhou

first: Huihua

last: Zhang

address: 601, west Huangpu avenue, Tianhe district

department: Biomedicine Institute & Cell Biology Department

country: China

institute: Jinan University

description:
HC 440
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.

hyb_protocol: 2-fold diluted culture supernatant was added to each well. After overnight incubation at 4°C and extensive washing, the biotin-labeled detection antibody was added for 2 hours and then washed away. AlexaFluor 555-conjugated streptavidin was then added and incubated for 1 hour at room temperature.

scan_protocol: The signals (532 nm excitation, 635 nm emission) were scanned and extracted using an InnoScan 300 scanner (Innopsys, Carbonne, France).

data_processing: Individual array spots were background subtracted locally by subtracting the median background across spot replicated in each sample, and then normalized using two positive controls. For protein quantification, standard curves were generated using purified proteins representing the proteins-of-interest.

label: AlexaFluor 555

molecule: protein

organism: Homo sapiens

source_name: Culture supernatant from Mtb-stimulated whole blood

extract_protocol: Culture supernatant from whole blood

treatment_protocol: Whole blood (250 µl) collected from participants using an EDTA anticoagulation tube was cultured in serum-free medium (DKW34-EHK0100, DAKEWE) in absence or presence of 2.5 µg/ml phytohemagglutinin (PHA, L8754, Sigma) or 10 µg/ml Mtb-antigen peptide pool for 24 h at 37°C, 5% CO2, and then the supernatant was collected.

tag: tissue

value: Whole blood

tag: histology

value: Healthy

tag: groups

value: Establish and test


title: PN 464-464

description:
PN 464
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.

label_protocol: AlexaFluor 555-conjugated streptavidin was then added and incubated for 1 hour at room temperature.

value: Non-TB pulmonary inflammations


title: LTBI 404-404

description:
LTBI 404
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.

value: Latent tuberculosis infection


title: HC 434-434

description:
HC 434
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 432-432

description:
Definite TB 432
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.

value: Pulmonary tuberculosis


title: HC 438-438

description:
HC 438
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Probable TB 430-430

description:
Probable TB 430
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Probable TB 424-424

description:
Probable TB 424
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 426-426

description:
Definite TB 426
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Probable TB 422-422

description:
Probable TB 422
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 416-416

description:
PN 416
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 412-412

description:
PN 412
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 418-418

description:
PN 418
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 420-420

description:
PN 420
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 410-410

description:
PN 410
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 406-406

description:
LTBI 406
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 400-400

description:
LTBI 400
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 398-398

description:
LTBI 398
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 394-394

description:
HC 394
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 392-392

description:
HC 392
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 402-402

description:
LTBI 402
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: NMJs2

type: RNA

city: nagoya

first: guiying

last: chen

address: 65 Tsurumai-cho, Showa-ku

country: Japan

institute: nagoya university

description: Exonarray data of NMJ region

hyb_protocol: Five ug of cDNA was hybridized for 16 hr at 45C on Affymetrix Mouse Exon 1.0 Array. Probe array was washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The hybridized arrays were scanned  with Affymetrix GeneChip Scanner 3000 7G.

data_processing: The microarray raw data (6 Affymetrix cell files) were processed using the robust multichip analysis (RMA) algorithm to normalize the array signals across chips with the Affymetrix Expression Console software, and were further analyzed using Affymetrix Transcriptome Analysis Console software.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse TA muscle, NMJ regions

label_protocol: Biotinilated cDNA was prepared using Ovation Pico WTA System V2 Kit from 10 ng total RNA for each sample according to the manufacture's instruction.

extract_protocol: We microdissected 9973 NMJs and equal area of non-NMJs from same fiber of TA muscle by laser capture. The total RNA was isolated with RNeasy Micro Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: For AChE staining, the slides placed in staining solution on ice for 10 min. Then washed with 70% ethanol for 30 s and four rounds of 100% ethanol for 1 min each, placed in xylene for 5 s, and finally air dry 5 min. Dehydration tissues were used immediately for neuromuscular junctions (NMJs) microdissection.

tag: strain

value: ICR mouse

value: TA muscle

tag: Stage

value: 16-week old

tag: region

value: NMJ


title: HC 386-386

description:
HC 386
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 382-382

description:
Definite TB 382
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: non-NMJs3

description: Exonarray data of non-NMJ region

source_name: Mouse TA muscle, non-NMJ regions

value: non-NMJ


title: HC 388-388

description:
HC 388
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Probable TB 376-376

description:
Probable TB 376
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 384-384

description:
Definite TB 384
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: NMJs3

description: Exonarray data of NMJ region


title: NMJs1

description: Exonarray data of NMJ region


title: Probable TB 380-380

description:
Probable TB 380
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 396-396

description:
HC 396
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Probable TB 378-378

description:
Probable TB 378
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: non-NMJs2

description: Exonarray data of non-NMJ region


title: Probable TB 374-374

description:
Probable TB 374
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 358-358

description:
LTBI 358
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: non-NMJs1

description: Exonarray data of non-NMJ region


title: HC 390-390

description:
HC 390
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 370-370

description:
PN 370
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 372-372

description:
PN 372
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: TFAP2a kd HH9 rep1

type: SRA

city: Ithaca

first: Marcos

last: Simoes-Costa

state: New York

address: 526 Campus Rd

department: Molecular Biology and Genetics

country: USA

institute: Cornell University

description: CUT&RUN for Tfap2a in the presence of Tfap2b knockdown

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Base calling was performed using CASAVA 1.8. Sequenced reads were trimmed for adaptor sequence using cutadapt v1.18, and mapped to the galGal5 genome using Bowtie 2 v2.3.4.3 with parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 1000. Duplicate reads were marked using MarkDuplicates function of Picard tools v 2.0.4 and reads were filtered using samtools  v1.9 -F 1804 -f 2. Bigwig plots were generated using deeptools v3.1.2 bamCoverage function with the following parameters: --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads.

molecule: genomic DNA

organism: Gallus gallus

source_name: Chicken neural crest

extract_protocol:
Neural crest dissections were performed on HH9 embryos (10 embryos/ 20 neural folds per experiment). Cells were dissociated in Accumax (Accutase, SCR006) cell dissociation solution for 20 minutes at RT under mild agitation. CUT&RUN experiments were carried out as described(Skene and Henikoff, 2017).
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645) and sequenced with paired-end 37bp reads on an Illumina NextSeq500 instrument.
Neural plate border/neural crest dissections were performed on HH6/HH9 embryos (10 embryos/ 20 neural folds per experiment). Cells were dissociated in Accumax (Accutase, SCR006) cell dissociation solution for 20 minutes at RT under mild agitation. CUT&RUN experiments were carried out as described(Skene and Henikoff, 2017).

value: Chicken neural crest

tag: antibody

value: anti-AP2 alpha (abcam, ab108311)


title: TFAP2a kd HH9 rep2


title: PN 362-362

description:
PN 362
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 366-366

description:
PN 366
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 368-368

description:
PN 368
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 364-364

description:
PN 364
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 352-352

description:
LTBI 352
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 360-360

description:
LTBI 360
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: NC RNAseq HH9 rep1

description: RNA-seq on isolated neural crest cells using AP2aE1

library_source: transcriptomic

data_processing: Base calling was performed using CASAVA 1.8. Sequenced reads were trimmed for adaptor sequence using cutadapt v1.18, and mapped to the galGal5 genome using HiSat2(Kim et al., 2019). Read counts were obtained using featureCounts(Liao et al., 2014). Bigwig plots were generated using deeptools v3.1.2 bamCoverage function with the following parameters: --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 1218492533.

extract_protocol:
For isolation of neural crest cells, embryos were transfected with the enhancer reporter construct PTK-AP2aE1-eGPF. To obtain neural crest cells from different stages, embryos were cultured until HH6 (8 hours) and HH10 (15-16hours), and screened for robust GFP expression in neural crest cells. Embryo heads were dissected and incubated in Accumax (Accutase, SCR006) cell dissociation solution, for 40 minutes at RT under mild agitation. At least 5,000 GFP+ cells from each stage were sorted directly into 100uL of lysis buffer from the RNAqueous-Micro Total RNA Isolation Kit (ThermoFisher, AM1931). Total RNA was isolated according to the kit’s protocol.
RNA was poly(A) selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490). TruSeq-barcoded RNAseq libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760) and sequenced on an Illumina NextSeq500 instrument.
Neural plate border/neural crest dissections were performed on HH6/HH9 embryos (10 embryos/ 20 neural folds per experiment). Cells were dissociated in Accumax (Accutase, SCR006) cell dissociation solution for 20 minutes at RT under mild agitation. CUT&RUN experiments were carried out as described(Skene and Henikoff, 2017).


title: HC 348-348

description:
HC 348
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: TFAP2a control HH9 rep2

description: CUT&RUN for Tfap2a in control tissue


title: LTBI 356-356

description:
LTBI 356
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: NC RNAseq HH6 rep1


title: ATAC HH9 rep2

description: ATAC-seq on isolated neural crest cells using AP2aE1

data_processing: Base calling was performed using CASAVA 1.8. Sequenced reads were trimmed for adaptor sequence using cutadapt v1.18, and mapped to the galGal5 genome using Bowtie 2 v2.3.4.3 with parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000. Duplicate reads were marked using MarkDuplicates function of Picard tools v 2.0.4 and reads were filtered using samtools  v1.9 -F 1804 -f 2. Bigwig plots were generated using deeptools v3.1.2 bamCoverage function with the following parameters: --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads.

extract_protocol:
For isolation of neural crest cells, embryos were transfected with the enhancer reporter construct PTK-AP2aE1-eGPF. To obtain neural crest cells from different stages, embryos were cultured until HH6 (8 hours) and HH9 (13-14hours), and screened for robust GFP expression in neural crest cells. Embryo heads were dissected and incubated in Accumax (Accutase, SCR006) cell dissociation solution, for 40 minutes at RT under mild agitation. At least 20,000 GFP+ cells from each stage were sorted into 200uL of HANKS buffer supplemented with 0.5% BSA.
ATAC-seq library preparation was performed as previously described (Buenrostro et al., 2015).
Neural plate border/neural crest dissections were performed on HH6/HH9 embryos (10 embryos/ 20 neural folds per experiment). Cells were dissociated in Accumax (Accutase, SCR006) cell dissociation solution for 20 minutes at RT under mild agitation. CUT&RUN experiments were carried out as described(Skene and Henikoff, 2017).


