title: CUS_3

city: Nanjing

first: Xiaoyu

last: Yu

state: Jiangsu

address: Dingjiaqiao 87

institute: Southeast univeristy

data_processing:
A cDNA library constructed by technology from the pooled RNA from brain samples of mouse was sequenced run with Illumina sequence platform. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the UCSC (http://genome.ucsc.edu/) C57BL_6NJ mouse reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Assembly: mm9
Supplementary files format and content: Excel file include FPKM  and count values for each Sample

source_name: hippocampus

growth_protocol: hippocampus tissue were obtained from brain of  C57BL/6J and Rag1-/- mice.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base is then added to the blunt ends of each strand, then ligated to modified Illumina multiplex barcode adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012), and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Novaseq TM 6000 following the vendor's recommended protocol.

treatment_protocol: mice were injected with 2´10^5  CD8+TSCM cells for 3 times.

value: brain

tag: brain region

value: hippocampus


title: S2-siRen.H3K27me3.3 [CUT&RUN]

status: Public on Apr 18 2025

type: SRA

city: Cambridge

first: Susanne

last: Bornelöv

address: Robinson Way

department: Cancer Research UK - Cambridge Institute

country: United Kingdom

institute: University of Cambridge

library_source: genomic

data_processing:
Sequencing adapters were removed using Trim Galore! (v0.6.4, ‑‑paired ‑‑stringency 6 ‑a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC).
The resulting reads were mapped to their respective reference genome using Bowtie (v1.2.3, ‑S ‑y ‑M 1 ‑‑best ‑‑strata ‑‑fr ‑‑minins 10 ‑‑maxins 600 ‑‑chunkmbs 2000 ‑‑nomaqround), reporting at most one hit for each read and considering insert sizes between 10 and 600nt.
Uniquely mapped reads were converted into BigWig files using the deepTools bamCoverage module (v3.3.2, ‑‑binSize 1 ‑‑ignoreForNormalization chrM ‑‑normalizeUsing CPM  ‑‑exactScaling ‑‑scaleFactor s ‑‑skipNonCoveredRegions ‑‑minMappingQuality 50 --extendReads --centerReads), where the scale factor, s, was set to the number of uniquely mapped reads divided by all mapped reads.
Peaks were called using MACS2 to capture either narrow (callpeak -f BAMPE -g dm -q 0.01) or broad (callpeak -f BAMPE -g dm -q 0.05 --broad --broad-cutoff 0.1) peaks. Only uniquely mapped reads were used for the peak calling.  As controls we used the corresponding IgG libraries.
Differential binding affinity analysis was performed using DiffBind (v2.14.0) applied on the MACS2 narrow or broad peaks siRen and siEz samples, using the corresponding IgG libraries as controls and without specifying any blacklist regions. For the analysis, we used the dba, dba.count, dba.normalize, dba.contrast, and dba.analyze modules with default options.
Assembly: dm6
Supplementary files format and content: BigWig with read coverage per position across the genome.
Supplementary files format and content: BED-like files with differentially bound peaks, fields include: chromosome, start, end, log2(mean), log2(mean siRen), log2(mean siEz), log2FC, p, padj.
Supplementary files format and content: BroadPeak files from MACS2.
Supplementary files format and content: NarrowPeak files from MACS2.
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Drosophila melanogaster

growth_protocol: Drosophila Schneider 2 (S2) cells were purchased from Thermo Fisher Scientific (R69007) and were grown at 26 °C in Schneider media (Gibco) supplemented with 10% Heat-Inactivated FBS (Sigma).

extract_protocol:
1 million cells per sample were harvested and washed three times with Wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM spermidine supplemented with protease inhibitors) and resuspended in 1 ml of Wash buffer.   Following sample preparation, CUT&RUN was performed according to instructions in CUT&RUN protocol V.3 with some modifications ).  10 µl of activated Concanavalin A-coated magnetic beads (Bangs Laboratories) were added to each sample and rotated for 10 min at RT.  Bead-bound cells were incubated with 5 µl of antibody (Table S3) and 95 µl of antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.05% digitonin) overnight at 4 °C.  Bead-bound cells were washed twice with Dig-wash buffer (0.05% digitonin in Wash buffer).  Bead-bound cells were resuspended in Dig-wash buffer containing 1x CUTANA™ pAG-MNase (Epicypher) and rotated for 1 hr at RT.  Following pAG-MNase binding, bead-bound cells were washed twice with Dig-wash buffer and resuspended in 100 µl Dig-wash buffer.  Chromatin digestion was performed on ice for 30 min by adding 2 μL 100  CaCl2 mM.  Digestion was stopped by the addition of 2x STOP Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% digitonin, 100 µg/ml RNase A (Thermo Fisher Scientific), 50 µg/ml glycogen) and samples were incubated at 37 °C for 30 min to release DNA fragments into the solution.  After centrifugation, 0.1% SDS and 0.2 μg/μl Proteinase K were added to the supernatant and samples were incubated for 1 hour at 50 °C.  DNA was extracted using Phenol:Chloroform:Isoamyl Alcohol 25:24:1 (Sigma) according to the manufacturer’s instructions.
Libraries were prepared following the manufacturer’s instructions with NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: For knockdown experiments, two rounds of electroporation (48hrs apart) were performed using the Cell Line Nucleofector kit V (Amaxa Biosystems) and the program G-030, as described (Batki et al. 2019).  Chromodomain constructs were co-transfected with 200 pmol of siRNA duplexes during the second nucleofection round or transfected using the TransIT®-Insect Transfection Reagent 24hrs after the second nucleofection round.  Cells were collected 5 days after the first nucleofection round.

tag: cell line

tag: genotype

value: siRen

tag: antibody

value: H3K27me3 (cell signalling 9733S)


title: Healthy control-derived i3LMNs, ND CSF-treated, rep 4

city: Worcester

first: Alberto

last: Brusati

state: MA

address: N Lake Ave 55

department: Neurology

country: USA

institute: UMass Chan Medical School

description: Library name: ND biol rep 4

library_source: transcriptomic

data_processing:
Reads were realigned on the reference genome (GRCh38) with the STAR tool using Genecode.v45 as gene annotation file. Post-alignment quality control was performed using Qualimap.
Quantification was performed using Salmon.
Assembly: GRCh38
Supplementary files format and content: Quant file provided by salmon for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: i3 LMNs

extract_protocol:
RNA was extracted using TRIzol™ reagent
RNA libraries for RNA -seq were prepared in service (N/A)

treatment_protocol: For CSF treatment: 10% CSF for 24 h; for ARS treatment: 10 uM ARS for 24 h

tag: cell type

value: i3 LMNs

value: WT

tag: treatment

value: ND CSF

tag: batch

value: D


title: Sxl binding in male larval neurons

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

data_processing:
The forward sequencing reads were mapped to release 6 of the Drosophila genome using Bowtie2 (see PMID: 26112292 for details of the damidseq_pipeline)
Reads were extended to adjacent GATC sites and binned for each GATC fragment
GATC fragments without any reads were excluded, followed by quantile normalisation and pseudocount addition.
Ratio files (log2) were then generated from the experimental and Dam-only control data.
Assembly: BDGP6
Supplementary files format and content: log2 normalised fold changes between the experimental and Dam-only control as a gff file produced by the damidseq_pipeline

source_name: Larval CNS

growth_protocol: Flies were maintained on standard fly media.

extract_protocol:
Genomic DNA was isolated,RNAseA treated and DpnI digested. DamID adaptors were ligated to DpnI digested DNA followed by DpnII digestion PCR amplification, sonication and removal of DamID adaptors (Marshall et al., 2016).
Libraries were generated using the Illumina Truseq Library Kit
DamID-seq

treatment_protocol: Animals were raised at 18 degrees, then shifted to 29 degrees 24 h before DNA extraction

tag: tissue

value: Larval CNS

value: neurons

value: DamID material


title: Healthy control-derived i3LMNs, C9 CSF-treated, rep 4

description: Library name: C9 biol rep 4

value: C9 CSF


title: CUS_1

country: China

organism: Mus musculus


title: Healthy control-derived i3LMNs, C9 CSF-treated, rep 3

description: Library name: C9 biol rep 3

value: C


title: S2-siRen.H3K27me3.2 [CUT&RUN]


title: Healthy control-derived i3LMNs, C9 CSF-treated, rep 2

description: Library name: C9 biol rep 2

value: B


title: Sxl binding in female larval neurons


title: S2-siEz.H3K9me3.5 [CUT&RUN]

value: siE(z)

value: H3K9me3 (active motif 39161)


title: Sxl binding in larval neurons


title: S2-siEz.H3K9me3.4 [CUT&RUN]


title: Sxl binding in larval neurons 1


title: ctrl_3


title: Healthy control-derived i3LMNs, C9 CSF-treated, rep 1

description: Library name: C9 biol rep 1

value: A


title: S2-siEz.H3K9me3.3 [CUT&RUN]


title: S2-siRen.H3K27me3.4 [CUT&RUN]


title: Healthy control-derived i3LMNs, UNC13A AA CSF-treated, rep 5

description: Library name: UNC13A AA biol rep 5

value: UNC13A AA CSF

value: E


title: Healthy control-derived i3LMNs, UNC13A AA CSF-treated, rep 4

description: Library name: UNC13A AA biol rep 4


title: S2-siEz.H3K9me3.2 [CUT&RUN]


title: Total liver from alcohol-fed mice with AKAP12 overexpression, sample F

city: Los Angeles

first: Komal

last: Ramani

state: CA

address: 8700 Beverly Blvd.

institute: Cedars-Sinai Medical Center

description: Library name: F

data_processing:
Data were processed by Azenta Inc.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: liver

extract_protocol:
Total RNA was extracted by the services of Azenta Inc.
Libraries were constructed by Azenta Inc. and sequenced on Illumina platform

treatment_protocol: Mice were fed a control lieber-de carli or an ethanol diet for 10 days during which they were injected with an empty vector backbone or a CMV-AKAP12 vector using in vivo JETPEI gal reagent (polyplus-sartorius) at day 3, 6,9. On the 11th day of feeding, mice were oral gavaged with binge 5% alcohol and sacrificed after 9h. Livers were isolated and snap frozen. Hepatocytes were isolated from livers.

