title: H3K4me3(replicate 2)

city: Ipswich

first: Sriharsa

last: Pradhan

state: MA

address: 240 County Road

institute: New England Biolabs

data_processing:
Library Strategy: NEED-seq
Adaptor and low-quality sequences were trimmed from paired-end sequencing reads using Trim Galore v 0.5.0
NEED-seq:Trimmed read pairs were mapped to the reference genome (human: hg38) using Bowtie2 v. 2.3.4.3. PCR duplicates and mitochondrial reads were removed using Picard tools and samtools. The aligned bam files of technical replicates were merged using samtools. Open chromatin regions were identified by calling narrow peaks and Closed chromatin were identified by calling broad peaks using MACS2.
EM-seq: Trimmed read pairs were mapped to the reference genome (human: hg38) using Bwa-meth. PCR duplicates and mitochondrial reads were removed using samblaster and samtools.
ChIP-seq: Trimmed read pairs were mapped to the reference genome (human: hg38) using Bowtie2 v. 2.3.4.3. PCR duplicates and mitochondrial reads were removed using Picard tools and samtools. The aligned bam files of technical replicates were merged using samtools.  Open chromatin regions were identified by calling narrow peaks and Closed chromatin were identified by calling broad peaks using MACS2 where Input were used as control
Hi-C: HiC data were analysed using HicPro.
Assembly: hg38
Supplementary files format and content: Bigwigs were generated using bins using deeptools bamCoverage with the following parameters: --normalizeUsing RPKM

growth_protocol: HT1080 and HCT116 cells were grown in 6 well plates until 70-80% confluency. After one wash with 1XPBS, cells were crosslinked in 1XPBS with 4% formaldehyde (Thermo Fisher Scientific # 28908) for 10 min at RT. K562 crosslinked cells with 4% formaldehyde were decrosslinked overnight at 58°C in 1X PBS. Cytoplasmic extraction was performed for 30 min with end-over-end mixing at 4°C. After 300 g centrifugation at 4°C for 5 min, cell pellet was washed once with 1X PBS and nuclei concentration was defined using Luna automated cell counter.