title: HC 342-342

description:
HC 342
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 344-344

description:
HC 344
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 354-354

description:
LTBI 354
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: NC RNAseq HH9 rep2


title: NC RNAseq HH6 rep2


title: ATAC HH6 rep2


title: HC 346-346

description:
HC 346
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: ATAC HH9 rep1


title: HC 340-340

description:
HC 340
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: MP_18_chicken_3A.M

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: single end protocol R2 used for 7N barcode + 8N UMI in fastq header

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: hisat 0.1.5  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
Read count by homer (http://homer.salk.edu/homer/ngs/)
Genome_build: hg38
Genome_build: Mmul 8.0.1
Genome_build: calJac3
Genome_build: Oar v3.1
Genome_build: Rnor 6.0
Genome_build: mm10
Genome_build: S.galili v1.0
Genome_build: MesAur1.0
Genome_build: galGal5
Genome_build: danRer10
Supplementary_files_format_and_content: text files include mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: Total brain

extract_protocol:
10,000 cells from each sample were sorted into lysis/binding buffer (Life Technologies). mRNA was captured with 6.5ul of Dynabeads oligo(dT) (Life Technologies), washed, and eluted at 85C with 10ul of 10 mM Tris-HCl (pH7.5).
We used a derivation of the MARS-seq as described (Jaitin et al. Science 2014), developed for single cell MARS-seq to produce 3' exprssion libraries with a minimum of 3 replicates per sample.

value: Brain

tag: selection markers

value: mPEG+ (NA)

tag: source

value: Southern Biotech

tag: catalog #

tag: age


title: HC 338-338

description:
HC 338
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: ATAC HH6 rep1


title: TFAP2a control HH9 rep1

description: CUT&RUN for Tfap2a in control tissue


title: Probable TB 334-334

description:
Probable TB 334
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: MP_17_chicken_2A.M


title: Probable TB 336-336

description:
Probable TB 336
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 332-332

description:
Definite TB 332
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: MP_16_chicken_1A.M


title: AB5658

description: paired-end (read2 used to read cell and molecule barcodes only)

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: hg38
Genome_build: Mmul 8.0.1
Genome_build: calJac3
Genome_build: Oar v3.1
Genome_build: Rnor 6.0
Genome_build: mm10
Genome_build: S.galili v1.0
Genome_build: MesAur1.0
Genome_build: galGal5
Genome_build: danRer10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

extract_protocol:
Single-cell libraries were prepared as previously described (Keren-Shaul, Nature Protocols, 2019). In brief, mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription, and the resulting RNA is fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier (Keren-Shaul, Nature Protocols, 2019).
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

tag: cell type

value: Immune cells

tag: selection marker

tag: catalog#


title: AB3013


title: Probable TB 326-326

description:
Probable TB 326
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.

value: Whole blood


title: TFAP2c HH9 rep2

data_processing:
Library strategy: CUT&RUN
Base calling was performed using CASAVA 1.8
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.18, and mapped to the galGal5 genome using Bowtie 2 v2.3.4.3 with parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 1000
Duplicate reads were marked using MarkDuplicates function of Picard tools v 2.0.4 and reads were filtered using samtools  v1.9 -F 1804 -f 2
Bigwig plots were generated using deeptools v3.1.2 bamCoverage function with the following parameters: --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads
Genome_build: galGal5
Supplementary_files_format_and_content: bigwig files (scores represent enrichment normalized to 1x genome coverage)

source_name: neural crest

extract_protocol:
Neural plate border/neural crest dissections were performed on HH6/HH9 embryos (10 embryos/ 20 neural folds per experiment). Cells were dissociated in Accumax (Accutase, SCR006) cell dissociation solution for 20 minutes at RT under mild agitation. CUT&RUN experiments were carried out as described(Skene and Henikoff, 2017).
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645) and sequenced with paired-end 37bp reads on an Illumina NextSeq500 instrument.

value: neural crest

value: anti-AP2 gamma (abcam, ab218107)


title: Definite TB 330-330

description:
Definite TB 330
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.

value: Establish and test


title: IgG control

value: anti-IgG (abcam, ab46540)


title: PN 322-322

description:
PN 322
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.

value: Non-TB pulmonary inflammations


title: PN 324-324

description:
PN 324
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 320-320

description:
PN 320
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 318-318

description:
PN 318
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 316-316

description:
PN 316
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: TFAP2b HH9 rep2

value: anti-AP2 beta (abcam, ab221094)


title: PN 314-314

description:
PN 314
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: TFAP2c HH6 rep2


title: TFAP2b HH6 rep1


title: TFAP2c HH9 rep1


title: H3K27ac HH9 rep2

value: anti-Histone H3 (acetyl K27) (abcam, ab177178)


title: TFAP2a HH9 rep2


title: TFAP2c HH6 rep1


title: TFAP2a HH6 rep1


title: H3K27ac HH9 rep3


title: H3K27ac HH9 rep1


title: Probable TB 328-328

description:
Probable TB 328
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.

value: Pulmonary tuberculosis


title: AB6899

organism: Nannospalax galili

value: BD  Biosciences


title: H3K27ac HH6 rep3


title: TFAP2b HH6 rep2


title: TFAP2b HH9 rep1


title: TFAP2a HH6 rep2


title: AB6898


title: H3K27ac HH6 rep2


title: AB6897


title: H3K27ac HH6 rep1


title: AB6896


title: H9

city: Seoul

first: Kinarm

last: Ko

address: 120, Neungdong-ro, Gwangjin-gu

country: South Korea

institute: Konkuk University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Check the rRNA ratio using Fastq screen v0.11.1
Using bowtie to align RNA-seq data to reference genome(human hg19) and get histogram for insert size
Using Tophat v2.0.13 to mapping the read to reference(hg19) and generate bam files.
Fragments Per Kilobase of transcript per Million(FPKM) was calculated from mapped reads using cufflinks v2.2.0.
Genome_build: hg19
Supplementary_files_format_and_content: "expression.csv.gz" contains FPKM values for genes

source_name: Human embryonic stem cells

growth_protocol: AgHiPSCs were cultured on matrigel coated plated using mTeSR. AgFib cells were grown in BIOAMF-2 complete medium.

extract_protocol:
RNA extraction was performed using QIAGEN standard protocols. Illumina TruSeq Stranded mRNA Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic stem cells


title: AgHiPSC

source_name: Induced pluripotent stem cells

value: Androgenetic induced pluripotent stem cells


title: AgFib

source_name: Fibroblasts

value: Androgenetic fibroblasts


title: Wt rep1

city: Boston

first: Tatsuya

last: Kobayashi

state: MA

address: 50 Blossom St

department: Endocrine Unit

institute: Massachusetts General Hospital

data_processing:
Illumina Hiseq 2000/2500 software used for basecalling.
Low quality reads were filtered with adaptors and reads with unknown bases with software SOAPnuke v1.5.2 with parameters -l 10 -q 0.5 -n 0.001 -A 0.25. Assembled clean reads into Unigenes followed with Unigene functional annotation, SSR detection, and calculated the Unigene expression levels and SNPs of each sample. Mapped clean reads to mm9 reference using Bowtie v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: Rib Cartilage

extract_protocol:
Rib cartilage was treated with .2% Collagenase II in Dmem 10% FBS medium overnight. Cells were filtered and plated. RNA was extracted using trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Rib Chondrocytes

value: 10 Days


title: KO rep2


title: MP_21_monkey_3A.M

organism: Callithrix jacchus

value: Brain

value: BioLegend


title: MP_19_monkey_1A.M


title: MP_20_monkey_2A.M


title: TFAP2a HH9 rep1

value: anti-AP2 alpha (abcam, ab108311)


title: mic_sheep2.M

organism: Ovis aries

value: Bio-Rad


title: mic_macaca1.M

organism: Macaca fascicularis

value: Miltenyi Biotec


title: AB3016

organism: Mesocricetus auratus

value: Immune cells


title: AB5656


title: mic_macaca3.M


title: MP_11_hamster_3A.M


title: MP_12_hamster_5A.M


title: AB3499


title: AB5659


title: AB5660


title: mic_sheep3.M


title: AB3015


title: mic_macaca2.M


title: mic_sheep1.M


title: AB3498

source_name: Brain cortex


title: Wt rep2


title: ExpI-IL6KD

status: Public on Dec 11 2019

city: Orebro

first: Liza

middle: U

last: Ljungberg

address: Sodra Grev Rosengatan 32

department: Medical Sciences

country: Sweden

institute: Örebro University

description:
IL6KD
raw count per gene (ENSEMBL ID)

data_processing:
Demultiplexing and conversion to FASTQ format was performed using the CASAVA software (version 1.8.4), provided by Illumina.
fastQC: quality control
cutadapt: trimming adapters (AGATCGGAAGAGC), quality cutoff 20, min_length 20
STAR: alignment to Human Transcriptome SAM
samtools: sam to bam conversion, sorting and indexing bam-files
Supplementary_files_format_and_content: text files with ENSEMBL Gene IDs and transcript counts summarised per gene

source_name: Endothelial cells

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were cultured in VascuLife basal medium supplemented with VEGF LifeFactors kit (LifeLine Cell Technologies, Frederick, MD, USA), penicillin 0.1 U/ml and streptomycin 100 ng/ml. The cells were grown in uncoated plastic cell culture flasks and kept at 37ᵒC in 95% air and 5% CO2. Medium was replaced every 48-72 h and the cells were sub-cultured when confluent.

extract_protocol:
RNA was isolated from HUVECs using E.Z.N.A.® Total RNA Kit I (Omega Bio-tek, Norcross, GA, USA) according to the manufacturer’s instructions. The cell lysate was treated with PureLink® DNAse (Thermo Fisher Scientific) for 15 min after being loaded onto the column. RNA was from eluted in RNAse free water and RNA concentration was measured using Nano-drop.
Sequencing libraries were prepared from 1 ug total RNA using the TruSeq stranded mRNA sample prep kit including poly-A selection (Illumina) according to the manufacturer’s protocol. The quality of the libraries was evaluated using the Fragment Analyzer (Advanced Analytical Technologies, Ankeny, IA) with the dsDNA Reagent kit (Advanced Analytical Technologies). The adapter-ligated fragments were quantified by qPCR using the Library quantification kit for Illumina (KAPA Biosystems, Wilmington, MA) on a StepOnePlus instrument (Applied Biosystems, Thermo Fisher Scientific) prior to cluster generation and sequencing. Sequencing was performed on a Illumina HiSeq2500 instrument according to the manufacturer's instructions.