value: liver

value: WT mice with AKAP12 overexpression vector

value: Ethanol diet


title: ctrl_1

value: brain

value: hippocampus


title: PBS_3


title: Total liver from alcohol-fed mice with AKAP12-PKA binding domain CRISPR vector, sample D

description: Library name: D

value: WT mice with AKAP12-PKA binding domain CRISPR vector


title: PBS_2


title: Total liver from WT mice with AKAP12 overexpression vector, sample E

description: Library name: E

value: Control diet


title: S2-siEz.H3K27me3.5 [CUT&RUN]

value: H3K27me3 (cell signalling 9733S)


title: Healthy control-derived i3LMNs, UNC13A AA CSF-treated, rep 3

description: Library name: UNC13A AA biol rep 3

value: i3 LMNs

value: WT


title: CUS_2


title: S2-siEz.H3K27me3.4 [CUT&RUN]


title: Healthy control-derived i3LMNs, UNC13A AA CSF-treated, rep 2

description: Library name: UNC13A AA biol rep 2


title: S2-siEz.H3K27me3.3 [CUT&RUN]


title: Total liver from alcohol-fed mice with empty vector (EV), sample B

description: Library name: B

value: WT mice with empty vector (EV)


title: WT_3


title: Healthy control-derived i3LMNs, UNC13A CC CSF-treated, rep 4

description: Library name: UNC13A CC biol rep 4

value: UNC13A CC CSF


title: Healthy control-derived i3LMNs, UNC13A AA CSF-treated, rep 1

description: Library name: UNC13A AA biol rep 1


title: S2-siEz.H3K27me3.2 [CUT&RUN]

value: siE(z)


title: PBS_1


title: Total liver from WT mice with empty vector (EV), sample A

description: Library name: A


title: S2.IgG.3 [CUT&RUN]

value: wildtype

value: Rabbit Anti-mouse (Abcam ab6709)


title: WT_2


title: Healthy control-derived i3LMNs, UNC13A CC CSF-treated, rep 3

description: Library name: UNC13A CC biol rep 3

value: C


title: ctrl_2


title: WT_1


title: Healthy control-derived i3LMNs, UNC13A CC CSF-treated, rep 2

description: Library name: UNC13A CC biol rep 2

value: B


title: S2.IgG.2 [CUT&RUN]


title: Female_B

city: Baltimore

first: Mahashweta

last: Basu

state: MD

address: 670 W. Baltimore Street

institute: Institute for Genome Sciences

description: Library name: Sample 4

library_source: transcriptomic single cell

data_processing:
The raw scRNA-seq data were processed to counts of unique molecular identifers (UMIs) in each droplet using CellRanger, then passed through SoupX to reduce artifacts from ambient RNA.Quality control, normalization, and analysis were performed using the Seurat (v2) Standard Workflow. Cells were clustered using the Louvain method.
Assembly: Rattus_norvegicus.Rnor_6.0.91
Supplementary files format and content: Seurat Rdata objects

organism: Rattus norvegicus

source_name: 4-day-old amygdala

extract_protocol:
On P4, neonates of both sexes (n=6) were deeply anesthetized with Fatal Plus and decapitated. Brains were removed and placed on ice, and the amygdala of both hemispheres was dissected out and placed in Hibernate A solution (Thermo Fisher Scientific, Waltham, MA) while the remaining brains were dissected. Single cells were isolated for transcriptional profiling by proteolytic enzymatic digestion using the Worthington Papain Dissociation System (Worthington Biochemical Corporation, Lakewood, NJ), following the manufacturer’s protocol. Samples were centrifuged, then resuspended in 0.05% bovine serum albumin in phosphate-buffered saline. Cell suspensions were then pooled, resulting in four final samples prepared for submission: 2 male samples and 2 female samples, each containing cells from 3 animals per sex. Pooled suspensions were counted using a hemocytometer and delivered for further processing using the 10x Genomics system.
A total of 3,000 cells per sample were loaded by GRC staff into each well of a chromium microfluidics container (10x Genomics, Pleasanton, CA). Sequencing libraries were prepared using the Chromium Next GEM Single Cell 3’ Kit v2 per the manufacturer’s instructions. Samples were sequenced across 4 lanes (1 sample per channel) using the 75 base pair paired-end protocol on an Illumina HiSeq4000 sequencer.

value: 4-day-old amygdala

tag: Sex

value: Female


title: nos-white-KD.2 [total RNA]

data_processing:
Adapters were removed using Trim Galore! (v0.6.4, ‑‑stringency 6 ‑‑length 18 ‑‑max_length 29 ‑q 0)
The resulting reads were mapped to dm6 using Bowtie (v2.3.1, -S -n 2 -M 1 ‑‑best ‑‑strata ‑‑nomaqround ‑‑chunkmbs 1024 ‑‑no-unal)
Uniquely mapped reads were converted into BigWig files using the deepTools bamCoverage module (v3.3.2, ‑‑binSize 1 ‑‑ignoreForNormalization chrM ‑‑normalizeUsing CPM  ‑‑exactScaling ‑‑scaleFactor s ‑‑skipNonCoveredRegions ‑‑minMappingQuality 255), where the scale factor, s, was set to the to the number of uniquely mapped reads divided by all mapped reads.
Additionally, ‘‑‑filterRNAstrand’ and ‘‑‑minFragmentLength 23 ‑‑maxFragmentLength 30’ was used to select piRNAs for each strand, separately.
Assembly: dm6
Supplementary files format and content: BigWig with read coverage per position across the genome for each strand.

source_name: ovary

growth_protocol:
Flies were kept at standard conditon at 25°C
All flies were kept at 18 C or 25 C on standard cornmeal or propionic food.

extract_protocol:
Total RNA was extracted from 10 to 20 ovaries from 3-6 day-old flies using TRizol (Thermo Fisher Scientific). rRNA depletion was performed from 1µg total RNA using the RNA Depletion stranded Library Prep kit (BGI).
RNA-seq libraries were produced using NEBNext Ultra Directional Library Prep Kit for Illumina, following the manufacturer’s instructions for rRNA depleted RNA.

value: ovary

tag: age

value: 3-6 day old

value: female

value: Nanos Gal4 VP16-expressed dsRNA-white BDSC_35573


title: Healthy control-derived i3LMNs, UNC13A CC CSF-treated, rep 1

description: Library name: UNC13A CC biol rep 1

value: A


title: Female_A

description: Library name: Sample 3


title: S2.IgG.1 [CUT&RUN]


title: Male_B

description: Library name: Sample 2

value: Male


title: Healthy control-derived i3LMNs, ARS-treated, rep 5

description: Library name: ARS biol rep 5

value: i3 LMNs

value: Chronic ARS

value: E


title: nos-white-KD.1 [total RNA]


title: S2.H3K9me3.2 [CUT&RUN]

value: H3K9me3 (active motif 39161)


title: nos-Ez-KD.2 [total RNA]

value: Nanos Gal4 VP16-expressed dsRNA-E(z) BDSC_33659


title: Male_A

description: Library name: Sample 1


title: Healthy control-derived i3LMNs, ARS-treated, rep 4

description: Library name: ARS biol rep 4

value: WT

value: D


title: AZA_2

type: genomic

city: Salt Lake City

first: Li

last: Li

state: Utah

address: 201 PRESIDENTS CIRCLE

institute: University of Utah

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to mouse Illumina MethylationEPIC BeadChip (Illumina) using Infinium HD Methylation Assay, manual protocol

scan_protocol: Arrays were imaged using Illumina iScan System using standard recommended Illumina scanner setting

data_processing: IDAT files were processed using SeSAMe package (v1.20.0) in R environment (v4.3.2).

label: Cy3 and Cy5

source_name: Tumor

label_protocol: Genomic DNA was bisulfite converted using Infinium HD Methylation Assay, manual protocol

extract_protocol: DNA was extracted from mouse tumors using dneasy blood & tissue kit (Qiagen)

value: Tumor

value: Rosa26hSS2 and Myf5Cre mouse

value: SS18-SSX fusion

value: AZA


title: Total liver from WT mice with AKAP12-PKA binding domain CRISPR vector, sample C

description: Library name: C

value: liver

value: Control diet


title: S2.H3K9me3.1 [CUT&RUN]

value: wildtype


title: nos-Ez-KD.1 [total RNA]

value: ovary

value: 3-6 day old

value: female


title: S2.H3K27me3.2 [CUT&RUN]

value: H3K27me3 (cell signalling 9733S)


title: DAC_4

value: Decitabine


title: Healthy control-derived i3LMNs, ARS-treated, rep 2

description: Library name: ARS biol rep 2

value: i3 LMNs

value: Chronic ARS

value: B


title: S2.H3K27me3.1 [CUT&RUN]


title: Healthy control-derived i3LMNs, ARS-treated, rep 3

description: Library name: ARS biol rep 3

value: WT

value: C


title: AZA_1

value: Tumor


title: S2.H2AK119ub.2 [CUT&RUN]

value: H2AK119ub (cell signaling, D27C4)


title: Healthy control-derived i3LMNs, ARS-treated, rep 1

description: Library name: ARS biol rep 1

value: A


title: DAC_3

value: Rosa26hSS2 and Myf5Cre mouse

value: SS18-SSX fusion


title: DAC_2


title: DAC_1


title: Healthy control-derived i3LMNs, untreated, rep 5

description: Library name: NT biol rep 5

value: Untreated

value: E


title: Healthy control-derived i3LMNs, untreated, rep 4

description: Library name: NT biol rep 4

value: D


title: S2.H2AK119ub.1 [CUT&RUN]

value: wildtype


title: S2.IgG.6 [CUT&RUN]

extract_protocol:
1 million cells per sample were harvested and washed three times with Wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM spermidine supplemented with protease inhibitors) and resuspended in 1 ml of Wash buffer. Following sample preparation, CUT&RUN was performed according to instructions in CUT&RUN protocol V.3 with some modifications ).  10 µl of activated Concanavalin A-coated magnetic beads (Bangs Laboratories) were added to each sample and rotated for 10 min at RT.  Bead-bound cells were incubated with 5 µl of antibody (Table S3) and 95 µl of antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.05% digitonin) overnight at 4 °C.  Bead-bound cells were washed twice with Dig-wash buffer (0.05% digitonin in Wash buffer).  Bead-bound cells were resuspended in Dig-wash buffer containing 1x CUTANA™ pAG-MNase (Epicypher) and rotated for 1 hr at RT.  Following pAG-MNase binding, bead-bound cells were washed twice with Dig-wash buffer and resuspended in 100 µl Dig-wash buffer.  Chromatin digestion was performed on ice for 30 min by adding 2 μL 100  CaCl2 mM.  Digestion was stopped by the addition of 2x STOP Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% digitonin, 100 µg/ml RNase A (Thermo Fisher Scientific), 50 µg/ml glycogen) and samples were incubated at 37 °C for 30 min to release DNA fragments into the solution.  After centrifugation, 0.1% SDS and 0.2 μg/μl Proteinase K were added to the supernatant and samples were incubated for 1 hour at 50 °C.  DNA was extracted using Phenol:Chloroform:Isoamyl Alcohol 25:24:1 (Sigma) according to the manufacturer’s instructions.
Libraries were prepared following the manufacturer’s instructions with NEBNext Ultra II DNA Library Prep Kit for Illumina.

value: Rabbit Anti-mouse (Abcam ab6709)


title: S2.IgG.5 [CUT&RUN]


title: Control_2

value: Vehicle


title: Dsim.IgG.2 [CUT&RUN]

data_processing:
Assembly: GCF_016746395
Sequencing adapters were removed using Trim Galore! (v0.6.4, ‑‑paired ‑‑stringency 6 ‑a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC).
The resulting reads were mapped to their respective reference genome using Bowtie (v1.2.3, ‑S ‑y ‑M 1 ‑‑best ‑‑strata ‑‑fr ‑‑minins 10 ‑‑maxins 600 ‑‑chunkmbs 2000 ‑‑nomaqround), reporting at most one hit for each read and considering insert sizes between 10 and 600nt.
Uniquely mapped reads were converted into BigWig files using the deepTools bamCoverage module (v3.3.2, ‑‑binSize 1 ‑‑ignoreForNormalization chrM ‑‑normalizeUsing CPM  ‑‑exactScaling ‑‑scaleFactor s ‑‑skipNonCoveredRegions ‑‑minMappingQuality 50 --extendReads --centerReads), where the scale factor, s, was set to the number of uniquely mapped reads divided by all mapped reads.
Supplementary files format and content: BigWig with read coverage per position across the genome.
Library strategy: CUT&RUN

organism: Drosophila simulans

growth_protocol: All flies were kept at 18 C or 25 C on standard cornmeal or propionic food.