extract_protocol:
Cells were fixed with 1% and 4% formaldehyde
HT1080 and HCT116 cells were grown in 6 well plates until 70-80% confluency. After one wash with 1X PBS (GIBCO # 770011-044), cells were crosslinked in 1X PBS with 4% formaldehyde (Thermo Fisher Scientific # 28908) for 10 min at room temperature (RT). In some crosslinking conditions, 1% formaldehyde was used. Crosslink was quenched using 0.25 M Glycine for 5 min at RT. Cells were de-crosslinked overnight at 58°C in 1X PBS. Cytoplasm was extracted for 10-30 min on ice using cytosolic buffer (15mM Tris-HCl, pH7.5, 5mM MgCl2, 60mM KCl, 0.5mM DTT, 15mM NaCl, 300mM sucrose, and 1% NP40) with occasional agitation. After 1X PBS wash, cells were incubated with 1X PBS / 5% BSA / 0.3% Triton™ X-100 for 1 hr at RT with gentle rocking. Primary antibodies were added (1/400 dilution per well) and incubated overnight at 4°C with gentle rocking. After 3 washes with 1X T-PBS (PBS + 0.1% Tween 20) for 5 min at RT, secondary antibodies were added , Alexa Fluor® 488 conjugated goat anti-Mouse IgG (H+L) Superclonal™ or goat anti-Rabbit IgG (H+L) Superclonal™ (corresponding to species of primary antibody; Thermo Fisher # A-28175 and A-27034 respectively) at a dilution of 1:1000 in PBS / 0.3% Triton™ X-100/ 5% BSA for 1 hr at RT with gentle rocking. After 3 washes with 1X T-PBS for 5 min at RT, cells were incubated for 1 hr at RT with 1 µl of Nt.CviPII-pGL (NEB, 0.5 units) in 800 µl binding buffer per well (20 mM potassium phosphate pH 7.0, 20 mM NaCl, 0.3% Triton™ X-100). In some experiments, heparin (Sigma-Aldrich # H3149) was added at different concentrations to prevent non-specific DNA binding. Plates were then washed 3 times with washing buffer (20 mM potassium phosphate buffer  pH 7.0, 500 mM NaCl, 0.3% Triton™ X-100) for 15 min at RT. Cells were incubated with 10 units of DNA Polymerase I (NEB # M0209S), 5 mM of dNTP mix including Biotin-14-dCTP (Thermo Fisher # 19518018), 5-methyl-dCTP (NEB # N0356S), dATP, dTTP and dGTP for 1 hr at 37°C in 800 µl of 1X NEBuffer 2 per well to allow nick translation to occur. Plates were then washed 3 times with washing buffer (20 mM potassium phosphate buffer, pH 7.0, 500 mM NaCl, 0.3% Triton™ X-100) for 15 min at RT with an additional wash with 1X PBS. Cells were then covered with 100 µl of 1X PBS and DNA was extracted using Monarch genomic DNA purification kit (NEB # T3010S) according to manufacturer’s recommendations. After DNA purification, 100-500 ng of genomic DNA was fragmented using 2 units of Nt.CviPII (NEB # R0626S) in 500  µl of 1X NEBuffer 2 at 37°C overnight. Nt.CviPII was inactivated at 65°C for 20 min. NaCl 5M stock was added to reach 1 M final concentration along with 30 µl of Streptavidin magnetic beads (NEB # S1420S) for 2 hrs with end-over-end mixing at 4°C to capture biotinylated DNA fragments. Streptavidin bound DNA beads were washed twice with 1X TE buffer supplemented with 2 M NaCl and 0.05 % Triton™ X-100. A third wash was performed with 1X TE buffer. Beads were resuspended in 50 µl of TE buffer and libraries were made on beads using NEBNext®Ultra™ II DNA Library Prep Kit for Illumina® (NEB # E7645S) according to manufacturer’s protocol. 8 to 12 PCR cycles were used to amplify barcoded DNA. NEED-seq protocol described above was used with some modifications. Briefly, K562 crosslinked cells with 4% formaldehyde were decrosslinked overnight at 58°C in 1X PBS. Cytoplasmic extraction was performed for 30 min with end-over-end mixing at 4°C. After 300 x g centrifugation at 4°C for 5 min, cell pellet was washed once with 1X PBS and nuclei number was calculated using Luna automated cell counter. Nuclei resuspended in 1X PBS were then captured by adding 10 µl of preactivated Concanavalin A magnetic beads (Cell Signaling Technology # 93569) for 10 min with end-over-end mixing at RT. Bead-bound nuclei were incubated with 1X PBS including 0.3 % Triton X-100 and 5% BSA for 1 hr at RT. Primary antibodies were added (1/400 final dilution) and incubated overnight with end-over-end mixing at 4°C. After 3 washes with 1X T-PBS for 5 min at RT, blocking buffer was added with anti-mouse IgG or anti-rabbit IgG coupled with Alexa 488 for 1h at RT with gentle rocking. After 3 washes with 1X T-PBS for 5 min at RT, beads were resuspended in 1 ml binding buffer (as described above) including 1 ul of fusion enzyme Nt.CviPII-pGL (NEB) for 1 hr at RT. Beads were then washed 3 times with washing buffer (as described above) for 15 min at RT. After 1 wash with 1X PBS, beads were incubated with 10 units of DNA Polymerase I, 5 uM of dNTP mix including Biotin-14-dCTP, 5-methyl-dCTP, dATP, dTTP and dGTP for 1 hr at 37°C in 800 µl of 1X NEBuffer 2 with end-over-end mixing. After 3 washes with washing buffer for 15 min at RT, beads were resuspended in 50 mM Tris-Cl, pH 7.5, 1 % SDS, 200 mM NaCl and 2 µl of proteinase K (NEB # P8107S) and incubated overnight at 65°C to lyse nuclei bound to the beads and DNA was extracted using phenol-chloroform and precipitated using glycogen. 