treatment_protocol: HUVECs were seeded at a density of 200 000 cells per well in 6-well plates in complete endothelial medium. The following morning, the cells were rinsed in Opti-MEM I reduced serum medium (Gibco) and tranfection was performed in 700 µl Opti-MEM I reduced serum medium containing 4µl lipofectamine 2000 and 20 pmol of 3 IL6-targeting Stealth RNAi™ siRNAs (Thermo Fisher Scientific) or 60 pmol non-target Stealth RNAi™ siRNAs negative control (Thermo Fisher Scientific) per well. The plates were incubated at 37ᵒC in 95% air and 5% CO2 for 4 hours followed by addition of 1.3 ml VascuLife basal medium supplemented with VEGF LifeFactors kit per well. Knockdown of IL6 was performed both in the presence and absence of the soluble IL6 receptor. Recombinant human sIL6Rα 100 ng/ml (RnD systems, Minneapolis, MN, USA) was added to the wells 6h after introducing siRNA. Cells were collected after 48h and stored at -80°C pending RNA extraction.

value: Human vein umbilical endothelial cells (HUVECs)

tag: passage

tag: donor

value: pooled from multiple donors


title: ExpG-IL6KD-IL6R

description:
IL6R+IL6KD
raw count per gene (ENSEMBL ID)


title: ExpB-IL6KD-IL6R


title: ExpI-IL6R

description:
IL6R
raw count per gene (ENSEMBL ID)


title: ExpH-IL6R

description:
IL6R
raw count per gene (ENSEMBL ID)


title: ExpG-IL6R

description:
IL6R
raw count per gene (ENSEMBL ID)


title: ExpH-IL6KD

description:
IL6KD
raw count per gene (ENSEMBL ID)


title: KO rep1


title: ExpI-IL6KD-IL6R


title: MP_10_hamster_2A.M


title: AB5661


title: ExpG-IL6KD

description:
IL6KD
raw count per gene (ENSEMBL ID)


title: ExpG-CTL

description:
CTL
raw count per gene (ENSEMBL ID)


title: ExpB-IL6R

description:
IL6R
raw count per gene (ENSEMBL ID)


title: 11C_KO_DNA_DMSO_16_R1

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina)
A base call trimming step was applied to remove low-confidence base calls from read ends
FASTQs were aligned using STAR v.2.4.2a
Gene counts were generated using htseq-count
QC and metrics was performed using the Picard family of tools (v1.134)
Genome_build: GRCh38.91

source_name: U937 cell line

growth_protocol: Cells were passaged at sub 1 million/mL confluency in RPMI.

extract_protocol:
RNA was extracted by freezing samples in Trizol before purification by miniprep.
Total RNA was added directly to lysis buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), and reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries

treatment_protocol: Cells were differentiated by stimulation with 100 nM PMA for 24 hours and rested 24 hours prior to sample specific stimulations.

value: derived from histiocytic lymphoma

tag: treatment

value: lipofectamine + DNA

tag: timepoint (hours)

tag: genotype

value: knockout


title: 12B_KO_DNA_2uM_16_R1

value: lipofectamine + Nu7441 inhibitor


title: 12A_KO_DNA_2uM_16_R1


title: 12C_KO_DNA_2uM_16_R1


title: ExpB-CTL

description:
CTL
raw count per gene (ENSEMBL ID)


title: ExpI-CTL

description:
CTL
raw count per gene (ENSEMBL ID)


title: 10B_KO_DNA_2uM_8_R1


title: 11A_KO_DNA_DMSO_16_R1


title: ExpB-IL6KD

description:
IL6KD
raw count per gene (ENSEMBL ID)


title: 9C_KO_DNA_DMSO_8_R1


title: 10C_KO_DNA_2uM_8_R1


title: 11B_KO_DNA_DMSO_16_R1


title: 9B_KO_DNA_DMSO_8_R1


title: 10A_KO_DNA_2uM_8_R1


title: ExpH-IL6KD-IL6R


title: 8B_KO_lipo_2uM_8_R1


title: 9A_KO_DNA_DMSO_8_R1


title: 6A_WT_DNA_2uM_16_R1

value: wild-type


title: 6C_WT_DNA_2uM_16_R1


title: 8A_KO_lipo_2uM_8_R1


title: 7C_KO_lipo_DMSO_8_R1

value: lipofectamine


title: 7B_KO_lipo_DMSO_8_R1


title: ExpH-CTL

description:
CTL
raw count per gene (ENSEMBL ID)


title: 6B_WT_DNA_2uM_16_R1


title: 5A_WT_DNA_DMSO_16_R1


title: 5B_WT_DNA_DMSO_16_R1


title: 3B_WT_DNA_DMSO_8_R1


title: 4B_WT_DNA_2uM_8_R1


title: 4C_WT_DNA_2uM_8_R1


title: 2A_WT_lipo_2uM_8_R1


title: 4A_WT_DNA_2uM_8_R1


title: 1C_WT_lipo_DMSO_8_R1


title: 2B_WT_lipo_2uM_8_R1


title: 3A_WT_DNA_DMSO_8_R1


title: 1A_WT_lipo_DMSO_8_R1


title: 5C_WT_DNA_DMSO_16_R1


title: 1B_WT_lipo_DMSO_8_R1


title: 3C_WT_DNA_DMSO_8_R1


title: 8C_KO_lipo_2uM_8_R1


title: RNA-seq FASR Replicate 2

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

country: Australia

institute: South Australian Immunogenomics Cancer Institute

description:
Rep2.FASR.TPM
TKCC20150326_Rep2_FASR_C60DTACXX_8

data_processing:
100bp paired-end reads for MCF7, TAMR and FASR cell lines in biological triplicate were processed using Trim Galore (version 0.11.2) for adapter trimming (parameter settings: --fastqc --paired --retain_unpaired --length 16) and STAR (version 2.4.0j) for mapping reads to the hg38/GRCh38 human genome build with GENCODE v21 used as a reference transcriptome (parameter settings: --quantMode TranscriptomeSAM --outFilterMatchNmin 101).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: normalized transcript abundance measurment

source_name: FASR

growth_protocol: MCF7 breast cancer cells, and the corresponding endocrine resistant sub cell lines were kindly given to our laboratory by Dr Julia Gee (Cardiff University, UK). MCF7 cells were maintained in RPMI-1640 based medium containing 5% (v/v) fetal calf serum (FCS). Tamoxifen-resistant MCF7 (TAMR) cells were generated by the long-term culture of MCF7 cells in phenol-red-free RPMI medium containing 5% charcoal stripped FCS and 4-OH-tamoxifen (1×10－7 M) (TAM). Fulvestrant-resistant MCF7 (FASR) cells were generated by the long-term culture of MCF7 cells in phenol-red-free RPMI medium containing 5% charcoal stripped FCS and fulvestrant (1×10－7 M) (FAS). Endocrine resistant sub lines were established and characterised following 6 months endocrine challenge. All cell lines were authenticated by short-tandem repeat (STR) profiling (Cell Bank, Australia) and cultured for less than 6 months after authentication.

extract_protocol:
Total RNA was isolated with TRIzol reagent. 500ng of total RNA was spiked with external controls (ERCC RNA spike-in Mix, Thermo Fischer #4456740) and libraries constructed with the Illumina TruSeq Stranded mRNA sample preparation kit (ref. RS-930-1001, Illumina).
Illumina TrueSeq

tag: cell line

value: breast cancer cells

tag: resistant phenotype

value: fulvestrant-resistant


title: RNA-seq FASR Replicate 1

description:
Rep1.FASR.TPM
TKCC20150326_Rep1_FASR_C60DTACXX_8


title: 7A_KO_lipo_DMSO_8_R1


title: RNA-seq TAMR Replicate 2

description:
Rep2.TAMR.TPM
TKCC20150326_Rep2_TAMR_C60DTACXX_8

source_name: TAMR

value: tamoxifen-resistant


title: RNA-seq TAMR Replicate 3

description:
Rep3.TAMR.TPM
TKCC20150326_Rep3_TAMR_C60DTACXX_8


title: RNA-seq MCF7 Replicate 1

description:
Rep1.MCF7.TPM
TKCC20150326_Rep1_MCF7_C60DTACXX_6

value: responsive


title: RNA-seq MCF7 Replicate 2

description:
Rep2.MCF7.TPM
TKCC20150326_Rep2_MCF7_C60DTACXX_6


title: RNA-seq TAMR Replicate 1

description:
Rep1.TAMR.TPM
TKCC20150326_Rep1_TAMR_C60DTACXX_8


title: Hi-C FASR Replicate 3

data_processing:
Raw sequence data was mapped and processed using HiC-Pro v2.7.7 (Servant et al., 2015). The paired end reads were aligned separately using bowtie2 against the hg38 human build. Contact matrices were constructed at multiple resolutions and normalized suing ICE normalization algorithm (Imakaev et al. 2012).
Juicebox hic files were prepared using hicpro2juicebox script (Servant et al., 2015). Topologically Associating Domains were annotated using domain-caller (Dixon et al., 2012). Sub-compartments A and B were annotated using Homer Sub-nuclear Compartment Analysis (Heinz et al., 2010). Differential interactions were identified using diffHiC v1.8.1 (Lun et al., 2015) at 20kb resolution.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: allValidPairs files contain all valid interactions identified at multiple resolutions (10kb, 20kb, 40kb, 150kb, 500kb and 1Mb) using HiC-Pro pipeline. The validPairs are stored using a tab-delimited text format as described in (Servant et al., 2015). hic files contain compressed contact matrices at all resolutions. hic format can also be used to visualise Hi-C data in Juicebox (Durand et al., 2016; Robinson et al., 2018) or WashU Epigenome Browser (Zhou et al., 2013). TADs.txt files contain domain calls generated via domain-caller in a bed format. pcaOut files contain sub-nuclear compartment calls created by Homer software. DIs.tsv files contain all differential interactions identified by diffHic (Lun et al., 2015) at 20kb resolution.