extract_protocol:
10-20 fly ovaries were dissected in ice cold PBS per sample.  Ovaries were digested in 250 µl of dissociation buffer (0.5% Trypsin and 2.5 mg/ml Collagenase A in PBS) for an hour with shaking at 800 rpm at 30 °C.  The digestion was stopped with 250 µl of Schneider medium containing 10% FBS.  Cell suspensions were filtered through 40 µm strainers, pelleted and washed three times with Wash buffer and resuspended in 1 ml of Wash buffer. Following sample preparation, CUT&RUN was performed according to instructions in CUT&RUN protocol V.3 with some modifications ).  10 µl of activated Concanavalin A-coated magnetic beads (Bangs Laboratories) were added to each sample and rotated for 10 min at RT.  Bead-bound cells were incubated with 5 µl of antibody (Table S3) and 95 µl of antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.05% digitonin) overnight at 4 °C.  Bead-bound cells were washed twice with Dig-wash buffer (0.05% digitonin in Wash buffer).  Bead-bound cells were resuspended in Dig-wash buffer containing 1x CUTANA™ pAG-MNase (Epicypher) and rotated for 1 hr at RT.  Following pAG-MNase binding, bead-bound cells were washed twice with Dig-wash buffer and resuspended in 100 µl Dig-wash buffer.  Chromatin digestion was performed on ice for 30 min by adding 2 μL 100  CaCl2 mM.  Digestion was stopped by the addition of 2x STOP Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% digitonin, 100 µg/ml RNase A (Thermo Fisher Scientific), 50 µg/ml glycogen) and samples were incubated at 37 °C for 30 min to release DNA fragments into the solution.  After centrifugation, 0.1% SDS and 0.2 μg/μl Proteinase K were added to the supernatant and samples were incubated for 1 hour at 50 °C.  DNA was extracted using Phenol:Chloroform:Isoamyl Alcohol 25:24:1 (Sigma) according to the manufacturer’s instructions.
Libraries were prepared following the manufacturer’s instructions with NEBNext Ultra II DNA Library Prep Kit for Illumina.

value: ovary


title: Dsim.IgG.1 [CUT&RUN]


title: Healthy control-derived i3LMNs, untreated, rep 3

description: Library name: NT biol rep 3

value: i3 LMNs


title: Healthy control-derived i3LMNs, untreated, rep 1

description: Library name: NT biol rep 1


title: Dyak.IgG.2 [CUT&RUN]

data_processing:
Assembly: GCF_016746365
Sequencing adapters were removed using Trim Galore! (v0.6.4, ‑‑paired ‑‑stringency 6 ‑a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC).
The resulting reads were mapped to their respective reference genome using Bowtie (v1.2.3, ‑S ‑y ‑M 1 ‑‑best ‑‑strata ‑‑fr ‑‑minins 10 ‑‑maxins 600 ‑‑chunkmbs 2000 ‑‑nomaqround), reporting at most one hit for each read and considering insert sizes between 10 and 600nt.
Uniquely mapped reads were converted into BigWig files using the deepTools bamCoverage module (v3.3.2, ‑‑binSize 1 ‑‑ignoreForNormalization chrM ‑‑normalizeUsing CPM  ‑‑exactScaling ‑‑scaleFactor s ‑‑skipNonCoveredRegions ‑‑minMappingQuality 50 --extendReads --centerReads), where the scale factor, s, was set to the number of uniquely mapped reads divided by all mapped reads.
Supplementary files format and content: BigWig with read coverage per position across the genome.
Library strategy: CUT&RUN

organism: Drosophila yakuba

tag: qc fail

value: TRUE


title: S2.IgG.2 [CUT&RUN]


title: S2.IgG.3 [CUT&RUN]


title: S2.IgG.1 [CUT&RUN]


title: Dyak.IgG.1 [CUT&RUN]


title: Dsim.H3K9me3.2 [CUT&RUN]

value: H3K9me3 (active motif 39161)


title: Dsim.H3K9me3.1 [CUT&RUN]

value: WT


title: Dyak.H3K9me3.2 [CUT&RUN]


title: Dyak.H3K9me3.1 [CUT&RUN]


title: Dsim.H3K27me3.2 [CUT&RUN]

value: H3K27me3 (cell signalling 9733S)


title: ovary.IgG.2 [CUT&RUN]

data_processing:
Sequencing adapters were removed using Trim Galore! (v0.6.4, ‑‑paired ‑‑stringency 6 ‑a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC).
The resulting reads were mapped to their respective reference genome using Bowtie (v1.2.3, ‑S ‑y ‑M 1 ‑‑best ‑‑strata ‑‑fr ‑‑minins 10 ‑‑maxins 600 ‑‑chunkmbs 2000 ‑‑nomaqround), reporting at most one hit for each read and considering insert sizes between 10 and 600nt.
Uniquely mapped reads were converted into BigWig files using the deepTools bamCoverage module (v3.3.2, ‑‑binSize 1 ‑‑ignoreForNormalization chrM ‑‑normalizeUsing CPM  ‑‑exactScaling ‑‑scaleFactor s ‑‑skipNonCoveredRegions ‑‑minMappingQuality 50 --extendReads --centerReads), where the scale factor, s, was set to the number of uniquely mapped reads divided by all mapped reads.
Assembly: dm6
Supplementary files format and content: BigWig with read coverage per position across the genome.
Library strategy: CUT&RUN

value: Rabbit Anti-Mouse (abcam ab6709)


title: Dsim.H3K27me3.1 [CUT&RUN]


title: Dyak.H3K27me3.2 [CUT&RUN]


title: ovary.IgG.1 [CUT&RUN]


title: ovary.H3K9me3.3 [CUT&RUN]


title: TDZ treated, 4 week, replicate 3

city: Nyíregyháza

first: Judit

last: Dobránszki

state: Szabolcs-Szatmár-Bereg

address: Westsik Vilmos út 4-6.

department: Centre for Agricultural Genomics and Biotechnology

country: Hungary

institute: University of Debrecen

description: Library name: HR22b

data_processing:
Original image data file from Illumina NovaSeq X Series high-throughput sequencing platform were transformed to sequenced reads by CASAVA base recognition and stored in .fq format.
Fastp software was used to trim raw reads for adapter sequences and filter out reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%) or  low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Trimmed sequence reads were mapped using Hisat2 (v2.0.5) to GCA_004115385.1 Malus domestica reference genome.
Gene level read quantification was performed with featureCounts (v1.5.0-p3)
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GCA_004115385.1
Supplementary files format and content: Tab-delimited text file, including gene level raw read counts for each sample
Supplementary files format and content: Tab-delimited text file including gene level fpkm for each sample

molecule: polyA RNA

organism: Malus domestica

source_name: axillary shoot

growth_protocol: in vitro shoot culture

extract_protocol:
Total RNA was purified from the samples as three biological replicates each using Quick-RNATM Plant Miniprep kit (Zymo Research, Irvine, CA, USA) based on the manufacturer’s protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. The process was completed after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: MS medium contained either thidiazuron or benzylaminopurine riboside

tag: cultivar

value: Husveti rozmaring

value: axillary shoot

value: thidiazuron treated

tag: time

value: 4 week


title: Control_1

value: Tumor

value: Rosa26hSS2 and Myf5Cre mouse

value: SS18-SSX fusion


title: Healthy control-derived i3LMNs, untreated, rep 2

description: Library name: NT biol rep 2

value: Untreated

value: B


title: TDZ treated, 4 week, replicate 2

description: Library name: HR23


title: S2.IgG.4 [CUT&RUN]

value: wildtype

value: Rabbit Anti-mouse (Abcam ab6709)


title: ovary.H3K9me3.2 [CUT&RUN]

value: ovary


title: BAR treated, 4 week, replicate 3

description: Library name: HR25b

value: benzylaminopurine riboside treated


title: ovary.H3K9me3.1 [CUT&RUN]

value: H3K9me3 (active motif 39161)


title: ovary.H3K27me3.3 [CUT&RUN]


title: BAR treated, 4 week, replicate 2

description: Library name: HR26


title: BAR treated, 4 week, replicate 1

description: Library name: HR25


title: ovary.H3K27me3.2 [CUT&RUN]


title: small_RNA-seq_Sxl-RAC_1

description:
Library name: Sample 1
Over/misexpression of Sxl-RAC in male adult neurons

data_processing:
TrimGalore! (v0.6.7)
falco (v1.2.4)
bowtie2 (v2.5.3) and subsequent analysis on R1 only
featureCounts (v.2.0.8) with gene annotation file dmel-all-r6.58.gtf.gz
DESeq2 (v.2.11.40.8)
Assembly: dmel-all-r6.58.gtf.gz
Supplementary files format and content: DESeq2 with differentially expressed features from count tables in .csv format

source_name: Adult heads

growth_protocol: Raised at 18oC and shifted to 29oC after eclosion for 4 days.

extract_protocol:
Trizol extraction, DNAse treatment.
Small RNA Library Prep Set for Illumina (Multiplex Compatible)
Illumina library preparation by Genewiz/Azenta

value: Adult heads

value: ;tub-GAL80ts;nSyb-GAL4 x UAS-SxlRAC (and nSyb-GAL4 x UAS-mCherry attP2 control)


title: ovary.IgG.3 [CUT&RUN]

value: Rabbit Anti-Mouse (abcam ab6709)


title: ovary.H3K27me3.1 [CUT&RUN]

value: H3K27me3 (cell signalling 9733S)


title: Control, 4 week, replicate 3

description: Library name: HR3

value: Husveti rozmaring

value: axillary shoot

value: control (untreated)


title: Control, 4 week, replicate 2

description: Library name: HR2

value: 4 week


title: Sxl-RAC_2

description:
Library name: Sample 11
Over/misexpression of Sxl-RAC  in male adult neurons

data_processing:
Trimmomatic (v0.39) with ILLUMINACLIP
FASTQC (v.0.74)
HISAT2 (v.2.2.1) using R1 and R2.
featureCounts (v.2.0.8) with gene annotation file dmel-all-r6.58.gtf.gz
DESeq2 (v.2.11.40.8)
Assembly: dmel-all-r6.58.gtf.gz
Supplementary files format and content: DESeq2 with differentially expressed features from count tables in .csv format

extract_protocol:
Trizol extraction, DNAse treatment.
PolyA selection for mRNA species (eukaryotic)
Illumina library preperation by Genewiz/Azenta


title: Dyak.H3K27me3.1 [CUT&RUN]

value: WT


title: Sxl-RAC_1

description:
Library name: Sample 10
Over/misexpression of Sxl-RAC  in male adult neurons


title: TDZ treated, 4 week, replicate 1

description: Library name: HR22

value: thidiazuron treated


title: Sxl-RNA_3

description:
Library name: Sample 9
Over/misexpression of Sxl with mutated RNA binding regions in male adult neurons

value: ;tub-GAL80ts;nSyb-GAL4 x UAS-SxlRNA (and nSyb-GAL4 x UAS-mCherry attP2 control)


title: TDZ treated, 48 hour, replicate 3

description: Library name: HR486

value: 48 hour


title: Sxl-RAC_3

description:
Library name: Sample 12
Over/misexpression of Sxl-RAC  in male adult neurons


title: Control, 4 week, replicate 1

description: Library name: HR1


title: VIP-GABAergic cell from the VIP-eGFP mouse hippocampus 6

city: Quebec

first: Lisa

last: Topolnik

state: Quebec

department: Biochemistry, Microbiology and Bio-informatics

country: Canada

institute: Université Laval

description: Library name: Sample 6

data_processing:
Sequencing raw data were de-multiplexed to discriminate reads from different samples and then trimmed to remove sequencing adapters, low confidence bases, sequencing-specific bias and PCR artifacts. We computed reads alignments as a measure of quality, specifically the fraction of reads that could be mapped back to the mouse genome (mm10 assembly) as indicated by the aligner STAR (v2.5.2a). For reads quantification we computed pseudo-alignments using Kallisto (Pachter Lab, UC Berkeley). The average number of pseudo-aligned reads per cell was 2.1 million.
Assembly: mm10
Supplementary files format and content: 6 tab excel files containing 1 sample per tab with target_id, eff_length, est_counts, tpm and gene name.