200 ng of DNA was fragmented using Nt.CviPII and used to make libraries as described above. For low number of cells, barcoded DNA was amplified using ~18 PCR cycles. To determine the dynamic range of NEED-seq, cells were serially diluted after the labeling reaction. In this modified NEED-seq method, HT1080 cells were grown on 6 well plate to 80% confluency. Cells were incubated for 10 min at 4°C using CSK buffer (10 mM PIPES pH 6.8, 300 mM sucrose, 100 mM NaCl, 1.5 mM MgCl2 and 0.5 % Triton X-100) followed by crosslinking with 4% formaldehyde for 10 min at RT. Glycine was used to quench formaldehyde for 5 min at RT (final concentration 0.25M). After 1X PBS wash, blocking buffer was added to cells for 1h at RT (5% BSA, 1X PBS and 0.3% Triton X-100). Different antibodies (see Table S2) were then added at dilutions recommended by the manufacturer and incubated with cells for 16 hrs at 4°C. After 3 washes with T-PBS (PBS with 0.1 % Tween 20) for 5 min at RT, blocking buffer was added with anti-mouse IgG or anti-rabbit IgG coupled with Alexa 488 for 1h at RT. After 3 washes with T-PBS for 5 min at RT, NEED-seq binding buffer (20 mM KPO4, 150 mM NaCl and 0.3% TritonX-100) was added along with Nt.CviPII-pGL enzyme (1 unit per well) for 1h at 37°C. After 3 washes with NEED-seq washing buffer (20 mM KPO4, 500 mM NaCl and 1% TritonX-100) for 15 min at RT, 1X NEBuffer2.1 was added for 1h at 37°C to allow Nt.CviPII-pGL activity to fragment the targeted DNA. After 1 wash with 1X PBS, genomic DNA extraction was performed using Monarch genomic DNA purification kit (6 wells pooled per antibody) according to NEB recommendations with a minor modification which included a lysis step at 56°C for 1h instead of 10 min to reverse DNA crosslinking. 0.1 to 1 µg of genomic DNA was used for size selection using first 0.4x volume of NEBNext Sample Purification beads with 10 min incubation at RT. Supernatant containing 200-500 bp DNA sizes was separated from beads using 12-tube magnetic separation rack (NEB # S1509S) and collected. An additional 0.4x volume of NEBNext Sample Purification beads was added to the supernatant and incubated for 10 min at RT. After 2 washes with 80% EtOH, DNA was eluted form beads with 50 µl of low TE buffer and DNA libraries were prepared using NEBNext Ultra II DNA Library Prep (NEB # E7103L) with some modifications. Briefly, end repair/dA tailing was performed on size selected DNA and NEBNext Illumina adaptor (1/10 dilution) were ligated for 2 hrs at RT. USER enzyme (NEB # E7103L) was incubated for 20 min at 37°C and another round of library size selection was performed as described above. The library was amplified using 13 PCR cycles. PCR products were purified using 0.9x volume of NEBNext Sample Purification beads. 1 nM of size selected DNA library was sequenced on Novaseq 6000. HT1080 cells (0.5x10e6) were crosslinked with 4% formaldehyde for 10 min at RT and quenched with 1.5 M Tris-HCl (pH 8) for 5 min at RT. After 1X PBS wash, cells were permeabilized with Hi-C lysis buffer (10 mM Tris-HCl (pH 8), 10 mM NaCl and 0.2% NP40) for 30 min at 4°C, washed with 1X NEBuffer2 and incubated for 10 min at 58°C with 1X NEBuffer2, 0.3% SDS and 1 mM DTT. To quench SDS, Triton X-100 was added (1% final concentration per well) for 15 min at 37°C. 400 U of MboI (NEB # R0147M) were added and incubated for 16 hrs at 37°C. Enzyme was inactivated at 58°C for 20 min. Supernatant was discarded and DNA polymerase I mix containing  NEBuffer2.1 1X (NEB # B7002S), 30 µM of dNTPs (including dCTP/dGTP/dTTP (NEB # N0441S/ N0442S/N0443S respectively) with biotin-14-dATP (ThermoFisher Scientific # 19524016)) and 50 U of DNA polymerase I (NEB # M0210M) was added and incubated for 4 hrs at RT. Ligase mix was added and incubated for 16 hrs at RT. Ligase mix contains 2000 U of T4 DNA ligase (M0202M NEB), 140 µg of recombinant albumin (NEB # B9200S),  1X T4 DNA ligase buffer (NEB # B0202S) and 1 % Triton X-100. After ligation, supernatant was discarded, and cells were washed using 1X PBS. Genomic DNA was extracted from the wells using Monarch Genomic DNA purification Kit (NEB # T3010L). To remove biotin from un-ligated DNA ends, 10 µg of genomic DNA was incubated with 30 U of T4 DNA Polymerase (NEB # M0203L), 25 µM dATP/dGTP (NEB # N0440S/N0442S respectively) in 1X NEBuffer2 for 4 hrs at 20°C. Enzyme was inactivated for 20 min at 75°C. DNA was purified using 1X volume of NEBNext Sample Purification beads (NEB # E6178S) and sheared to 300 bp using Covaris (program : repeat/iterations # 7; repeat process treatment duration 10s; peak power 50W; duty factor 20%; cycles per burst 1000; total treatment time per sample 70s). To capture biotinylated DNA, DNA was incubated with NEB Magnetic Streptavidin beads (NEB # S1420S) for 30 min at RT in 10 mM Tris-HCl (pH 7.5) supplemented with 1 M NaCl. Beads were washed once with 10 mM Tris-HCl (pH 7.5) supplemented with 1 M NaCl and once with low TE buffer. Beads were resuspended in 50 µl of low TE buffer and DNA libraries were prepared on beads using NEBNext Ultra II DNA Library Prep (NEB # E7103L) with some modifications. Briefly, end repair/dA tailing was performed on beads and NEBNext Illumina adaptor (1/10 dilution) were ligated for 2 hrs at RT. 3 µl of USER (NEB # E7103L) was added for 20 min at 37°C. Beads were then washed once with 10 mM Tris-HCl (pH 7.5) supplemented with 1 M of NaCl and once with low TE. Beads were resuspended in 15 µl of low TE. 14 PCR cycles were performed. Supernatant containing PCR products were separated from beads using 12-tube magnetic separation rack (NEB # S1509S) and purified using 0.9x volume of NEBNext Sample Purification beads. 1 nM of DNA Hi-C library was loaded on Novaseq 6000.