extract_protocol:
Cells were cross-linked with formaldehyde, lysed and the intact nuclei was permeabilized. DNA was then cut with NcolI restriction enzyme, the overhangs filled in incorporating a biotinylated base and the free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and the biotinylated ligation junctions were pulled down with streptavidin beads.
Custom library construction protocol was followed. Briefly, DNA was end-repaired and dA-tailing using the NEBNext DNA Master Mixes kit and the ligation of universal adapter was performed on Streptavidin-bound DNA using the NEBNext Ultra DNA Library Prep kit. After adapter ligation DNA was PCR amplified with indexed Illumina primers for 8-12 cycles and library fragments of at least 200bp were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols.


title: Hi-C FASR Replicate 1


title: 2C_WT_lipo_2uM_8_R1


title: Hi-C TAMR Replicate 1


title: RNA-seq MCF7 Replicate 3

description:
Rep3.MCF7.TPM
TKCC20150326_Rep3_MCF7_C60DTACXX_6


title: Donor18.EC

city: Philadelphia

first: Sylvia

middle: T

last: Nurnberg

state: PA

address: 3400 Civic Center Blvd

department: Medicine

institute: University of Pennsylvania

description:
DR_ASE18.EC
083016_DESeq2_paired_hg19_ALL.csv

data_processing:
basecalling with bcl2fastq v2.15.0.4
2pass alignment with STAR-2.4.1d
Differential Gene Expression with DESeq2 v1.15.28
absolute gene expression with RSEM v1.2.31
Genome_build: hg19
Supplementary_files_format_and_content: csv (DESeq2 output): differential gene expression SMC v EC
Supplementary_files_format_and_content: RESULTS file (RSEM output): absolute gene expression per sample

source_name: coronary artery endothelial cell

extract_protocol:
large RNA (>200bp) isolation using the Macherey-Nagel Nucleospini miRNA kit (P/N 740971.50)
Illumina TruSeq stranded mRNA library prep kit according to the manufacturer's protocol

tag: lot number

value: EC

tag: individual


title: Donor15.EC

description:
DR_ASE15.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Hi-C FASR Replicate 2


title: Donor20.EC

description:
DR_ASE20.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor14.EC

description:
DR_ASE14.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Hi-C MCF7 Replicate 1


title: Hi-C MCF7 Replicate 3


title: Hi-C MCF7 Replicate 2


title: Donor12.EC

description:
DR_ASE12.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor13.EC

description:
DR_ASE13.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor11.EC

description:
DR_ASE11.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Hi-C TAMR Replicate 2


title: Donor10.EC

description:
DR_ASE10.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor19.EC

description:
DR_ASE19.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor9.EC

description:
DR_ASE09.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor17.EC

description:
DR_ASE17.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor1.EC

description:
DR_ASE01.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor7.EC

description:
DR_ASE07.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor2.EC

description:
DR_ASE02.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Hi-C TAMR Replicate 3


title: Donor4.EC

description:
DR_ASE04.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor6.EC

description:
DR_ASE06.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor3.EC

description:
DR_ASE03.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor20.SMC

description:
DR_ASE20.SMC
083016_DESeq2_paired_hg19_ALL.csv

source_name: coronary artery smooth muscle cell

value: SMC


title: Donor19.SMC

description:
DR_ASE19.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor17.SMC

description:
DR_ASE17.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor18.SMC

description:
DR_ASE18.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor14.SMC

description:
DR_ASE14.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor15.SMC

description:
DR_ASE15.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor12.SMC

description:
DR_ASE12.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor13.SMC

description:
DR_ASE13.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor11.SMC

description:
DR_ASE11.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor10.SMC

description:
DR_ASE10.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor8.EC

description:
DR_ASE08.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor7.SMC

description:
DR_ASE07.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor8.SMC

description:
DR_ASE08.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor6.SMC

description:
DR_ASE06.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor5.EC

description:
DR_ASE05.EC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor4.SMC

description:
DR_ASE04.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor3.SMC

description:
DR_ASE03.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor2.SMC

description:
DR_ASE02.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: Donor5.SMC

description:
DR_ASE05.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: Wilmar-A_Glycerol_2

city: Melbourne

first: Dane

middle: Aaron McKay

last: Vassiliadis

address: Parkville VIC 3000

institute: Peter MacCallum Cancer Centre

description:
R116
wilmar_counts_combined.csv

data_processing:
basecalls were performed using Illumina CASAVA v1.8.4 pipeline
raw reads were cleaned using Cutadapt v1.9.1 with default parameters and assessed for quality using FastQC
cleaned reads were aligned to the S. pombe ASM294v2.25 genome using Tophat2 v2.1.1 with a max intron size of 5000bp and library-type of fr-firststrand (for stranded samples) or fr-unstranded (for unstranded samples)
reads mapping to gene features were counted with featureCounts v1.5.2 using -s 2 (for stranded samples)
Differential gene expression was performed using DESeq2 v1.12.3
Genome_build: ASM294v2
Supplementary_files_format_and_content: individual raw counts files for each sample

organism: Schizosaccharomyces pombe

source_name: Whole cell

growth_protocol: Cells were cultured in YES 3% glucose for four hours at 32 degrees before being collected by centrifugation, washed twice in sterile water and shifted to YES 3% glucose, YES 3% glycerol + 0.1% glucose or YES 3% glycerol and cultured at 32 degrees for a further four hours. For molasses samples, cells were cultured in molasses medium for four hours

extract_protocol:
Cells were harvested by centrifugation and the hot phenol method (Lyne et al. 2003, BMC Genomics 4:27) was used to isolate total RNA from cells
Libraries were prepared from ribo-depleted RNA using the Illumina TruSeq stranded protocols. Samples R75 R77 R80 were prepared as TruSeq unstranded libraries. All other libraries were prepared as Truseq stranded libraries.

tag: strain

value: Wilmar-A

value: 3% glycerol


title: Wilmar-P_Glycerol_glucose_2

description:
R127
wilmar_counts_combined.csv

value: Wilmar-P

value: 3% glycerol + 0.1% glucose


title: Wilmar-A_Glycerol_glucose_2

description:
R128
wilmar_counts_combined.csv


title: Wilmar-P_Glycerol_2

description:
R113
wilmar_counts_combined.csv


title: Wilmar-P_Molasses_2

description:
R107
wilmar_counts_combined.csv

value: molasses


title: Donor9.SMC

description:
DR_ASE09.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: WT_Molasses_2

description:
R106
wilmar_counts_combined.csv

value: h-


title: Wilmar-P_Molasses_1

description:
R105
wilmar_counts_combined.csv


title: WT_Molasses_1

description:
R104
wilmar_counts_combined.csv


title: Wilmar-A_Glucose_2

description:
R92
wilmar_counts_combined.csv

value: 3% glucose


title: Wilmar-A_Glycerol_1

description:
R94
wilmar_counts_combined.csv


title: Wilmar-P_Glycerol_1

description:
R91
wilmar_counts_combined.csv


title: dBET6-gH2AX

city: Durham

first: Drake

last: Edwards

state: NC

address: 11 Pilatus Dr

department: Radiation Oncology

institute: Duke University

description:
dBET6_gH2AX_Input_log2_50.bw
For R-ChIP, once cells reached 70% confluence, a transfection mixture was created for each 10 cm plate. 750 fmol of DNA, along with a 6:1 ratio of Xtremegene HP (Roche), was diluted in 1mL Opti-mem media (Thermo Fisher Scientific) before being added dropwise to cells in 7 mL of media

data_processing:
Trimming and alignment were done by Genewiz: "Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality at 3’ end (error rate > 0.01) using CLC Genomics Server 9.0. Trimmed data was then aligned to reference genome for human (GRCh38 or called hg20)"
Genome_build: hg38
Supplementary_files_format_and_content: To normalize ChIP-seq reads to the appropriate input files, bamCompare by deepTools was used to find a log2 ratio. The bigWig files provided are the output of this software.

source_name: HeLa cells

growth_protocol: HeLa cells were grown as a monolayer on 10cm plates, typically seeded at ~1 million cells per plate. Cells were grown in DMEM High Glucose (Genessee Scientific) supplemented with 10% fetal bovine serum (Summerlin Scientific Products) and 1% penicillin/streptomycin (Thermo Fisher Scientific)

extract_protocol:
Cells were fixated with 1% formaldehyde for 13 minutes before extracting ChIP DNA using the SimpleChIP plus sonication kit (Cell Signaling Technology)
Libraries were prepared using Illumina standard protocols by Genewiz

treatment_protocol: Cells were treated with 100nM dBET6 or equivalent volume of DMSO for 2 hours before fixation

tag: transfection

tag: chip antibody

value: γH2AX (Abcam, ab2893)


title: DMSO-R-ChIP

description:
DMSO_R-ChIP_Input_log2_50.bw
For R-ChIP, once cells reached 70% confluence, a transfection mixture was created for each 10 cm plate. 750 fmol of DNA, along with a 6:1 ratio of Xtremegene HP (Roche), was diluted in 1mL Opti-mem media (Thermo Fisher Scientific) before being added dropwise to cells in 7 mL of media

value: V5 (Abcam, ab9116)


title: dBET6-R-ChIP

description:
dBET6_R-ChIP_Input_log2_50.bw
For R-ChIP, once cells reached 70% confluence, a transfection mixture was created for each 10 cm plate. 750 fmol of DNA, along with a 6:1 ratio of Xtremegene HP (Roche), was diluted in 1mL Opti-mem media (Thermo Fisher Scientific) before being added dropwise to cells in 7 mL of media


title: DMSO-R-ChIP-5pct-Input


title: Donor1.SMC

description:
DR_ASE01.SMC
083016_DESeq2_paired_hg19_ALL.csv


title: DMSO-gH2AX

description:
DMSO_gH2AX_Input_log2_50.bw
For R-ChIP, once cells reached 70% confluence, a transfection mixture was created for each 10 cm plate. 750 fmol of DNA, along with a 6:1 ratio of Xtremegene HP (Roche), was diluted in 1mL Opti-mem media (Thermo Fisher Scientific) before being added dropwise to cells in 7 mL of media


title: dBET6-R-ChIP-5pct-Input


title: DMSO-5pct-Input


title: dBET6-5pct-Input


title: ADAM10 flox/flox-Col2a1-Cre mouse #2

city: Tokorozawa

first: Keisuke

last: Horiuchi

address: 3-2 Namiki, Tokorozawa

department: Department of Orthopedic Surgery

institute: National Defense Medical College

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent   SurePrint G3 Mouse GE Microarray (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B).