source_name: Hippocampus, CA1 area

growth_protocol: mice housed in 12hr day light cycle, fed ad libitum

extract_protocol:
acute hippocampal slices in ACSF, patch-clamp recordings followed by cell mechanical aspiration, the cell content was extracted in the lysis buffer containing the RNAse inhibitor
The cDNA libraries were constructed using SMART-Seq v4 Ultra low input RNA Kit. cDNA from SMART sequences was amplified by PCR Primer II A. After 17 cycles of long-distance PCR, amplified cDNA was purified using the Agencourt AMPure XP Kit.The quality of cDNA library construction was validated using the Agilent Tapestation 2200 system. The threshold cDNA concentration of 200 pg/ml was achieved in all samples. cDNA libraries from 23 cells were prepared for Illumina Next Generation sequencing using Nextera XT DNA Library Preparation Kits. Libraries with unique index were then pooled together in equimolar ratio and sequenced for paired-end sequencing using both lanes of a rapid run flow-cell on the Illumina HiSeq 2500 system. The average insert size for the paired-end libraries was 225 base pairs.

treatment_protocol: no experimental treatment

value: Hippocampus, CA1 area

value: VIP interneuron

value: GABAergic cell

value: VIP-eGFP (MMRRC strain #31009)

value: Hippocampal slice in vitro


title: VIP-GABAergic cell from the VIP-eGFP mouse hippocampus 4

description: Library name: Sample 4


title: VIP-GABAergic cell from the VIP-eGFP mouse hippocampus 3

description: Library name: Sample 3


title: Sxl-RNA_2

description:
Library name: Sample 8
Over/misexpression of Sxl with mutated RNA binding regions in male adult neurons

value: Adult heads

value: tub-GAL80ts;nSyb-GAL4 x UAS-SxlRNA (and nSyb-GAL4 x UAS-mCherry attP2 control)


title: VIP-GABAergic cell from the VIP-eGFP mouse hippocampus 2

description: Library name: Sample 2


title: TDZ treated, 48 hour, replicate 1

description: Library name: HR484


title: TDZ treated, 48 hour, replicate 2

description: Library name: HR485


title: small_RNA-seq_Sxl-RAC_3

description:
Library name: Sample 3
Over/misexpression of Sxl-RAC in male adult neurons

value: ;tub-GAL80ts;nSyb-GAL4 x UAS-SxlRAC (and nSyb-GAL4 x UAS-mCherry attP2 control)


title: Sxl-RNA_1

description:
Library name: Sample 7
Over/misexpression of Sxl with mutated RNA binding regions in male adult neurons


title: small_RNA-seq_Sxl-RAC_2

description:
Library name: Sample 2
Over/misexpression of Sxl-RAC in male adult neurons


title: VIP-GABAergic cell from the VIP-eGFP mouse hippocampus 1

description: Library name: Sample 1


title: BAR treated, 48 hour, replicate 3

description: Library name: HR487b

value: benzylaminopurine riboside treated


title: Sxl_RNAi_3

description:
Library name: Sample 6
RNAi KD of Sxl in male adult brain neurons

value: ;tub-GAL80ts;nSyb-GAL4 x UAS-Sxl RNAi (and nSyb-GAL4 x UAS-KK RNAi control)


title: Blood DDC neutrophil sample 3

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: Circulating neutrophils (3)

data_processing:
raw reads were analyzed for data quality using FastQC v0.11.5 (Babraham Bioinformatics) and filtered using skewer v0.2.2 (Jiang et al., 2014) for removing the low quality reads and trimming the Illumina adapter
Mapping of the reads were obtained using the STAR program against human genome (GRCm38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE.vM15 database .
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Assembly: mus musculus (GRCm38)
Supplementary files format and content: RSEM expected counts

source_name: Blood neutrophils

growth_protocol: Liver and circulating neutrophils were isolated by Ly6G immunomagnetic separation after liver suspension percoll gradient and blood lysis.

extract_protocol:
RNA was isolated using the commercial kit miReasy Micro Kit (Qiagen) following manufacturer’s instructions. The quantity and quality of the RNAs were evaluated using Nanodrop and Agilent RNA 6000 Pico Chips (Agilent Technologies, Cat.# 5067-1513).
Sequencing libraries were prepared using “SMARTer Stranded Total RNA-seq Kit v2 – Pico Input Mammalian” kit (Takara Bio USA, Cat.# 634411), following “SMARTer Stranded Total RNA-seq Kit v2 – Pico Input Mammalian User Manual (Rev. 063017)”. Paired-ended sequencing was performed on Illumina platform.

value: BLOOD


title: Sxl_RNAi_2

description:
Library name: Sample 5
RNAi KD of Sxl in male adult brain neurons


title: Sxl_RNAi_1

description:
Library name: Sample 4
RNAi KD of Sxl in male adult brain neurons

value: tub-GAL80ts;nSyb-GAL4 x UAS-Sxl RNAi (and nSyb-GAL4 x UAS-KK RNAi control)


title: BAR treated, 48 hour, replicate 2

description: Library name: HR489

value: Husveti rozmaring

value: axillary shoot


title: BAR treated, 48 hour, replicate 1

description: Library name: HR487


title: Blood DDC neutrophil sample 1

description: Circulating neutrophils (1)


title: VIP-GABAergic cell from the VIP-eGFP mouse hippocampus 5

description: Library name: Sample 5


title: Polr3E_RNAi_2

description:
Library name: Sample 2
RNAi KD of Polr3E in male adult brain neurons

value: ;tub-GAL80ts;nSyb-GAL4 x UAS-Polr3E RNAi (and nSyb-GAL4 x UAS-attP40 RNAi control)


title: Liver DDC neutrophil sample 2

description: Liver infiltrating neutrophils (2)

source_name: Liver neutrophils

value: LIVER


title: Liver DDC neutrophil sample 1

description: Liver infiltrating neutrophils (1)


title: Polr3E_RNAi_3

description:
Library name: Sample 3
RNAi KD of Polr3E in male adult brain neurons


title: RNA sequencing from primary neurons_anti-miR-129_1

status: Public on Apr 17 2025

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

description: Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.

data_processing:
The sequencing data were processed using a customized in-house software pipeline. Illumina’s conversion software bcl2fastq (v2.20.2) was employed for adapter trimming and converting the base calls in the per-cycle BCL files to the per-read FASTQ format from raw images. Quality control of raw sequencing data was carried out using FastQC (v0.11.5)(http://www.bioinformatics.babraham. ac.uk/projects/fastqc/). Reads were aligned using the STAR aligner (v2.5.2b) and read counts were generated using featureCounts (v1.5.1). The mouse genome version mm10 was utilized.
Assembly: mm10
Supplementary files format and content: processed data files contain raw counts from individual samples.

source_name: Mouse primary neuron culture

growth_protocol:
primary neurons were derived from mouse embryos at embryonic day 17.5 according to Animal Welfare regulations. Neurons were seeded onto poly-D-lysine-coated cell culture dishes in plating medium (DMEM media, 100U/ml Penicillin and 0,1mg/ml Streptomycin). Plating medium was replaced with maintenance medium (MEM supplemented, 2% B27 supplement (Gibco), 2mM Glutamax, 100U/ml Penicillin and 0,1mg/ml Streptomycin) 2-3 hours later and kept in a humidified incubator, 37C, 5% CO2.
P0 to P2 mice pups of CD1 background were sacrificed by decapitation and their cortex dissected, careful to remove all meninges from each hemisphere. 2 brains were pooled per 15-mL falcon containing ice-cold PBS. Tissue was dissociated in a pre-warmed solution of 0.05% trypsin-EDTA (in PBS) at 37°C for 20-minutes. Trypsinization was stopped by adding processing medium (10 mM HEPES in HBSS) and cells were washed twice to wash off remaining trypsin-EDTA. Dissociated tissues were homogenized in the processing media, filtered through a 100μm cell strainer, and transferred into a coated T75 flask.

extract_protocol:
RNA was isolated using trizol and with Zymo RNA isolation kit.
Total RNA was used for the library preparation using the TrueSeq RNA library prep kit v2 (Illumina, USA) according to the manufacturer's protocol. 500 ng RNA was used as starting material. The quality of the libraries was assessed using the Bioanalyzer (Agilent Technologies). Library concentration was measured by Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, USA). Multiplexed libraries were directly loaded onto a Hiseq2000 (Ilumina) with 50 bp single read setup.

treatment_protocol:
Primary astrocytes were treated with miR-129-5p inhibitor or scramble sequence.
Primary astrocytes were treated with miR-129-5p inhibitor or scramble sequence and co-cultured with primary neurons.

value: Mouse primary neuron culture

value: Primary neuron

value: miR-129-5p inhibitor treated

tag: mouse age

value: Primary neurons from E17.5


title: RNA sequencing from primary neurons_anti-miR-129_4


title: Control, 48 hour, replicate 2

description: Library name: HR483

value: control (untreated)

value: 48 hour


title: Blood DDC neutrophil sample 2

description: Circulating neutrophils (2)


title: Liver DDC neutrophil sample 3

description: Liver infiltrating neutrophils (3)


title: RNA sequencing from primary neurons_sc-control_4

value: Scramble treated


title: RNA sequencing from primary neurons_sc-control_6


title: RNA sequencing from primary neurons_sc-control_5


title: Polr3E_RNAi_1

description:
Library name: Sample 1
RNAi KD of Polr3E in male adult brain neurons

value: Adult heads


title: RNA sequencing from primary neurons_sc-control_3


title: RNA sequencing from primary neurons_anti-miR-129_5


title: Control, 48 hour, replicate 1

description: Library name: HR481


title: RNA sequencing from primary neurons_sc-control_1


title: RNA sequencing from primary neurons_anti-miR-129_2


title: RNA sequencing from primary neurons_anti-miR-129_3


title: RNA sequencing from primary neurons_sc-control_2


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary astrocytes_anti-miR-129_5

source_name: Mouse cortical neuron + primary astrocyte co-culture

value: Primary cortical neuron and Primary astrocyte co-culture

value: Astrocytes treated with miR-129-5p inhibitor and co-cultured with primary cortical neurons

value: Primary neurons from E17.5 and Primary astrocyte from P1


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary astrocytes_anti-miR-129_2

value: Mouse cortical neuron + primary astrocyte co-culture


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary astrocytes_sc-control_3

value: Astrocytes treated with scramble sequence and co-cultured with primary cortical neurons


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary astrocytes_sc-control_2


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary astrocytes_sc-control_4


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary astrocytes_anti-miR-129_3


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary astrocytes_anti-miR-129_4


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary astrocytes_anti-miR-129_1


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary astrocytes_sc-control_1


title: RNA sequencing from primary astrocytes_anti-miR-129_6

source_name: Mouse primary astrocyte culture

value: Mouse primary astrocyte culture

value: Primary astrocyte


title: RNA sequencing from primary astrocytes_anti-miR-129_5


title: RNA sequencing from primary astrocytes_sc-control_6


title: RNA sequencing from primary astrocytes_anti-miR-129_4


title: RNA sequencing from primary astrocytes_sc-control_5


title: RNA sequencing from primary astrocytes_sc-control_4


title: RNA sequencing from primary astrocytes_sc-control_3


title: MCF-7 control rep1

type: RNA

city: Turku

first: Otto

last: Kauko

address: Tykistökatu 6

department: Turku Bioscience Centre

country: Finland

institute: University of Turku

description: Gene expression data from  MCF-7 cancer cell line

hyb_protocol: 10 ug of cRNA were hybridized for 16 hr at 45C onto Affymetrix human genome U133plus2.0 arrays  according to the manufacturer's protocol.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A

data_processing:
Raw data from hgu133plus2 was normalized using the robust multiarray average with GC-correction (GCRMA), implemented in the R package gcrma
The only processed data available are the differentially expressed genes.