value: fibrosarcoma cells

tag: condition


title: H3K27ac(replicate 2)

status: Public on Jan 16 2025

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: P2S5_breast_tumor_5_(20240201_SH_Hs_P2S5_BrT2_0128)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Human Breast Tumor RNAPiiS5p

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads. 2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the repeat-masked hg19 Homo sapiens reference sequence obtained from UCSC. 3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments. 4. We used bedtools 2.30.0 "genomecov" to make a normalized count hg19 track which is the fraction of counts at each base pair scaled by the size of the hg19 reference sequence (3095693983) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .hg19.bw)
Assembly: hg19
Supplementary files format and content: bw
Library strategy: CUT&Tag

source_name: Breast

extract_protocol:
https://www.protocols.io/edit/cutac-for-ffpes-c5huy36w
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

tag: tissue

value: Breast

tag: group

value: Normal

tag: tumor biochain

value: Tumor Biochain T8235086PT

tag: antibody

value: RNAP2Ser5P Cell Signaling Technology cat# 13523


title: P2S5_colon_normal_1_(20240118_SH_Hs_P2S5_CoN_0113)

description: Human Colon Normal RNAPIIS5p

source_name: Colon

value: Colon

value: Tumor Biochain T8235090PP


title: H3K27ac(replicate 1)


title: H3K4me1(replicate 2)


title: P2S5_breast_tumor_3_(20240118_SH_Hs_P2S5_BrT_0113)

description: Human Breast Tumor RNAPiiS5p


title: P2S5_breast_normal_3_(20240201_SH_Hs_P2S5_BrN2_0128)

description: Human Breast Normal RNAPiiS5p

value: Tumor Biochain T8235086PP


title: P2S5_breast_tumor_2_(20240108_SH_Hs_P2S5_BrT2_1225)

description: Human Breast Tumor RNAPiiS5p


title: H3K4me3(replicate 1)


title: H3K9me3(replicate 2)


title: H3K9me3(replicate 1)


title: H4K20me1(replicate 2)


title: H4K20me1(replicate 1)


title: H4K20me3(replicate 1)


title: H2AK119ub1(replicate 4)


title: H3K27me3(replicate 1)


title: H2AK119ub1(replicate 2)


title: H3K4me1(replicate 1)