data_processing: The scanned images were analyzed with the Feature Extraction ver 10.7.1.1 software (protocol: GE1_107 sep 09 and Grid: 028005_D_F_20131202).

source_name: Cartilage tissue from ADAM10 flox/flox-Col2a1-Cre mouse

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One Color Spike Mix Kit and Low Input Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using QIAzol Lysis Reagent and miRNeasy Micro Kit (Qiagen) as instructed by the manufacture. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: genotype/variation

value: ADAM10 flox/flox-Col2a1-Cre

tag: tissue

value: cartilage (tibia)


title: Control mouse #1

source_name: mouse cartilage tissue

value: control


title: ADAM10 flox/flox-Col2a1-Cre mouse #3


title: SS-nano-2

city: Montreal

first: Marie-Josée

last: Hébert

state: QC

address: 900 Rue Saint-Denis

country: Canada

institute: CRCHUM

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35[1] and aligned to the reference human genome version GRCh38 (gene annotation from Gencode version 24) using STAR version 2.5.1b
Gene expression were obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain transcript level expression.
Genome_build: GRCh38
Supplementary_files_format_and_content: XLS files include FPKM values for each sample and readcount values for each sample

source_name: primary human umbilical vein endothelial cells from Cell Applications

growth_protocol: Human umbilical vein endothelial cells (HUVEC) were purchased from Cell Applications, cultured in EGM-2MV complete medium (Lonza) or Medium 200 + LSGS (Gibco, Waltham, MA, USA) on a gelatin-coated surface and used at passage 4.

extract_protocol:
Total RNA was isolated from a 6-well by directly lysing the cells with TRIzol Reagent according to the manufacturer’s protocol (ThermoFisher) and then further purified using RNeasy columns (Qiagen, Germantown, MD, USA). The presence of contamination with chemicals was assessed by Nanodrop using 260/280 and 260/230 ratios. Quantification of total RNA was made by QuBit (Applied Biosystems, Waltham, MA, USA) and 1000 ng of total RNA was used for library preparation. Quality of total RNA was assessed with the BioAnalyzer Nano (Agilent, Santa Clara, CA, USA) and all samples had a RIN above 9.
Library preparation was done with the KAPA mRNAseq stranded kit (KAPA, Cat no. KK8420). Ligation was made with 11 nM final concentration of Illumina index and 9 PCR cycles were required to amplify cDNA libraries. Libraries were quantified by QuBit and BioAnalyzer. All libraries were diluted to 10 nM and normalized by qPCR using the KAPA library quantification kit (KAPA; Cat no. KK4973). Libraries were pooled to equimolar concentration.

treatment_protocol: Cells were exposed to RPMI serum-free medium (Gibco) for 2 hours +/- ApoExo (nano)

tag: cell type

value: HUVEC

tag: agent

value: ApoEx


title: Control mouse #2


title: Control mouse #3


title: SS-nano


title: Wilmar-A_Glycerol_glucose_1

description:
R80
wilmar_counts_combined.csv


title: SS-2h-2


title: Wilmar-P_Glycerol_glucose_1

description:
R77
wilmar_counts_combined.csv


title: Wilmar-A_Glucose_1

description:
R78
wilmar_counts_combined.csv


title: FASR_input_ChIP-seq

data_processing:
ChIP-seq reads were aligned to hg38 using bowtie v2.2.4 allowing up to 3 mismatches, discarding ambiguous and clonal reads. Peaks were called with Macs2 version 2.0.10.
Genome_build: hg38
Supplementary_files_format_and_content: Bigbed files were generated using Macs2 version 2.0.10.

extract_protocol:
Nuclei were purified after formaldehyde crosslinking, collected and resuspended in SDS Lysis buffer before sonication. Chromatin was sonicated to generate a majority of fragments between 200 and 600 bp. 10µg of each antibody was used per ChIP.
Libraries for ChIP-Seq were prepared following Illumina protocols. The resulting libraries were sequenced on the Illumina HiSeq 2000 platform configured for 50bp single-end reads.

value: breast cancer cells

tag: resistant phynotype

value: fulvestrant-resistant


title: TAMR_input_ChIP-seq

value: tamoxifen-resistant


title: Wilmar-P_Glucose_2

description:
R89
wilmar_counts_combined.csv


title: FASR_CTCF_ChIP-seq

value: CTCF millipore 07-729


title: ADAM10 flox/flox-Col2a1-Cre mouse #1


title: TAMR_CTCF_ChIP-seq


title: FASR_H3K27ac_ChIP-seq

value: H3K27Ac Active Motif 39133


title: TAMR_H3K27ac_ChIP-seq


title: TAMR_H3K27me3_ChIP-seq

value: H3K27Me3 millipore ab 07-449


title: sample10: C 005

city: Madison

first: Rozalyn

last: Anderson

state: WI

address: 2500 Overlook Terrace

department: Department of Medicine

institute: University of Wisconsin-Madison

data_processing:
mapper.pl <input>.fastq -e -j -k TGGAATTCTCGGGTGCCAAGG -l 18 -m -p mm801.93 -s <input>.collapsed.fa -t <input>_collapsed_vs_mm801.93.arf -v -h
map raw fastq to mm801.93 genome
commit: dc71ea882ef1e92aaf2cd8baf47361c1b8c3b7ee (v0.1.2)
miRDeep2_patch.pl <input>.collapsed.fa mm801.93.fa <input>.reads_collapsed_vs_mm801.93.arf mature_ref.fa mature_other.fa hairpin_ref.fa none 2>report.<input>.log -T 32
run miRDeep2 pipeline
commit: a61a06a1b1214d18f8e22ec19cb4fe9f351c6759 (patch for miRDeep2 version 0.1.2)
miR source: miRBase v22 (2018-03-05)
Genome_build: Mmul_8.0.1 (Ensembl release 93)
Genome_build: NCBI_Assembly:GCA_000772875.3

organism: Macaca mulatta

source_name: skeletal muscle biopsy

extract_protocol:
50 mg of tissue was homogenized in Trizol and total RNA was purified according to manufacturer's specifications.
RNA integrity was confirmed using the Agilent 2100 Bioanalyzer. 5 ug of total RNA was used to gel isolate 17-35 nt-sized fragments. Isolated small RNAs were then used to make small RNA-seq libraries using TruSeq Small RNA Library Prep Kit from Illumina (Cat#: RS-200-0024).
Small RNA-seq libraries were then run 1x100bp on an Illumina 2500.

value: vastus lateralis muscle

tag: animal diet

value: Control


title: sample13: R 008

value: CR


title: sample9: R 005


title: sample12: R 007


title: sample11: R 006


title: SS-2h


title: FASR_H3K4me1_ChIP-seq

value: H3K4Me1 Active Motif 39297


title: FASR_H3K4me3_ChIP-seq

value: H3K4Me3 Active Motif 39159


title: TAMR_H3K4me3_ChIP-seq


title: Wilmar-P_Glucose_1

description:
R75
wilmar_counts_combined.csv

value: Wilmar-P

value: 3% glucose


title: sample6: R 002


title: sample7: R 003


title: sample5: C 004


title: TAMR_H3K4me1_ChIP-seq


title: sample8: R 004


title: FASR_H2AZac_ChIP-seq

value: H2A.Zac abcam 18262


title: sample3: R 001


title: sample2: C 002


title: sample4: C 003


title: TAMR_H2AZac_ChIP-seq


title: MCF7_H2AZac_ChIP-seq

value: responsive


title: sample1: C 001


title: 2363t

city: Changchun

first: ren

last: shengnan

state: State...

address: NO.126 Xiantai street

institute: China-Japan union hospital of Jilin university

data_processing:
 Basecalls performed using cutadapt software (v1.9.3).
The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4).
Guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA
Genome_build: hg19
Supplementary_files_format_and_content: excel format

source_name: colorectal cancer tissues

extract_protocol:
Total tissue RNA was extracted from the frozen tissue block  using TRI reagent (Sigma, USA)
rRNA was removed by Ribo-Zero™ rRNA Removal Kit (Illumina, USA) and construct library with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA).

tag: tissue type

value: colorectal cancer tissues

tag: tumor stage


title: 2254t


title: 2239t


title: 0783t


title: 1995t


title: 1995n

source_name: normal colorectal epithelial tissues

value: normal colorectal epithelial tissues


title: EPI_seCLIP_AKAP8_Rep2

city: Houston

first: Samuel

middle: Emerson

last: Harvey

state: TEXAS

address: One Baylor Plaza

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

data_processing:
RNA-seq reads were aligned to the human genome (GRCh37, primary assembly) and transcriptome (Gencode version 24 backmap 37 comprehensive gene annotation) using STAR version 2.6.1a59 with the following non-standard parameters --outFilterMultimapNmax 1 --outSAMstrandField intronMotif --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 3 --alignEndsType EndToEnd. Only uniquely aligned reads were retained for downstream analysis.
Differential gene expression analysis was performed by counting reads over genes from the same annotation as alignment using featureCounts version 1.5.0 with the following non-default parameters -s 2 -p -C -B. Differential gene expression analysis was conducted using DESeq2 performed on genes with at least 10 counts present in the library with the lowest sequencing depth61. Significantly regulated genes were defined as genes with an | log2FC | > 1 and FDR < 0.05
Differential alternative splicing was quantified using rMATS version 4.0.260 with the following non-default parameters --readLength 100 --cstat 0.01 --libType fr-secondstrand. To identify significant differential splicing events, we set up the following cutoffs: FDR < 0.05, ∆PSI ≥ 0.1, and average junction reads per event per replicate ≥ 20.
Specifically, input and AKAP8 antibody IP-ed fractions were run on an SDS-PAGE. Protein-RNA complexes between 95 KD to 180 KD were collected for RNA isolation followed by library generation. eCLIP libraries were sent to Genomic Facility at University of Chicago for single-end sequencing. eCLIP data processing was conducted using the public eCLIP pipeline version 0.2.1a (https://github.com/YeoLab/eclip/releases/tag/0.2.1a) and public merge-peaks pipeline version 0.0.6 (https://github.com/YeoLab/merge_peaks/ releases/tag/0.0.6), derived from the previously published eCLIP pipeline. High confidence eCLIP peaks for each cell state were called by selecting AKAP8 binding peaks with a minimum log2FC IP / Input signal > 2 among the replicates and an adjusted p-value < 0.05, resulting in 21,668 and 26,230 AKAP8 binding peaks in the epithelial and mesenchymal states, respectively.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited file with counts for each gene in each sample; rMATS output for five alternative splicing types comparing control and knockdown samples, replicate merged, input normalized seCLIP AKAP8 peaks in bed format

source_name: HMLE Twist-ER Untreated Cells

growth_protocol: HMLE/Twist-ER cells were grown in Mammary Epithelial Cell Growth Medium (Lonza, USA). To induce EMT in HMLE/Twist-ER cells, a final concentration of 20 nM tamoxifen (TAM) was added to its culture medium, and cells were split every other day until the mesenchymal morphology was fully observed.