label: biotin

source_name: cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: MCF7, CRL-2061, and VCaP cells were purchased from ATCC and cultured according to the vendor’s guidelines in the media specified by the vendor. GP5D cells (Sigma, 95090715) in DMEM supplemented with 10% fetal bovine serum, 2 nM l-glutamine and 1% penicillin–streptomycin.

extract_protocol: Total RNA were prepared by QIAshedder (Cat. 79656, QIAGEN) and Qiagen RNAeasy Kit (catalog no. 74104) according to manufacturer's instructions.

treatment_protocol: Predesigned FlexiTube siRNAs (QIAGEN) for the transcription factors PAX3, GLI1, and CTNNB1, siRNAs SI03064726 and SI03089443(QIAGEN) for ERG, or control siRNA (SI03650325, QIAGEN), were transfected into cells using HiPerFect Transfection Reagent (Cat. 301704, QIAGEN)Transfections were performed in two steps with 24h interval, and the cells were harvested 48h after the transfections. Expression profiling of ER  was done by adding either 100 nM Estradiol (E2),  or mock ligand (Ethanol) to MCF-7 cells cells 4h prior lysis, and expression profiling of AR by adding  1 nM of the synthetic androgen methyltrienolone to VCaP cells. The cells were hormone starved for 48h prior to ligand addition.

value: breast


title: MCF-7 control rep2


title: RNA sequencing from primary astrocytes_anti-miR-129_3


title: MCF-7 estradiol rep2

description: Gene expression data from  MCF-7 cancer cell line treated with estradiol

source_name: cancer cell line treated with estradiol

value: estradiol


title: MCF-7 estradiol rep3


title: VCaP androgen rep2

description: Gene expression data from  VCaP cancer cell line treated with androgen

source_name: cancer cell line treated with androgen

value: prostate

value: VCaP

value: androgen


title: RNA sequencing from primary astrocytes_sc-control_2


title: mng_bap1_42

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

institute: University Hospital Heidelberg, Intitute of Pathology

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta

source_name: MNG BAP1

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: material

value: FFPE

value: Female

tag: disease state

tag: outcome


title: RNA sequencing from primary astrocytes anti-miR-129_1

value: miR-129-5p inhibitor treated


title: MCF-7 control rep3


title: mng_bap1_41

value: Male

value: progressive

value: alive


title: MCF-7 estradiol rep1


title: VCaP mock siRNA rep2

description: Gene expression data from  VCaP cancer cell line treated with negative control RNAi

source_name: cancer cell line, negative control RNAi

value: negative control RNAi


title: mng_bap1_40


title: VCaP mock siRNA rep1


title: mng_bap1_38


title: RNA sequencing from primary astrocytes anti-miR-129_2


title: RNA sequencing from primary astrocytes sc-control_1

value: Scramble treated


title: VCaP ERG siRNA2 rep2

description: Gene expression data from  VCaP cancer cell line treated with ERG RNAi

source_name: cancer cell line, ERG RNAi

value: ERG RNAi


title: VCaP androgen rep1


title: mng_bap1_39


title: mng_bap1_37

value: Frozen


title: VCaP ERG siRNA2 rep1


title: VCaP ERG siRNA1 rep2


title: mng_bap1_36


title: VCaP ERG siRNA1 rep1


title: mng_bap1_31


title: mng_bap1_30


title: VCaP control rep2

description: Gene expression data from  VCaP cancer cell line


title: CRL-2061 mock siRNA rep1

description: Gene expression data from  CRL-2061 cancer cell line treated with negative control RNAi

value: skeletal muscle


title: mng_bap1_27


title: VCaP control rep1


title: mng_bap1_26

value: dead


title: CRL-2061 control rep2

description: Gene expression data from  CRL-2061 cancer cell line


title: CRL-2061 PAX3 siRNA2 rep2

description: Gene expression data from  CRL-2061 cancer cell line treated with PAX3 RNAi

source_name: cancer cell line, PAX3 RNAi

value: PAX3 RNAi


title: CRL-2061 mock siRNA rep2


title: mng_bap1_28


title: CRL-2061 control rep1


title: mng_bap1_22


title: mng_bap1_21


title: CRL-2061 PAX3 siRNA2 rep1


title: mng_bap1_18


title: CRL-2061 GLI1 siRNA2 rep2

description: Gene expression data from  CRL-2061 cancer cell line treated with GLI1 RNAi

source_name: cancer cell line, GLI1 RNAi

value: GLI1 RNAi


title: mng_bap1_20


title: CRL-2061 PAX3 siRNA1 rep2


title: mng_bap1_33


title: CRL-2061 PAX3 siRNA1 rep1


title: mng_bap1_19


title: mng_bap1_25


title: CRL-2061 GLI1 siRNA2 rep1


title: mng_bap1_17


title: mng_bap1_16


title: CRL-2061 GLI1 siRNA1 rep2


title: mng_bap1_15


title: GP5d CTNNB1 siRNA2 rep1

description: Gene expression data from  GP5d cancer cell line treated with CTNNB1 RNAi

source_name: cancer cell line, CTNNB1 RNAi

value: colon

value: CTNNB1 RNAi


title: CRL-2061 GLI1 siRNA1 rep1


title: mng_bap1_13

value: stable


title: mng_bap1_05

value: FFPE


title: GP5d mock siRNA rep1

description: Gene expression data from  GP5d cancer cell line treated with negative control RNAi


title: mng_bap1_07


title: mng_bap1_12

value: Female


title: GP5d CTNNB1 siRNA1 rep2


title: GP5d mock siRNA rep2


title: GP5d control rep1

description: Gene expression data from  GP5d cancer cell line


title: LN319 cells overexpressing TRA2B, TRA2A KO, replicate 3

city: Philadelphia

first: Peter

last: Choi

state: PA

address: 3501 Civic Center Blvd, CTRB 4400

department: Pathology and Laboratory Medicine

institute: The Children's Hospital of Philadelphia

description: Library name: LN319-TRA2B_TRA2A-KO_rep3

data_processing:
Reads were aligned to the GRCh38 genome and Gencode v34 annotation using STAR v2.7.3.
Alternative splicing events were quantified using MAJIQ v2.5.
Transcript levels were quantified with kallisto v0.48.0.
Assembly: GRCh38
Supplementary files format and content: excel files for each cell line containing MAJIQ dPSI values
Supplementary files format and content: csv files for each cell line containing gene TPM values

extract_protocol:
Total RNA was extracted from cells using the Maxwell RSC simplyRNA Cells Kit (Promega, AS1390) and the Maxwell RSC48 Instrument (Promega).
RNA-seq library preparation was performed by Novogene. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, PCR amplification, and purification.

value: TRA2A knockout by CRISPR


title: mng_bap1_09

value: Male


title: mng_bap1_11


title: GP5d control rep2


title: GP5d CTNNB1 siRNA1 rep1


title: GP5d CTNNB1 siRNA2 rep2


title: mng_bap1_04


title: LN319 cells overexpressing TRA2B, TRA2A KO, replicate 2

description: Library name: LN319-TRA2B_TRA2A-KO_rep2


title: Control, 48 hour, replicate 3

description: Library name: HR481b

source_name: axillary shoot

value: Husveti rozmaring

value: axillary shoot

value: control (untreated)

value: 48 hour


title: mng_bap1_03


title: mng_bap1_02

value: alive


title: mng_bap1_01

value: progressive


title: mng_bap1_10


title: LN319 cells overexpressing TRA2B, Control KO, replicate 1

description: Library name: LN319-TRA2B_CTRL-KO_rep1

value: Control knockout by CRISPR


title: LN319 cells overexpressing TRA2B, Control KO, replicate 2

description: Library name: LN319-TRA2B_CTRL-KO_rep2


title: LN319 cells overexpressing Luc, TRA2B KO, replicate 3

description: Library name: LN319-Luc_TRA2B-KO_rep3

value: Luciferase-overexpressing

value: TRA2B knockout by CRISPR


title: LN319 cells overexpressing Luc, TRA2B KO, replicate 1

description: Library name: LN319-Luc_TRA2B-KO_rep1


title: LN319 cells overexpressing Luc, TRA2B KO, replicate 2

description: Library name: LN319-Luc_TRA2B-KO_rep2


title: LN319 cells overexpressing Luc, TRA2A KO, replicate 2

description: Library name: LN319-Luc_TRA2A-KO_rep2


title: LN319 cells overexpressing TRA2B, Control KO, replicate 3

description: Library name: LN319-TRA2B_CTRL-KO_rep3


title: LN319 cells overexpressing Luc, TRA2A KO, replicate 1

description: Library name: LN319-Luc_TRA2A-KO_rep1


title: LN319 cells overexpressing Luc, TRA2A KO, replicate 3

description: Library name: LN319-Luc_TRA2A-KO_rep3


title: LN319 cells overexpressing Luc, Control KO, replicate 2

description: Library name: LN319-Luc_CTRL-KO_rep2


title: LN319 cells overexpressing Luc, Control KO, replicate 3

description: Library name: LN319-Luc_CTRL-KO_rep3


title: P36-T0

city: Valencia

first: Angela

middle: L.

last: Riffo-Campos

state: Valencia

address: Avda. Blasco Ibáñes, 17

department: Department of Biochemistry and Molecular Biology

institute: University of Valencia, and INCLIVA

hyb_protocol: The hybridization of the samples was carried out on SurePrint G3 Human Gene Expression v3 8x60K crystals (AMADID 72363).

scan_protocol: The scanning of the crystals after hybridization was carried out on the Agilent G2600D Scanner and finally the data was extracted with the Agilent Feature Extraction 12.0.3.2 program.

data_processing: The background correction was performed using the ”normexp” method implemented in the R "limma" package. Normalization of expression intensities was performed using the "normalizeBetweenArrays" function, by the "quantile" method of the "limma" package. Statistical analysis of the data was performed by adjusting a linear model for each gene using the "lmFit" function, the coefficients and standard errors are estimated using the "contrasts.fit" function, and finally the moderate t-statistics, the moderate F-statistic and the logarithmic probabilities of differential expression using the "ebayes" function of the R "limma" package.

source_name: Gene expression of responders before of spinal cord stimulator in patient 36

label_protocol: The arrays were carried out following the Agilent protocol (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling).