title: H3K27me3_K562(replicate 2)

value: Chronic myelogenous leukemia cells


title: H2AK119ub1(replicate 1)


title: H3K4me3_K562_50 (50 cells)

value: H3K4me3 (50 cells)


title: H3K4me3 K562


title: H3K4me3_K562_50K(replicate 2 from 50K cells)

value: H3K4me3 (50K cells)


title: P2S5_normal_4_(20240201_SH_Mm_P2S5_N4_0128)

description: Mouse Normal Brain RNAPIIS5p

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads. 2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the repeat-masked mm10 Homo sapiens reference sequence obtained from UCSC. 3. We used samtools 1.14 "view" to extract properly paired reads from the mm10 alignments. 4. We used bedtools 2.30.0 "genomecov" to make a normalized count mm10 track which is the fraction of counts at each base pair scaled by the size of the mm10 reference sequence (2725537669) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .mm10.bw)
Assembly: mm10
Supplementary files format and content: bw
Library strategy: CUT&Tag

organism: Mus musculus

source_name: Brain

value: Brain

value: mouse brain tumor FFPE


title: H2AK119ub1(replicate 3)


title: H3K27me3_K562(replicate 1)


title: H4K20me3(replicate 2)


title: H3K4me3_K562_50K(replicate 1 from 50K cells)


title: P2S5_YAP1_tumor_2.1_(20240201_SH_Mm_P2S5_Y2_0128)

description: Mouse YAP1 Tumor RNAPIIS5p

value: Tumor


title: P2S5_normal_2_(20240201_SH_Mm_P2S5_N2_0128)

description: Mouse Normal Brain RNAPIIS5p


title: P2S5_normal_1_(20240201_SH_Mm_P2S5_N1_0128)

description: Mouse Normal Brain RNAPIIS5p


title: H3K27me3(replicate 2)


title: P2S5_normal_5_(20240201_SH_Mm_P2S5_N5_0128)

description: Mouse Normal Brain RNAPIIS5p


title: P2S5_YAP1_tumor_1.7_(20231010_SH_Mm_P2S5_Y43_1007)

description: Mouse YAP1 Tumor RNAPIIS5p


title: P2S5_YAP1_tumor_1.8_(20231010_SH_Mm_P2S5_Y44_1007)

description: Mouse YAP1 Tumor RNAPIIS5p


title: P2S5_YAP1_tumor_2.2_(20240201_SH_Mm_P2S5_Y4_0128)

description: Mouse YAP1 Tumor RNAPIIS5p


title: P2S5_YAP1_tumor_1.6_(20231010_SH_Mm_P2S5_Y42_1007)

description: Mouse YAP1 Tumor RNAPIIS5p


title: P2S5_normal_3_(20240201_SH_Mm_P2S5_N3_0128)

description: Mouse Normal Brain RNAPIIS5p


title: P2S5_YAP1_tumor_1.4_(20231010_SH_Mm_P2S5_Y34_1007)

description: Mouse YAP1 Tumor RNAPIIS5p


title: P2S5_YAP1_tumor_1.3_(20231010_SH_Mm_P2S5_Y33_1007)

description: Mouse YAP1 Tumor RNAPIIS5p


title: P2S5_YAP1_tumor_1.1_(20231010_SH_Mm_P2S5_Y31_1007)

description: Mouse YAP1 Tumor RNAPIIS5p


title: P2S5_YAP1_tumor_1.2_(20231010_SH_Mm_P2S5_Y32_1007)

description: Mouse YAP1 Tumor RNAPIIS5p


title: P2S5_YAP1_normal_2_(20240201_SH_Mm_P2S5_Y3_0128)

description: Mouse YAP1 Normal RNAPIIS5p


title: P2S5_YAP1_normal_1_(20240201_SH_Mm_P2S5_Y1_0128)

description: Mouse YAP1 Normal RNAPIIS5p


title: H3K4me3_K562_500 (500 cells)

value: H3K4me3 (500 cells)