extract_protocol:
Immunoprecipitated RNA after IP with AKAP8 antibody
seCLIP (single end enhanced Crosslinking and Immunoprecipitation) library generation per PMID: 28766298
seCLIP (single end enhanced Crosslinking and Immunoprecipitation) library generation per PMID: 28766298

treatment_protocol: UV crosslinked cells

value: Tert-immortalized human mammary epithelial cells

value: HMLE Twist-ER Untreated Cells

tag: antibody

value: AKAP8 immunoprecipitated processed through seCLIP library generation


title: MES_seCLIP_AKAP8_Rep1

source_name: HMLE Twist-ER Tamoxifen-Treated Cells

value: Tert-immortalized human mammary epithelial cells treated with tamoxifen

value: HMLE Twist-ER Tamoxifen-Treated Cells


title: 2363n


title: Non-irradiated biological replicate 2

city: Milwaukee

first: Heather

last: Himburg

state: Wisconsin

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

hyb_protocol: Affymetrix mouse 430 2.0 array.

scan_protocol: Affymetrix Fluidics Station and Scanner.

data_processing: Affymetrix Expression Console software to perform gene level normalization and signal summarizations. Affymetrix Transcriptome Analysis Console (TAC) software was used to analyze the differential gene expression between the irradiation time points.

source_name: adult mouse bone marrow

label_protocol: Nugen Ovation RNA Amplification System V2 (Cat. #3100-A01).

growth_protocol: 8-10 week old adult mice.

extract_protocol: Qiagen RNeasy micro kit.

treatment_protocol: 5 Gy total body irradiation.

tag: strain/background

value: Bone marrow VE-cadherin+ endothelial cells

tag: treatment

value: Non-irradiated


title: 2254n


title: Day 14 post TBI biological replicate 5

value: Total body irradiation (TBI)

tag: time point

value: Day 14 post TBI


title: 2239n


title: Non-irradiated biological replicate 1


title: Day 14 post TBI biological replicate 1


title: Day 14 post TBI biological replicate 4


title: 24 hours post TBI biological replicate 2

value: 24 hours post TBI


title: MES_seCLIP_Input_Rep1

extract_protocol:
Total RNA was extracted using standard Trizol extraction procedures
seCLIP (single end enhanced Crosslinking and Immunoprecipitation) library generation per PMID: 28766298
seCLIP (single end enhanced Crosslinking and Immunoprecipitation) library generation per PMID: 28766298

tag: cell line

value: Total RNA processed through seCLIP library generation


title: Day 14 post TBI biological replicate 2


title: Non-irradiated biological replicate 3


title: Non-irradiated biological replicate 4


title: 0783n


title: 24 hours post TBI biological replicate 3


title: EPI_seCLIP_Input_Rep2


title: Non-irradiated biological replicate 5


title: MES_seCLIP_AKAP8_Rep2


title: EPI_seCLIP_AKAP8_Rep1


title: 24 hours post TBI biological replicate 5


title: MES_seCLIP_Input_Rep2


title: EPI_seCLIP_Input_Rep1


title: RNA-seq FASR Replicate 3

description:
Rep3.FASR.TPM
TKCC20150326_Rep3_FASR_C60DTACXX_8

value: breast cancer cells

tag: resistant phenotype

value: fulvestrant-resistant


title: MES_Control_Rep3

description:
DESeq2_gene_table.txt.gz
DESeq2_gene_table.txt.gz
EPI_control_vs_MES_control_rMATS_A3SS.txt.gz
EPI_control_vs_MES_control_rMATS_A5SS.txt.gz
EPI_control_vs_MES_control_rMATS_MXE.txt.gz
EPI_control_vs_MES_control_rMATS_RI.txt.gz
EPI_control_vs_MES_control_rMATS_SE.txt.gz

extract_protocol:
Total RNA was extracted using standard Trizol extraction procedures
Stranded paired-end polyA-purified RNA sequencing libraries were prepared using Illumina TruSeq protocols
Stranded paired-end polyA-purified RNA sequencing libraries

treatment_protocol: Cell lines stably expressing the relevant shRNA were generated using lentiviral vectors using standard infection protocols

value: Non-specific shRNA treated


title: MES_shAKAP8_Rep2

description:
DESeq2_gene_table.txt.gz
MES_control_vs_AKAP8_KD_rMATS_A3SS.txt.gz
MES_control_vs_AKAP8_KD_rMATS_A5SS.txt.gz
MES_control_vs_AKAP8_KD_rMATS_MXE.txt.gz
MES_control_vs_AKAP8_KD_rMATS_RI.txt.gz
MES_control_vs_AKAP8_KD_rMATS_SE.txt.gz

value: AKAP8 targeting shRNA treated


title: MES_shAKAP8_Rep1


title: EPI_shAKAP8_Rep3

description:
DESeq2_gene_table.txt.gz
EPI_control_vs_AKAP8_KD_rMATS_A3SS.txt.gz
EPI_control_vs_AKAP8_KD_rMATS_A5SS.txt.gz
EPI_control_vs_AKAP8_KD_rMATS_MXE.txt.gz
EPI_control_vs_AKAP8_KD_rMATS_RI.txt.gz
EPI_control_vs_AKAP8_KD_rMATS_SE.txt.gz


title: 6 hours post TBI biological replicate 5

value: 6 hours post TBI


title: MES_Control_Rep1

description:
DESeq2_gene_table.txt.gz
MES_control_vs_AKAP8_KD_rMATS_A3SS.txt.gz
MES_control_vs_AKAP8_KD_rMATS_A5SS.txt.gz
MES_control_vs_AKAP8_KD_rMATS_MXE.txt.gz
MES_control_vs_AKAP8_KD_rMATS_RI.txt.gz
MES_control_vs_AKAP8_KD_rMATS_SE.txt.gz
EPI_control_vs_MES_control_rMATS_A3SS.txt.gz
EPI_control_vs_MES_control_rMATS_A5SS.txt.gz
EPI_control_vs_MES_control_rMATS_MXE.txt.gz
EPI_control_vs_MES_control_rMATS_RI.txt.gz
EPI_control_vs_MES_control_rMATS_SE.txt.gz


title: 38_L1.N702

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

data_processing:
Raw read data was aligned against mouse transcriptome (MouseEnsembl release 61) using Bowtie2 (Langmead and Salzberg, 2012). Splice junctions were defined as available in Ensembl v75. Read mappings were then mapped to genes and transcripts based on the transcript models annotated in Ensembl v75 using in-house tools and, again using in-house software, RPKM values were computed as described previously (Mortazavi et al., 2008).
Genome_build: MouseEnsembl release 61
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: MMTV-PyMT mammary tumors

extract_protocol:
Cell sorting was performed using FACS Aria II apparatus (BD). Each cell population (n=4) was isolated from an independent tumor. Typically, 2x104 to 2x105 cells were obtained for each cell population. Sorted cell populations were immediately homogenized in 700 µl Qiazol reagent (Qiagen). 140 µl of chloroform was added to the homogenate and the mixture centrifuged at 16,000 x g for 5 min at 4°C in Phase Lock Tubes (Qiagen). RNA was subsequently extracted from the aqueous phase using the RNeasy Micro kit (Qiagen) according to manufacturer’s instructions. Genomic DNA was removed using the RNase free DNase set (Qiagen) during the extraction. RNA was quality controlled on Agilent Eukaryote Total RNA pico chips (Agilent Technologies). High quality RNA (RIN >7) was obtained for all samples. SMARTer ultra low RNA kit for Illumina sequencing (Clontech) was used to prepare and amplify cDNA from 520 pg of total RNA according to manufacturer’s instructions.
Then, 1 ng of amplified cDNA was subjected to Nextera XT library preparation (Illumina) according to manufacturer’s instructions. Sequencing libraries were quantified using the Kapa Library Quantification kit (Kapa Biosystems) and quality controlled by capillary electrophoresis on a Bioanalyzer using High Sensitivity chips (Agilent Technologies). Libraries were sequenced on a HiSeq2500 sequencer (Illumina) for 2 x 50 cycles using version 4 cluster generation kits and version 4 sequencing reagents (Illumina).

treatment_protocol: When tumors reached a size of 300 mm3, mice were injected i.p with the following moAbs: mouse IgG1 (clone MOPC-21, 500 μg) + rat IgG2a (clone 2A3, 100 μg), designated as “IgG”; or anti-VEGFA/ANGPT2 (A2V, 500 μg) + rat IgG2a (clone 2A3, 100 μg), designated “A2V”.  Five days later, mice were euthanized and tumors harvested and prepared for fluorescence-activated cell sorting (FACS).