extract_protocol: Manual extraction of RNA with the Qiagen RNeasy Mini Kit (ref: 74104). Once the RNA was obtained, quality controls were performed with measurements on the Nanodrop spectrophotometer (thermo Fisher) and on TapeStation (Agilent)

value: Plasma

tag: group

value: Responders

tag: patient id


title: P25-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 25


title: LN319 cells overexpressing Luc, Control KO, replicate 1

description: Library name: LN319-Luc_CTRL-KO_rep1

tag: cell line

tag: genotype


title: LN319 cells overexpressing TRA2B, TRA2A KO, replicate 1

description: Library name: LN319-TRA2B_TRA2A-KO_rep1


title: P31-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 31


title: LN229 cells overexpressing TRA2B, TRA2A KO, replicate 3

description: Library name: LN229-TRA2B_TRA2A-KO_rep3


title: P20-T0

source_name: Gene expression of non-responders before of spinal cord stimulator in patient 20

value: Non-responders


title: P37-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 37


title: P15-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 15


title: P31-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 31


title: P23-T0

source_name: Gene expression of non-responders before of spinal cord stimulator in patient 23


title: LN229 cells overexpressing TRA2B, TRA2A KO, replicate 2

description: Library name: LN229-TRA2B_TRA2A-KO_rep2


title: P38-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 38


title: P28-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 28


title: LN229 cells overexpressing TRA2B, Control KO, replicate 3

description: Library name: LN229-TRA2B_CTRL-KO_rep3


title: P19-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 19


title: P29-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 29


title: P19-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 19


title: LN229 cells overexpressing TRA2B, Control KO, replicate 2

description: Library name: LN229-TRA2B_CTRL-KO_rep2


title: P39-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 39


title: P25-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 25


title: LN229 cells overexpressing TRA2B, Control KO, replicate 1

description: Library name: LN229-TRA2B_CTRL-KO_rep1


title: P28-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 28


title: P31-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 31


title: P33-T0

source_name: Gene expression of non-responders before of spinal cord stimulator in patient 33


title: LN229 cells overexpressing Luc, TRA2B KO, replicate 3

description: Library name: LN229-Luc_TRA2B-KO_rep3


title: LN229 cells overexpressing Luc, TRA2B KO, replicate 2

description: Library name: LN229-Luc_TRA2B-KO_rep2


title: P22-T0

source_name: Gene expression of non-responders before of spinal cord stimulator in patient 22


title: LN229 cells overexpressing TRA2B, TRA2A KO, replicate 1

description: Library name: LN229-TRA2B_TRA2A-KO_rep1


title: LN229 cells overexpressing Luc, TRA2B KO, replicate 1

description: Library name: LN229-Luc_TRA2B-KO_rep1


title: LN229 cells overexpressing Luc, TRA2A KO, replicate 3

description: Library name: LN229-Luc_TRA2A-KO_rep3


title: LN229 cells overexpressing Luc, TRA2A KO, replicate 2

description: Library name: LN229-Luc_TRA2A-KO_rep2


title: LN229 cells overexpressing Luc, Control KO, replicate 3

description: Library name: LN229-Luc_CTRL-KO_rep3


title: LN229 cells overexpressing Luc, TRA2A KO, replicate 1

description: Library name: LN229-Luc_TRA2A-KO_rep1


title: LN229 cells overexpressing Luc, Control KO, replicate 2

description: Library name: LN229-Luc_CTRL-KO_rep2


title: LN229 cells overexpressing Luc, Control KO, replicate 1

description: Library name: LN229-Luc_CTRL-KO_rep1


title: P5-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 5


title: P36-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 36


title: P20-T3

source_name: Gene expression of non-responders after 15 days of spinal cord stimulator in patient 20


title: P7-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 7


title: P6-T3

source_name: Gene expression of non-responders after 15 days of spinal cord stimulator in patient 6


title: P38-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 38


title: diff_SHROOM3_KD_3

city: Shanghai

first: Li-nan

last: Xu

address: No.399, Wanyuan Load, Minhang district, Shanghai.

institute: Children's Hospital of Fudan University

description:
Library name: Sample 7
KD37_3

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: GRCh38.p13
Supplementary files format and content: processed data_count.xlsx

source_name: podocyte

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions . The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq X Plus platform (PE150) using NovaSeq Reagent Kit.OR the sequencing library was performed on DNBSEQ-T7 platform (PE150) using DNBSEQ-T7RS Reagent Kit (FCL PE150) version 3.0.

value: podocyte


title: diff_SHROOM3_KD_4

description:
Library name: Sample 8
KD37_4


title: diff_SHROOM3_KD_2

description:
Library name: Sample 6
KD37_2


title: P16-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 16


title: P11-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 11


title: P26-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 26


title: diff_Control_4

description:
Library name: Sample 4
Con_4


title: P4-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 4


title: P21-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 21


title: P10-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 10


title: P8-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 8


title: diff_Control_2

description:
Library name: Sample 2
Con_2


title: P15-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 15


title: diff_Control_1

description:
Library name: Sample 1
Con_1


title: P11-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 11


title: diff_Control_3

description:
Library name: Sample 3
Con_3


title: diff_SHROOM3_KD_1

description:
Library name: Sample 5
KD37_1


title: P2-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 21


title: P16-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 16


title: AGS, RBM8A, rep3

city: Xi'an

first: Hang

last: Peng

address: No. 256 Youyi West Road

institute: Shaanxi Provincial People’s Hospital

description:
Library name: AGS_RBM8A_RIP_rep3
Processed data file inclued multiple processed files.

data_processing:
After obtaining the sequencing raw data, data filtering is first performed to remove low - quality data. Then, the filtered data is aligned with the reference genome to obtain the alignment results. The macs2 software is used to perform peak calling based on a model (Poisson distribution) to accurately identify the positions of protein - RNA interactions. Moreover, differential analysis is carried out on the peaks between different treatments, and functional enrichment analysis is performed on the genes associated with the differential peak regions.
Raw sequence files were subjected to quality control analysis using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
Use HISAT2 to align the quality - controlled sequencing reads with the reference genome. Then, use SAMtools to convert and sort the alignment results in the appropriate format and summarize the alignment outcomes. Finally, use MarkDuplicates in GATK to mark the duplicate sequences.
Assembly: hg38
Supplementary files format and content: Peak file represents a RBM8A - bound RNA peak, including the chromosome name, start position, end position, peak name, score, and strand information.

source_name: Stomach

growth_protocol: AGS cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin. Cells were maintained in a humidified incubator at 37°C with 5% CO₂. The medium was changed every 2 - 3 days, and cells were passaged when they reached approximately 80% confluence using 0.25% trypsin - EDTA solution.

extract_protocol:
Cell lysis: AGS cells were washed twice with ice-cold PBS and then lysed in RIP lysis buffer (50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, 1 mM EDTA) supplemented with protease inhibitors and RNase inhibitors on ice for 30 minutes. The cell lysate was centrifuged at 12,000 × g for 10 minutes at 4 °C to remove cell debris. RNA immunoprecipitation: The supernatant was pre-cleared with protein A/G magnetic beads for 1 hour at 4 °C. Then, the pre-cleared lysate was incubated with anti - RBM8A antibody overnight at 4 °C with gentle rotation. After that, protein A/G magnetic beads were added and incubated for another 2 hours at 4 °C. The beads were washed 5 times with RIP wash buffer (50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, 1 mM EDTA) to remove non - specifically bound proteins and RNAs. RNA extraction: The RNA bound to the beads was extracted using TRIzol reagent according to the manufacturer's instructions. The extracted RNA was treated with DNase I to remove genomic DNA contamination and then purified using an RNA purification kit.
RIP-seq

treatment_protocol: No specific treatment was applied to the AGS cells before the RIP experiment. The cells were in the normal growth state during the experiment.

value: Stomach

value: AGS

tag: cell type

value: Gastric adenocarcinoma cell

value: Wild type


title: AGS, RBM8A, rep2

description:
Library name: AGS_RBM8A_RIP_rep2
Processed data file inclued multiple processed files.


title: AGS, Input, rep1

description:
Library name: AGS_Input_RIP_rep1
Processed data file inclued multiple processed files.


title: AGS, Input, rep3

description:
Library name: AGS_Input_RIP_rep3
Processed data file inclued multiple processed files.


title: AGS, RBM8A, rep1

description:
Library name: AGS_RBM8A_RIP_rep1
Processed data file inclued multiple processed files.


title: P7-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 7


title: P9-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 9


title: K23/4903

city: Ghent

first: Jolien

last: Vanhooren

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

description: Library name: Sample 12

data_processing:
Sequencing reads were aligned to the human genome (GRCh38.p14) using STAR alignment (STAR/2.7.6a-GCC-10.2.0). After, BAM files were subjected to featureCounts program of the Subread package (Subread/2.0.3-GCC-9.3.0).
Assembly: GRCh38.p14
Supplementary files format and content: tab-deliminated text file with raw counts for each sample

source_name: peripheral blood

growth_protocol: Lentiviral transduced THP-1 and KASUMI-1 cells were maintained in RMPI medium supplemented with 20% FCS and antibiotics in humidified athmospheres with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using the QIAzol lysis reagent (Qiagen, Inc.) and purified using miRNeasy micro or mini kit (Qiagen, Inc.) according to manufacturer guidelines in combination with on-column DNase I digestion using a RNase-free DNase kit (Qiagen, Inc.).
RNA libraries for RNA sequencing were prepared by Eurofins Genomics Europe Sequencing GmbH

value: peripheral blood

value: acute myeloid leukemia

value: empty vector control


title: P19-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 19


title: K23/4901

description: Library name: Sample 11


title: P10-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 10


title: P14-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 14


title: P27-T0

source_name: Gene expression of non-responders before of spinal cord stimulator in patient 27


title: P7-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 7


title: K23/4818

description: Library name: Sample 10


title: P9-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 9


title: P15-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 15


title: K23/4902

description: Library name: Sample 9

value: NID1 overexpression


title: P2-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 25


title: AGS, Input, rep2

description:
Library name: AGS_Input_RIP_rep2
Processed data file inclued multiple processed files.


title: K23/3349

description: Library name: Sample 6

value: acute monocytic leukemia

value: non-targeting control


title: K23/3345

description: Library name: Sample 5


title: K23/4817

description: Library name: Sample 7


title: K23/2979

description: Library name: Sample 4


title: K23/3343

description: Library name: Sample 2

value: NID1 knockdown


title: K23/3347

description: Library name: Sample 3


title: K23/2977

description: Library name: Sample 1


title: SCHW25_CD45pos_p1_

city: Boston

first: L. Nicolas

last: Gonzalez Castro

address: 60 Fenwood Road

institute: Mass General Brigham

description: Library name: SCHW25_CD45pos_p1

data_processing:
We processed sequencing data from raw reads to gene expression matrices as previously described (Tirosh et al., 2016). Brieﬂy, we used bcl2fastq to generate demultiplexed FASTQ ﬁles, and aligned the resulting paired-end scRNA-seq reads to the human transcriptome (hg19) using Bowtie (v0.12.7) (Langmead et al., 2009). We quantiﬁed gene expression levels from these alignments as transcripts-per-million (TPM) values by running RSEM (v1.2.19) in paired-end mode (Li and Dewey, 2011). We normalized the total transcripts per cell to one-hundred thousand (TP100K), as this is our estimated complexity of single-cell libraries prepared by SMART-Seq2 (Tirosh et al., 2016), and then log-transformed these values to report gene expression as E = ln(TP100K+1).
Assembly: hg19
Supplementary files format and content: SCHW_samples.mtx

source_name: Schwannoma

extract_protocol:
Fresh tumors were collected directly from the operating room at the time of surgery and presence of schwannoma was confirmed by frozen section. Tumors were mechanically and enzymatically dissociated using a papain-based tumor dissociation kit (Miltenyi Biotec). Tumor cells were blocked in 1% bovine serum albumin in Hanks buffered saline solution (BSA / HBSS). Tumors were first stained first with CD45- Vioblue direct antibody conjugate (clone REA747, Miltenyi Biotec) for 30 min at 4deg C. Cells were washed with cold PBS, and then re- suspended in 1mL of BSA / HBSS containing 1 mM calcein AM (Life Technologies) and 0.33 mM TO-PRO-3 iodide (Life Technologies) to co-stain for 30 min before sorting. CD45 negative cells were stained with calcein AM (Life Technologies) for viability and CD24-APC (human antibody, clone REA832, Miltenyi Biotec) and CD44-VioBlue (human antibody, clone REA690, Miltenyi Biotec) to sort subpopulations of viable non-immune cells. Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter), 640nm (TO-PRO-3 or CD24-APC, 670/14 filter), and 405 nm (CD45-VioBlue or CD44-VioBlue, 450/50 filter) lasers. Standard, strict forward scatter height versus area criteria were used to discriminate doublets and gate only singleton cells. Viable single cells were identified as calcein AM positive and TO-PRO-3 negative. We sorted individual, viable, immune, and non-immune single cells into 96- well plates containing TCL buffer (QIAGEN) with 1% beta-mercaptoethanol. Plates were frozen on dry ice immediately after sorting and stored at -80deg C prior to whole transcriptome amplification, library preparation and sequencing. Smart-seq2 whole transcriptome amplification, library construction, and sequencing were performed.
Single cell cDNA and sequencing libraries were prepared using the SMART-seq2 protocol (Picelli et al., 2014) with several adaptations. Agencourt RNAClean beads were used to purify RNA prior to oligo (dT) hybridization. RNase inhibitor was added to the dT annealing step at 1U/ml. Trehalose (1M) was used instead of water to make up the reaction volume. For the reverse transcription step, Maxima RNaseH-minus RT (200 U/ml) was used as the RT enzyme at 2U/ml. MgCl2 was added at 0.01M and DTT was omitted from the reaction. Trehalose (1M) was used to stabilize the reaction rather than betaine. The RT step was performed at 50 C for 90 minutes followed by 85 C for 5 minutes. In the PCR pre-ampliﬁcation step, an ISPCR primer was used at 0.2 mM and PCR was per-formed for 21 cycles. PCR puriﬁcation was performed using AMpure XP beads at 0.8X. Libraries were tagmented and enriched with dual indexes using Illumina Nextera XT Library Prep kits. Libraries from 384 or 768 cells with unique indexes were pooled together and sequenced at 2pM on an Illumina Nextseq 500 sequencer, yielding paired-end 38 base pair reads (Tirosh et al., 2016).