value: Macrophages


title: 24 hours post TBI biological replicate 4


title: 7_L6

value: CD8+ cells


title: 27_L8


title: EPI_shAKAP8_Rep2

value: Tert-immortalized human mammary epithelial cells

value: HMLE Twist-ER Untreated Cells


title: 6 hours post TBI biological replicate 4


title: 26_L7


title: 44_L1.N708

value: CD4+ cells


title: 6 hours post TBI biological replicate 3


title: 6_L5


title: 6 hours post TBI biological replicate 2


title: 28_L1.N704


title: 58_L1.N709


title: EPI_Control_Rep3

description:
DESeq2_gene_table.txt.gz
EPI_control_vs_AKAP8_KD_rMATS_A3SS.txt.gz
EPI_control_vs_AKAP8_KD_rMATS_A5SS.txt.gz
EPI_control_vs_AKAP8_KD_rMATS_MXE.txt.gz
EPI_control_vs_AKAP8_KD_rMATS_RI.txt.gz
EPI_control_vs_AKAP8_KD_rMATS_SE.txt.gz
EPI_control_vs_MES_control_rMATS_A3SS.txt.gz
EPI_control_vs_MES_control_rMATS_A5SS.txt.gz
EPI_control_vs_MES_control_rMATS_MXE.txt.gz
EPI_control_vs_MES_control_rMATS_RI.txt.gz
EPI_control_vs_MES_control_rMATS_SE.txt.gz


title: 6 hours post TBI biological replicate 1


title: EPI_shAKAP8_Rep1


title: EPI_Control_Rep1


title: 22_L4


title: 10_L1.N710


title: MES_Control_Rep2

value: Tert-immortalized human mammary epithelial cells treated with tamoxifen

value: HMLE Twist-ER Tamoxifen-Treated Cells


title: HCC38 RP19 KD R2

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

description:
12_HCC38_KD_R2
RP11-1911.1 KD Replicate 2
Poly-A selected RNA

data_processing:
Basecalls performed using CASAVA version 1.8.4.
Reads were mapped to hg19 using TopHat v2.0.13 guided by GTF version GRCh37.70 with default parameters and calculated insert size and SD.
Read counting performed using HT-seq v0.6.0 (--mode=union --stranded=no --minaqual=30 --idattr=gene_name --type=exon).
Normalization and Differential expression analysis performed using DEseq v3.0.
BAM to bedgraph performed using bedtools v2.17.0.
bedgraph to bigwig performed using bedGraphToBigWig v4.
Statistics and plotting performed in R v3.1.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: BigWig (coverage for mapped reads).
Supplementary_files_format_and_content: Count tables (read counts for genomic features).

growth_protocol: Cells were cultured in 10cm Dish with complete growth medium.

extract_protocol:
RNA extraction was performed using TRIZOL extraction protocol.
The standard Agilent SureSelect Strand-Specific RNA sequencing protocol was followed. Briefly, the polyA fraction was purified using two rounds of oligo dT-magnetic bead purification. The resulting polyA fraction was fragmented and first strand cDNA was done with random primers in the presence of Actinomycin D using standard techniques. The resulting first stand cDNA was purified using AMPure Beads and second strand cDNA and end repair was done using standard techniques. The blunt ended double stranded cDNA was incubated with exo- E.coli DNA polymerase to add an adenosine to the ends for T/A cloning of the adaptors. PCR amplification was done in the presence of uracil DNA glycosylase to generate strand specificity. A second round of PCR amplification was done to add unique 6-bp barcodes to each sample and add sequences necessary for flow cell attachment. The resulting mRNA libraries were quantitated using qPCR following the manufacturer's instructions (Kapa Biosystems, Woburn MA).

treatment_protocol: Cells were transfected at the time of seeding with transfection mix containing LNA NS or LNA1/2 (50nM final). Media was changed after 6 hours. Cells were collected after 24h of transfection.

value: Breast Cancer Cell line

tag: condition


title: 24 hours post TBI biological replicate 1

value: Bone marrow VE-cadherin+ endothelial cells

value: Total body irradiation (TBI)


title: Day 14 post TBI biological replicate 3

value: Day 14 post TBI


title: HCC38 LNA NS R2

description:
11_HCC38_NS_R2
LNA CTR Replicate 2
Poly-A selected RNA

value: LNA CTR


title: EPI_Control_Rep2


title: HCC38 RP19 KD R1

description:
10_HCC38_KD_R1
RP11-1911.1 KD Replicate 1
Poly-A selected RNA


title: 9_L1.N709

value: CD31+ cells


title: HCC38 LNA NS R1

description:
9_HCC38_NS_R1
LNA CTR Replicate 1
Poly-A selected RNA


title: 40_L1.N704


title: 55_L1.N706


title: 42_L1


title: 41_L1.N705


title: 60_L3


title: 39_L1.N703


title: SUM149PT RP19 KD R1

description:
6_SUM149_KD_R1
RP11-1911.1 KD Replicate 1
Poly-A selected RNA


title: SUM149PT LNA NS R1

description:
5_SUM149_NS_R1
LNA CTR Replicate 1
Poly-A selected RNA


title: MDA-MB-468 RP19 KD R2

description:
4_468_KD_R2
RP11-1911.1 KD Replicate 2
Poly-A selected RNA


title: MDA-MB-468 RP19 KD R1

description:
2_468_KD_R1
RP11-1911.1 KD Replicate 1
Poly-A selected RNA


title: SUM149PT RP19 KD R2

description:
8_SUM149_KD_R2
RP11-1911.1 KD Replicate 2
Poly-A selected RNA


title: MDA-MB-468 LNA NS R1

description:
1_468_NS_R1
LNA CTR Replicate 1
Poly-A selected RNA


title: MDA-MB-468 LNA NS R2

description:
3_468_NS_R2
LNA CTR Replicate 2
Poly-A selected RNA


title: 37_L1.N701


title: 54_L1.N705


title: 24_L1.N712


title: 23_L5


title: 56_L1


title: 59_L2


title: 8_L7


title: 25_L6


title: WT CD45 TILs Rep 4

city: Baltimore

first: Gregory

middle: Lee

last: Szeto

state: MD

address: 1000 Hilltop Circle, ILSB room 415

institute: UMBC

data_processing:
Pass-filter Illumina reads may undergo one or both of adaptor and quality trimming upon completion of FastQC assessment. Sequence files that show adaptor contamination of 1% or higher undergo adaptor trimming using Trimmomatic enforcing a minimum Q20 trailing quality for every read. Quality trimming uses fastx_trimmer [2] to truncate reads where the quality drops below Phred scale quality of 20 (Q20). Reads that fail to meet a minimum read length of 30 bp (or 5bp for miRNA libraries) after adaptor and quality trimming are excluded from the trimmed files and so are their mates in the case of paired-end files.
Reads were assigned to transcripts using Salmon v0.9.1 in mapping mode to mouse transcriptome index.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated file with a header line containing names of all columns. Columns appear in the following order: Name, Length, Effective Length, TPM, NumReads  Each subsequent row describes a single transcript quantification. The columns have the following interpretation.    Name — ENSEMBL transcript ID with version identifier  Length — the length of the target transcript in nucleotides.  EffectiveLength — the computed effective length of the target transcript. .  TPM — the relative abundance in units of Transcripts Per Million (TPM).   NumReads — estimate of the number of reads mapping to transcript

source_name: subcutaneous B16F10 tumor

extract_protocol:
B16F10 tumors and lymph nodes from wild-type or CD4Cre Yap-floxed C57BL/6J mice were mechanically and enzymatically dissociated, and cells stained for flow sorting. Live, purified CD4+ T cells, CD8+ T cells or CD45+ CD4- CD8- cells were sorted directly into TRIzol LS reagent. RNA was purified by Qiagen miRNeasy kit.
Libraries were prepared using Takara SMART-Seq® v4 Ultra® Low Input RNA Kit following manufacturer's protocol.

value: CD45+ immune cells

tag: strain

tag: genotype

value: WT


title: YapKO CD45 TILs Rep 4

value: CD4Cre Yap flox


title: YapKO CD45 TILs Rep 3


title: YapKO CD45 TILs Rep 2


title: SUM149PT LNA NS R2

description:
7_SUM149_NS_R2
LNA CTR Replicate 2
Poly-A selected RNA


title: YapKO CD45 TILs Rep 1


title: 57_L1.N708


title: 21_L3


title: WT CD45 TILs Rep 1


title: WT CD45 TILs Rep 3


title: Ovaries, WT, H3K4me3-rep1 (ChIP-Seq)

city: Lyon

first: Gerard

last: BENOIT

address: 46 allée d'Italie

country: France

institute: CNRS/ENS Lyon/UMR5239

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Adapter dimer reads were removed using DimerRemover
ChIP-seq read alignment: bowtie2-2.3.3, default
Duplicated read removal using picard-tools 2.17.10
Peak Calling using MACS version 2.1.1.20160309
Genome_build: BDGP Release 6 + ISO1 MT/dm6
Supplementary_files_format_and_content: peak file (narrowPeak format) were generated using MACS 2.1.1 command callpeak with the following options -f BAMPE -g dm -s 50 -q 0.1 and an effective genome size of  1.20e+08
Supplementary_files_format_and_content: bigwig files for each sample were generated using Deeptools 3.0.1 command bamCoverage with the following options-p max --normalizeUsing BPM --smoothLength 30 --ignoreDuplicates --minMappingQuality 5 --centerReads --outFileFormat bigwig

organism: Drosophila melanogaster

source_name: Drosophila melanogaster ovaries

extract_protocol:
Pairs of ovary from young (0-1 day old) virgin female were dissected in PBS buffer. Ovaries were cross-linked with 1.8% formaldehyde and  nuclei were extracted by tissue homogeneization using Dounce with glass pistone (loose 4 times and tight 8 times) in total 10 min incubation at room temperature.Crosslinking was quenched by adding 125mM glycine followed by incubation for 5 min. Crosslinked isolated Nuclei were lysed in presence of 0.5% SDS and chromatin supernatant was sonicated using Bioruptor (18 cycles, 30s ON/30s OFF). H3K4me3-DNA complexes were isolated with antibody.
Libraries were synthesized using Diagenode MicroPlex Library Preparation kit v2 Instruction Manual, version v.2 02.15

value: Control KD (MTD-Gal4>+)

value: ovaries dissected from 3 day-old females

tag: chip antibody

value: H3K4me3 (abcam ab8580)


title: Ovaries, LidKD, H3K4me3-rep1 (ChIP-Seq)

value: lid KD (MTD-Gal4>shRNA lid)

tag: tissue


title: Ovaries, LidKD, H3K4me3-rep2 (ChIP-Seq)


title: Ovaries, WT, H3K4me3-rep2 (ChIP-Seq)


title: WT CD45 TILs Rep 2

tag: cell type


title: 11_L1.N711

value: CD8+ cells


title: Sin3A-2

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Adapter dimer reads were removed using DimerRemover
RNA-seq read alignment: Tophat version 2.1.1, default.
RNA-seq read assignment to genes: feautreCounts 1.4.6, default.
Differential gene expression detection: DESeq2
Genome_build: dm6 (dmel-all-chromosome-r6.15)
Supplementary_files_format_and_content: tab-delimited text files include read count values for each feature
Supplementary_files_format_and_content: DESeq2 results files in tab-separated format
Supplementary_files_format_and_content: bigwig files for each sample were generated using Deeptools command bamCoverage with the following options -bs 10  -p max --normalizeUsing CPM --smoothLength 30 --minMappingQuality 5 --outFileFormat bigwig

source_name: bioanalyzer validated (RIN>9) Drosophila ovaries total RNA samples

extract_protocol:
RNAs were extracted with the  Trizol (Invitrogen, Cat# 15596026) method according to supplier recommendations. RNA concentration wre measured using NanoDrop.  RNA integrity was assessed using an Agilent Bioanalyzer. RNA-seq libraries were made from samples with a RNA Integrity Number (RIN) of at least 9.0.
RNA-seq library was synthesized according to TruSeq Stranded mRNA Sample Preparation Guide - PN 15031047, version Rev.E Oct 2013

tag: genotype/variation

value: Sin3A KD (MTD-Gal4>shRNA Sin3A)

value: ovaries

tag: age

value: 3 day-old

tag: Sex

value: female


title: 12_L1.N712

value: CD4+ cells


title: 5_L4


title: WT CD4 TILs Rep 4

value: CD4+ T cells


title: Lid-1


title: Lid-2


title: Sin3A-1


title: Rod-P5-3

city: Bethesda

first: Koray Dogan

last: Kaya

address: 6 CENTER DR

department: NEI

institute: NIH

data_processing:
Paired end fastq files and single end fastq files of Rod samples from GSE74660 were aligned to protein coding cDNA fasta file annotated by Ensembl version 87 by using kallisto
Thw two types of data were summarized and normalized together by tximport

source_name: Isolated rods

growth_protocol: MEFs were grown in IMR90 medium and CiPC reprogramming was performed in photoreceptor induction medium

extract_protocol: Cells were sorted by promoter reporter expression and RNA was prepared by quick RNA micro kit from zymo research (R1050). Each sample contains 80ng of total RNA.

treatment_protocol: five chemical treatment for 11 days in induction medium

value: Isolated rods

value: Strain (Nrl-GFP)

tag: developmental stage

value: Postnatal day 5


title: YapKO CD4 TILs Rep 2


title: WT-1


title: YapKO CD4 TILs Rep 4


title: Rod-P5-2


title: Rod-P5-1


title: YapKO CD4 TILs Rep 3


title: RBP-J KO without stimulation

city: Beijing

first: Xiang

last: Zhang

address: Tsinghuayuan Street

institute: Tsinghua University

data_processing:
Illumina Casava v1.8.2 software used for basecalling
Sequenced reads were mapped to mouse miRNAs from the miRBase release 21 using miRDeep2
Number of raw counts was calculated using miRDeep2
The raw counts were then normalized by library size and multiplied by a factor of 1e6 which corresponds technically to counts per million (CPM) mapped miRNA reads
Genome_build: miRBase release 21

source_name: RBP-J KO_BMDM

growth_protocol: Murine Bone marrows cells were harvested from tibiae and femora, and  were cultured for 5 days in DMEM supplemented with 10% FBS and 10% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor to generate BMDMs

extract_protocol:
Total RNA were extracted from BMDMs with Trizol (Invitrogen)
Illumina TruSeq Small RNA Library preparation

treatment_protocol: without stimulation

tag: strain background

value: RBP-J KO; Rbpjf/f LyZ2 Cre

value: bone marrow macrophages


title: WT without stimulation

description: WT

value: WT


title: YapKO CD4 TILs Rep 1

value: CD4Cre Yap flox


title: Spt16_WT_2

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

data_processing:
ChIP-seq 50 bp single-end reads were aligned to the reference (Schizosaccharomyces pombe ASM294v2) using bowtie2 (version 2.2.9).
Reads were processed using the Homer software package (Heinz et al., 2010). Tag directories were created with the parameter -mapq 1 and bedgraph coverages were generated and normalized to the total number of reads and to the corresponding input using the makeUCSCfile command.
Genome_build: Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: Bedgraph format. Normalized coverage (ChIP/Input).

source_name: whole cell

extract_protocol:
100 ml yeast cultures were grown to mid-log phase to OD600=0.6. The cultures were cooled down at RT for 10 min and fixed with 1% FA for 20 min at RT on the shaker. Cross-linking was stopped with 150 mM Glycine for 10 min at RT on the shaker. Cells were spun down 2 min at 3000 rpm at 4°C, washed 2x with 30 ml cold dH2O, the pellet wash immediately frozen down in liquid nitrogen and kept at -80°C until further processing.  Pellets were resuspended in 1 ml FA(1) buffer (50 mM Hepes-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100 (v/v) , 0,1% NaDeoxycholate (w/v) , 0,1% SDS (w/v)0 supplemented with Roche protease inhibitors and phosSTOP (Roche). Cells were broken in a bead beater (Precellys): 9x30s. After centrifugation, the supernatant and the pellet were sonicated for 15 min at 4°C. Chromatin extracts were spun down for 10 min at 14000 rpm at 4°C. Different amount of chromatin was used for different antibodies: 100 ul chromatin (for H3, Spt16, Pob3 ChIP) or 500 ul chromatin (for RNAPIISer2, H3K9me2, H2Bub ChIP). Sampels were incubated with antibodies O/N at 4°C on the wheel. 25 ul of FA(1) buffer washed Dynabeads were added to each sample and they were incubated for 2 hours at 4°C on the wheel. Samples were then washed 3x for 5 min at RT with FA(1) buffer, FA(2) buffer (FA(1) buffer with 500 mM NaCl), once with LiCl buffer(10 mM TrisHCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0,5% NP-40 (v/v) , 0,5% NaDeoxycholate (w/v)) and once with TE buffer. DNA was eluted from the antibodies with ChIP Elution buffer (50 mM Tris HCl, pH 7.5, 10 mM EDTA, 1% SDS) for 15 min at 65°C in a thermomixer set to 1300 rpm.   DNA was treated with RNAseA (Thermo Fisher) for 1 hr at 37°C, followed by Proteinase K digestion and de-crosslinking O/N at 65°C. DNA was purified with Zymo Research ChIP DNA Clean and Concentrator kit according to the manual instructions. To obtain enough material for the library preparation usually 3 technical IP replicates were pulled.
ChIP-seq libraries were prepared with 2 ng of DNA with NEBNext®Ultra™ II DNA Library Prep Kit for Illumina® according to the manual instructions. The libraries were barcoded and sequenced at LAFUGA at the Gene Center (Munich).

value: Spt16  - Ladurner lab stock


title: WT CD4 TILs Rep 3


title: Rod-P3-3

value: Postnatal day 3


title: Spt16_pob3_1


title: Spt16_pob3_2


title: WT-2

value: Control KD (MTD-Gal4>+)


title: Spt16_H2BK119R_2


title: Spt16_H2BK119R_1


title: CiPC-3

source_name: Reprogrammed cells (CiPC) at d11

value: MEF derived photoreceptor like cells


title: RNAPII_WT_1

value: RNAPIISer2P - Dirk Eick lab


title: WT CD4 TILs Rep 1


title: RNAPII_WT_2


title: Rod-P3-1


title: YapKO CD8 TILs Rep 4

value: CD8+ T cells


title: CiPC-1


title: RNAPII_pob3_2


title: WT CD8 TILs Rep 4


title: RNAPII_pob3_ H2BK119R_2


title: RNAPII_pob3_ H2BK119R_1


title: CiPC-2


title: YapKO CD8 TILs Rep 3


title: RNAPII_pob3_1


title: RNAPII_H2BK119R_1


title: RNAPII_H2BK119R_2


title: YapKO CD8 TILs Rep 2


title: Rod-P3-2


title: WT CD4 TILs Rep 2


title: Pob3_WT_2

value: Pob3  - Ladurner lab stock


title: RI-d8-2

source_name: Chemically reprogrammed intermediates collected on day 8

value: MEF derived photoreceptor intermediates


title: Pob3_pob3_2


title: RI-d8-1


title: YapKO CD8 TILs Rep 1


title: WT CD8 TILs Rep 3


title: Pob3_H2BK119R_2


title: WT CD8 TILs Rep 2


title: Input_WT_2

value: Input


title: RI-d8-3


title: Input_pob3_2


title: Pob3_H2BK119R_1


title: Input_WT_1


title: RI-d5-3

source_name: Chemically reprogrammed intermediates collected on day 5


title: MEF-3

source_name: Mouse embryonic fibroblasts at passage2

value: Fibroblast like cells


title: Input_pob3_ H2BK119R_1


title: RI-d5-1


title: YapKO CD45 TDLNs Rep 4

source_name: tumor-draining inguinal lymph node

value: CD45+ immune cells


title: Input_pob3_1


title: Input_pob3_ H2BK119R_2


title: WT CD45 TDLNs Rep 4


title: Input_H2BK119R_2


title: H3_WT_2

value: H3 - Active Motif (#61475)


title: YapKO CD45 TDLNs Rep 3


title: Pob3_WT_1


title: Input_H2BK119R_1


title: Pob3_pob3_1


title: MEF-2

value: Strain (Nrl-GFP)


title: MEF-1


title: H3_WT_1


title: RI-d5-2


title: WT CD8 TILs Rep 1


title: H3_pob3_2


title: YapKO CD45 TDLNs Rep 2


title: YapKO CD45 TDLNs Rep 1


title: WT CD45 TDLNs Rep 3


title: Rod-P28-4

value: Isolated rods

value: Postnatal day 28


title: H3_pob3_ H2BK119R_1


title: H3_pob3_1


title: H3_pob3_ H2BK119R_2


title: Rod-P28-3


title: H3_H2BK119R_2


title: WT CD45 TDLNs Rep 2

value: WT


title: H3_H2BK119R_1


title: H3K9me2_WT_2

value: H3K9me2 - Abcam (ab1220)


title: Rod-P28-2


title: WT CD45 TDLNs Rep 1


title: H3K9me2_H2BK119R_2


title: H3K9me2_WT_1


title: Rod-P28-1


title: Spt16_WT_1

value: Spt16  - Ladurner lab stock


title: YapKO CD4 TDLNs Rep 4

value: CD4+ T cells

value: CD4Cre Yap flox


title: H3K9me2_H2BK119R_1


title: H2Bub_WT_2

value: H2Bub - Active Motif (#39623)


title: Rod-P14-2

value: Postnatal day 14


title: WT CD4 TDLNs Rep 4


title: H2Bub_pob3_2


title: H2Bub_WT_1


title: H2Bub_pob3_1