value: Schwannoma

tag: tissue type

value: tumor


title: TIGK 60C-3

city: Chicago

first: Chen

last: Han

state: IL

address: 801 S. Paulina St.

department: Center for Wound healing and Tissue Regeneration

institute: University of Illinois Chicago

description: Library name: Sample 18

data_processing:
Clean data was obtained by using in-house perl scripts (Novogene America) to remove reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Hisat2 (v2.0.5) was used to index and map reads to the human reference genome. The reference genome and gene model annotation files were downloaded from the genome website directly.
The mapped reads were assembled with StringTie (v1.3.3b).
Read numbers mapped to each gene were then counted in R with FeatureCounts (v1.5.0-p3) and an FPKM of each gene was calculated.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Gingival

extract_protocol:
RNA was harvested after 10 minutes in -25°C, 37°C, and 60°C using Trizol and purified with an RNA Clean & Concentrator-25 kit (Zymo, Tustin, CA, USA), and treated with DNAse (ThermoFisher Scientific, Waltham, MA). RNA integrity numbers (RIN) were checked with Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). All samples had an RIN between 8.9-9.4. 1 ug of total RNA was used for construction of sequencing libraries.
The library preparation, genome mapping, and raw gene counts for mRNA-sequencing analysis were performed by Novogene (Novogene America). The following methods were those provided by Novogene. Libraries generated for mRNA-sequencing were checked with Qubit and real-time (RT) PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina sequencing platforms (Illumina, Omaha, NE, USA) and clean data was obtained by using in-house Perl scripts from Novogene (Novogene America, Sacramento, CA, USA). Hisat2 (v2.0.5) was used to index and map reads to the human reference genome (GRCh38/hg38), and the mapped reads were assembled by StringTie (v1.3.3b) [22]. Read numbers mapped to each gene were counted in R using the FeatureCounts package (v1.5.0-p3) and an FPKM of each gene was calculated [23].

treatment_protocol: Cells were placed in -25°C for 10 min, 37°C for 10 min, or 60°C for 10 min before undergoing RNA extraction.

value: Gingival

value: TIGK

value: Gingival Keratinocytes

tag: treatment

value: 60°C Heat Injury


title: SCHW25_CD45neg_p3_

description: Library name: SCHW25_CD45neg_p3

tag: tissue


title: TIGK 60C-2

description: Library name: Sample 17


title: TIGK 60C-1

description: Library name: Sample 16


title: TIGK -25C-3

description: Library name: Sample 15

value: negative 25°C Cold Injury


title: P8-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 8

value: Plasma

value: Responders


title: TIGK -25C-2

description: Library name: Sample 14


title: P37-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 37


title: SCHW25_CD45neg_p1_

description: Library name: SCHW25_CD45neg_p1


title: TIGK -25C-1

description: Library name: Sample 13


title: TIGK 37C-3

description: Library name: Sample 12

value: 37°C Baseline


title: P14-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 14


title: TIGK 37C-2

description: Library name: Sample 11


title: SCHW24_CD45pos_p1_

description: Library name: SCHW24_CD45pos_p1


title: P2-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 2


title: TIGK 37C-1

description: Library name: Sample 10


title: P4-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 4


title: HaCaT 60C-3

description: Library name: Sample 9

source_name: Skin

value: Skin

value: HaCaT

value: Skin Keratinocytes


title: K23/4900

description: Library name: Sample 8

source_name: peripheral blood

value: peripheral blood

value: acute myeloid leukemia

value: NID1 overexpression


title: SCHW25_CD45neg_p2_

description: Library name: SCHW25_CD45neg_p2


title: P34-T3

source_name: Gene expression of non-responders after 15 days of spinal cord stimulator in patient 34

value: Non-responders


title: P39-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 39


title: P11-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 11


title: HaCaT 60C-2

description: Library name: Sample 8


title: P10-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 10


title: P22-T3

source_name: Gene expression of non-responders after 15 days of spinal cord stimulator in patient 22


title: P6-T0

source_name: Gene expression of non-responders before of spinal cord stimulator in patient 6


title: SCHW24_CD45neg_p2_

description: Library name: SCHW24_CD45neg_p2

value: Schwannoma


title: P5-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 5


title: HaCaT -25C-3

description: Library name: Sample 6


title: 6949166-C

source_name: Gene expression of control patient 6949166

value: C

value: Control


title: HaCaT 60C-1

description: Library name: Sample 7


title: 5439266-C

source_name: Gene expression of control patient 5439266


title: BB0052-C

source_name: Gene expression of control patient BB0052


title: HaCaT 37C-3

description: Library name: Sample 3


title: P36-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 36


title: SCHW23CD45pos_p1_

description: Library name: SCHW23CD45pos_p1

source_name: Schwannoma

value: tumor


title: HaCaT 37C-2

description: Library name: Sample 2


title: SCHW24_CD45neg_p3_

description: Library name: SCHW24_CD45neg_p3


title: SCHW23CD45neg_p5_

description: Library name: SCHW23CD45neg_p5


title: HaCaT 37C-1

description: Library name: Sample 1


title: 2862-C

source_name: Gene expression of control patient 2862


title: SCHW24_CD45neg_p1_

description: Library name: SCHW24_CD45neg_p1


title: SCHW23CD45neg_p4_

description: Library name: SCHW23CD45neg_p4


title: dTAG-SPT5-HCT116, dTAG_plus, Rep2

city: NYC

first: Rui

last: Sun

state: New York

address: 1425 Madison

institute: Icahn school of medicine at Mount Sinai

description: Library name: CR-dTAG-P-SPT5-Rep2

data_processing:
Reads were trimmed and filtered using TrimGalore (version 0.6.10) and aligned to the hg38 human genome (Ensembl) and other spike-in genomes with HISAT2 (version 2.2.1). Alignment files were converted to Bam files with Samtools (version 1.14) for the downstream analysis.
Bigwig files were generated in 10 bp bin through the BamCoverage function in Deeptools (version 3.5.1). Reads were normalized using CPM method and scaled based on the spike-in/intergenic region signal. The bigwig files of replicates in the experiment were averaged using wiggletools (version 1.2).
Assembly: hg38
Supplementary files format and content: bigwig files include RNAPII occupancy signals or Flag-SPT5 or dTAG-SPT5 occupancy or H3K4me3 signals as indicated
Supplementary files format and content: bed files include RNAPII wave tracks
Library strategy: CUT&RUN

growth_protocol: dTAG-SPT5 HCT116 cells were cultured in McCoy’s 5A medium (Corning) supplemented with 10% Fetal Bovine Serum (FBS) (Gibco) and 1× Penicillin-Streptomycin (Corning) at 37°C and 5% CO2.

extract_protocol:
About 2 million freshly prepared cell nuclei were used for one CUT&RUN experiment. The procedures were described in the manual of CUT&RUN kit (Epicypher). For DRB RNAPII CUT&RUN, dTAG-SPT5 cells grown on 100 mm dish were first treated with 125 nM dTAGv-1 for 4 hours, then followed by adding 100 μM DRB (5,6-dichloro-1-β-D-ribofuranosyl-1H-benzimidazole) for another 3 hours. DRB were washed out and cells were incubated in the fresh medium with 125 nM dTAGv-1 at 37 °C for the indicated time course. Cells were collected in the medium containing 1 µg/ml of actinomycin D on ice. Cell nuclei were extracted and proceeded with procedures above.
Spike-In DNA (E.coli) (Epicypher) were added to each sample and DNA libraries were prepared with NEBnext Ultra II DNA library kit (New England Biolabs).

treatment_protocol: 125 nM dTAGv-1 for 4 hours; 100 uM DRB for 3 hour in specified experiments

value: Human colon cancer cell line

tag: genetic modification

tag: cut&run antibody

value: Bethyl Laboratories; Cat. # A300-868A


title: 5256-C

source_name: Gene expression of control patient 5256


title: dTAG-SPT5-HCT116, dTAG_plus, Rep1

description: Library name: CR-dTAG-P-SPT5-Rep1


title: HaCaT -25C-2

description: Library name: Sample 5

value: negative 25°C Cold Injury


title: SCHW23CD45neg_p3_

description: Library name: SCHW23CD45neg_p3


title: dTAG-SPT5-HCT116, dTAG_minus, Rep2

description: Library name: CR-dTAG-M-SPT5-Rep2

value: DMSO


title: HaCaT -25C-1

description: Library name: Sample 4


title: dTAG-SPT5-HCT116, dTAG_minus, Rep1

description: Library name: CR-dTAG-M-SPT5-Rep1


title: dTAG-SPT5-HCT116, muR2_H3K4me3, Rep2

description: Library name: CR-muR2-H3K4me3-Rep2

value: Epicypher; Cat. # 14-1048


title: 5277-C

source_name: Gene expression of control patient 5277

value: Plasma


title: SCHW23CD45neg_p2_

description: Library name: SCHW23CD45neg_p2


title: dTAG-SPT5-HCT116, muR1R2_H3K4me3, Rep2

description: Library name: CR-muR1R2-H3K4me3-Rep2


title: dTAG-SPT5-HCT116, muR2_H3K4me3, Rep1

description: Library name: CR-muR2-H3K4me3-Rep1


title: SCHW23CD45neg_p1_

description: Library name: SCHW23CD45neg_p1


title: dTAG-SPT5-HCT116, muALL_H3K4me3, Rep2

description: Library name: CR-muALL-H3K4me3-Rep2

value: Flag-muALL


title: 4134-C

source_name: Gene expression of control patient4134


title: dTAG-SPT5-HCT116, muR1R2_H3K4me3, Rep1

description: Library name: CR-muR1R2-H3K4me3-Rep1


title: dTAG-SPT5-HCT116, muR1_H3K4me3, Rep2

description: Library name: CR-muR1-H3K4me3-Rep2


title: SCHW22_CD45n_P4_

description: Library name: SCHW22_CD45n_P4


title: dTAG-SPT5-HCT116, muALL_H3K4me3, Rep1

description: Library name: CR-muALL-H3K4me3-Rep1


title: dTAG-SPT5-HCT116, WT_H3K4me3, Rep1

description: Library name: CR-WT-H3K4me3-Rep1

value: Flag-WT


title: dTAG-SPT5-HCT116, WT_H3K4me3, Rep2

description: Library name: CR-WT-H3K4me3-Rep2


title: 4127-C

source_name: Gene expression of control patient 4127


title: dTAG-SPT5-HCT116, muR2_Flag, Rep2

description: Library name: CR-muR2-Flag-Rep2

value: Cell Signaling Technology; Cat. # 14793


title: SCHW22_CD45n_P2_

description: Library name: SCHW22_CD45n_P2


title: dTAG-SPT5-HCT116, muR2_Flag, Rep1

description: Library name: CR-muR2-Flag-Rep1


title: 180-C

source_name: Gene expression of control patient 180


title: dTAG-SPT5-HCT116, muR1R2_Flag, Rep2

description: Library name: CR-muR1R2-Flag-Rep2


title: SCHW22_CD45n_P1_

description: Library name: SCHW22_CD45n_P1


title: BB0060-C

source_name: Gene expression of control patient BB0060


title: dTAG-SPT5-HCT116, WT_Flag, Inde2

description: Library name: CR-WT-Flag-Inde2


title: SCHW22_CD45n_P5_

description: Library name: SCHW22_CD45n_P5


title: 3362-C

source_name: Gene expression of control patient 3362


title: dTAG-SPT5-HCT116, muR1_H3K4me3, Rep1

description: Library name: CR-muR1-H3K4me3-Rep1


title: BB0090-C

source_name: Gene expression of control patient BB0090


title: 893-C

source_name: Gene expression of control patient 893


title: dTAG-SPT5-HCT116, ChIP_RTF1, WT_Rep2

description: Library name: ChIP-RTF1-WT-Rep2

data_processing:
Reads were trimmed and filtered using TrimGalore (version 0.6.10) and aligned to the hg38 human genome (Ensembl) and other spike-in genomes with HISAT2 (version 2.2.1). PCR duplicates were removed using Picard Tools (version 3.1.1). Alignment files were converted to Bam files with Samtools (version 1.14) for the downstream analysis.
Bigwig files were generated in 10 bp bin through the BamCoverage function in Deeptools (version 3.5.1). Reads were normalized using CPM method and scaled based on the spike-in/intergenic region signal. The bigwig files of replicates in the experiment were averaged using wiggletools (version 1.2).
Assembly: hg38
Supplementary files format and content: bigwig files include RNAPII occupancy signals

extract_protocol:
About 20 million HCT116 cells grown on the 150 mm dish were cross-linked with 1% formaldehyde for 10 min at room temperature. Cross-linking was quenched with 125 mM glycine for 5 min. Cells were collected with a cell lifter (Costar) in 2 ml ChIP nuclei fractionation buffer [50 mM HEPES (pH 7.5), 140 mM NaCl, 1 mM EDTA (pH 8.0), 10% Glycerol, 1% NP-40, 0.25% Triton X-100] with proteinase and phosphatase inhibitors and incubated on ice for 10 min. Cell nuclei were collected by centrifugation at 4 °C at 600 × g for 10 min and washed with wash buffer [10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0)]. The pellets were lysed in 1.8 mL RIPA buffer with proteinase and phosphatase inhibitors and sheared by sonication in a Bioruptor (Diagenode) at high power, for 2× 20 min with cycles of 30 s ON and 30 s OFF. Lysates were clarified by centrifugation at 16,000 × g for 10 min at 4 °C. 600 μL pre-cleared lysates were incubated with 4 μg antibodies overnight at 4 °C with end-to-end rotation. 22 μL Protein G magnetic beads (New England Biolabs) were added to the tube on the second day and the samples were incubated for another 4 hours at 4 °C with end-to-end rotation. The beads were washed with RIPA buffer three times, IP wash buffer [100 mM Tris-HCl (pH 8.0), 500 mM lithium chloride, 1% NP-40, 1% sodium deoxycholate] three times and TE buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0)] twice. Reversal of cross-linking was done by incubating beads in the elution buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0), 1% SDS, 200mM NaCl, 0.8 U Proteinase K] at 55 °C with heated lid for 16 h. On the third day, 1 μg of RNase A was added and the samples were incubated at 37 °C for 30 min. DNA was purified by using DNA Cleanup Kit (5 μg) (New England Biolabs).
The purified DNA was used for qPCR and library preparation. Spike-In DNA (S. cerevisiae) (Cell Signaling Technology) were added to each sample and DNA libraries were prepared with NEBnext Ultra II DNA library kit (New England Biolabs).

treatment_protocol: 125 nM dTAGv-1 for 4 hours; 250 nM NVP2 for 1 hour in specified experiments

tag: chip antibody

value: Bethyl Laboratories; Cat. # A300-179A


title: SCHW22_CD45n_P3_

description: Library name: SCHW22_CD45n_P3


title: dTAG-SPT5-HCT116, ChIP_RTF1, muR2_Rep2

description: Library name: ChIP-RTF1-muR2-Rep2


title: dTAG-SPT5-HCT116, ChIP_RTF1, muR2_Rep1

description: Library name: ChIP-RTF1-muR2-Rep1


title: 41-C

source_name: Gene expression of control patient 41


title: SCHW21_CD45N_P2_

description: Library name: SCHW21_CD45N_P2


title: dTAG-SPT5-HCT116, ChIP_RTF1, WT_Rep1

description: Library name: ChIP-RTF1-WT-Rep1


title: dTAG-SPT5-HCT116, ChIP_RTF1, muR1R2_Rep2

description: Library name: ChIP-RTF1-muR1R2-Rep2


title: dTAG-SPT5-HCT116, muR1R2_Flag, Rep1

description: Library name: CR-muR1R2-Flag-Rep1


title: SCHW21_CD45N_P6_

description: Library name: SCHW21_CD45N_P6


title: dTAG-SPT5-HCT116, ChIP_RTF1, muR1R2_Rep1

description: Library name: ChIP-RTF1-muR1R2-Rep1


title: SCHW21_CD45N_P1_

description: Library name: SCHW21_CD45N_P1


title: dTAG-SPT5-HCT116, ChIP_RTF1, muR1_Rep2

description: Library name: ChIP-RTF1-muR1-Rep2


title: SCHW20_P9_

description: Library name: SCHW20_P9


title: P5-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 5

value: Responders


title: BB0055-C

source_name: Gene expression of control patient BB0055


title: dTAG-SPT5-HCT116, ChIP_RTF1, muALL_Rep2

description: Library name: ChIP-RTF1-muALL-Rep2


title: dTAG-SPT5-HCT116, ChIP_RTF1, muR1_Rep1

description: Library name: ChIP-RTF1-muR1-Rep1


title: P26-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 26


title: dTAG-SPT5-HCT116, ChIP_RTF1, muALL_Rep1

description: Library name: ChIP-RTF1-muALL-Rep1


title: SCHW20_P8_

description: Library name: SCHW20_P8


title: SCHW21_CD45N_P3_

description: Library name: SCHW21_CD45N_P3


title: SCHW20_P7_

description: Library name: SCHW20_P7


title: dTAG-SPT5-HCT116, ChIP_pSer5, WT_Rep2

description: Library name: ChIP-WT-pSer5-Rep2

value: Cell Signaling Technology; Cat. # 13523


title: dTAG-SPT5-HCT116, ChIP_pSer5, WT_Rep1

description: Library name: ChIP-WT-pSer5-Rep1


title: dTAG-SPT5-HCT116, ChIP_pSer5, muR2_Rep2

description: Library name: ChIP-muR2-pSer5-Rep2


title: SCHW20_P4_

description: Library name: SCHW20_P4


title: P38-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 38


title: dTAG-SPT5-HCT116, ChIP_pSer5, muR2_Rep1

description: Library name: ChIP-muR2-pSer5-Rep1


title: P32-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 32


title: P39-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 39


title: dTAG-SPT5-HCT116, ChIP_pSer5, muR1R2_Rep2

description: Library name: ChIP-muR1R2-pSer5-Rep2


title: P16-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 16


title: P4-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 4


title: SCHW20_P10_

description: Library name: SCHW20_P10

source_name: Schwannoma


title: P32-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 32


title: dTAG-SPT5-HCT116, ChIP_pSer5, muR1_Rep2

description: Library name: ChIP-muR1-pSer5-Rep2


title: dTAG-SPT5-HCT116, ChIP_pSer5, muALL_Rep2

description: Library name: ChIP-muALL-pSer5-Rep2


title: dTAG-SPT5-HCT116, ChIP_pSer5, muR1_Rep1

description: Library name: ChIP-muR1-pSer5-Rep1


title: dTAG-SPT5-HCT116, ChIP_pSer5, muALL_Rep1

description: Library name: ChIP-muALL-pSer5-Rep1


title: SCHW20_CD45p_P1_

description: Library name: SCHW20_CD45p_P1


title: SCHW20_CD45N_P6_

description: Library name: SCHW20_CD45N_P6


title: dTAG-SPT5-HCT116, ChIP_pSer2, WT_Rep1

description: Library name: ChIP-WT-pSer2-Rep1

value: Cell Signaling Technology; Cat. # 13499


title: dTAG-SPT5-HCT116, ChIP_pSer2, WT_Rep2

description: Library name: ChIP-WT-pSer2-Rep2


title: SCHW20_CD45n_P5_

description: Library name: SCHW20_CD45n_P5

value: Schwannoma


title: dTAG-SPT5-HCT116, ChIP_pSer2, muR2_Rep1

description: Library name: ChIP-muR2-pSer2-Rep1


title: dTAG-SPT5-HCT116, ChIP_pSer2, muR2_Rep2

description: Library name: ChIP-muR2-pSer2-Rep2


title: dTAG-SPT5-HCT116, ChIP_pSer5, muR1R2_Rep1

description: Library name: ChIP-muR1R2-pSer5-Rep1


title: dTAG-SPT5-HCT116, ChIP_pSer2, muR1R2_Rep2

description: Library name: ChIP-muR1R2-pSer2-Rep2


title: SCHW20_CD45N_P3_

description: Library name: SCHW20_CD45N_P3


title: dTAG-SPT5-HCT116, ChIP_pSer2, muR1_Rep1

description: Library name: ChIP-muR1-pSer2-Rep1


title: SCHW20_CD45P_P2_

description: Library name: SCHW20_CD45P_P2


title: dTAG-SPT5-HCT116, ChIP_pSer2, muALL_Rep2

description: Library name: ChIP-muALL-pSer2-Rep2


title: P34-T0

source_name: Gene expression of non-responders before of spinal cord stimulator in patient 34

value: Non-responders


title: P21-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 21


title: dTAG-SPT5-HCT116, ChIP_pSer2, muR1_Rep2

description: Library name: ChIP-muR1-pSer2-Rep2


title: P28-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 28


title: P33-T3

source_name: Gene expression of non-responders after 15 days of spinal cord stimulator in patient 33


title: P9-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 9


title: SCHW20_CD45N_P2_

description: Library name: SCHW20_CD45N_P2


title: P29-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 29


title: dTAG-SPT5-HCT116, ChIP_NELFC, WT_Rep2

description: Library name: ChIP-WT-NELFC-Rep2

value: Cell Signaling Technology; Cat. # 12265


title: dTAG-SPT5-HCT116, ChIP_pSer2, muR1R2_Rep1

description: Library name: ChIP-muR1R2-pSer2-Rep1


title: dTAG-SPT5-HCT116, ChIP_NELFC, muR1R2_Rep2

description: Library name: ChIP-muR1R2-NELFC-Rep2


title: SCHW20_CD45n_P1_

description: Library name: SCHW20_CD45n_P1

value: tumor


title: dTAG-SPT5-HCT116, ChIP_pSer2, muALL_Rep1

description: Library name: ChIP-muALL-pSer2-Rep1

value: Human colon cancer cell line