title: P2S5_RELA_tumor_7.1_(20240118_SH_Mm_P2S5_R9_0114)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_tumor_7.3_(20240201_SH_Mm_P2S5_R22_0128)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_tumor_7.2_(20240201_SH_Mm_P2S5_R21_0128)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_tumor_6.4_(20240118_SH_Mm_P2S5_R3_0114)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_tumor_6.3_(20240118_SH_Mm_P2S5_R2_0114)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_tumor_6.1_(20240118_SH_Mm_P2S5_R1_0114)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_tumor_6.2_(20240118_SH_Mm_P2S5_R10_0114)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_tumor_5.2_(20240108_SH_Mm_P2S5_R2_1223)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_tumor_3.2_(20231010_SH_Mm_P2S5_R32_1007)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_tumor_5.1_(20240108_SH_Mm_P2S5_R1_1223)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_tumor_3.1_(20231010_SH_Mm_P2S5_R31_1007)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_YAP1_tumor_1.5_(20231010_SH_Mm_P2S5_Y41_1007)

description: Mouse YAP1 Tumor RNAPIIS5p


title: P2S5_YAP1_normal_3_(20240201_SH_Mm_P2S5_Y5_0128)

description: Mouse YAP1 Normal RNAPIIS5p


title: P2S5_RELA_tumor_4.1_(20231010_SH_Mm_P2S5_R42_1007)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_tumor_2.3_(20231017_SH_Mm_P2S5_R33_1004)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_normal_9.4_(20231003_SH_Mm_P2S5_R8_0930)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_tumor_1.9_(20231017_SH_Mm_P2S5_R11_1004)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_tumor_2.4_(20231017_SH_Mm_P2S5_R34_1004)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_tumor_1.4_(20231003_SH_Mm_P2S5_R4_0930)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_normal_9.3_(20231003_SH_Mm_P2S5_R7_0930)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_9.2_(20231003_SH_Mm_P2S5_R6_0930)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_tumor_1.3_(20231003_SH_Mm_P2S5_R3_0930)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_normal_9.1_(20231003_SH_Mm_P2S5_R5_0930)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_tumor_1.2_(20231003_SH_Mm_P2S5_R2_0930)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_tumor_1.13_(20231017_SH_Mm_P2S5_R15_1004)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_tumor_1.11_(20231017_SH_Mm_P2S5_R13_1004)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_tumor_1.10_(20231017_SH_Mm_P2S5_R12_1004)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_tumor_1.12_(20231017_SH_Mm_P2S5_R14_1004)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_normal_8.4_(20240201_SH_Mm_P2S5_R26_0128)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_8.3_(20240201_SH_Mm_P2S5_R25_0128)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_tumor_2.1_(20231017_SH_Mm_P2S5_R31_1004)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_normal_8.2_(20240201_SH_Mm_P2S5_R24_0128)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_tumor_2.2_(20231017_SH_Mm_P2S5_R32_1004)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_normal_8.1_(20240201_SH_Mm_P2S5_R23_0128)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_7.4_(20240118_SH_Mm_P2S5_R7_0114)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_7.2_(20240118_SH_Mm_P2S5_R5_0114)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_6.2_(20240108_SH_Mm_P2S5_R4_1223)

description: ouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_5.2_(20231010_SH_Mm_P2S5_R44_1007)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_6.1_(20240108_SH_Mm_P2S5_R3_1223)

description: ouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_4.1_(20231010_SH_Mm_P2S5_R33_1007)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_5.1_(20231010_SH_Mm_P2S5_R43_1007)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_3.3_(20231017_SH_Mm_P2S5_R37_1004)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_4.2_(20231010_SH_Mm_P2S5_R34_1007)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_3.4_(20231017_SH_Mm_P2S5_R38_1004)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_3.2_(20231017_SH_Mm_P2S5_R36_1004)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_2.2_(20231017_SH_Mm_P2S5_R17_1004)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_2.3_(20231017_SH_Mm_P2S5_R18_1004)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_3.1_(20231017_SH_Mm_P2S5_R35_1004)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_tumor_1.1_(20231003_SH_Mm_P2S5_R1_0930)

description: Mouse RELA Tumor RNAPIIS5p


title: P2S5_RELA_normal_1.4_(20231003_SH_Mm_P2S2_R8_0927)

description: Mouse RELA Normal RNAPIIS2p

value: RNAP2Ser2P Cell Signaling Technology cat# 13523


title: P2S5_RELA_normal_1.3_(20231003_SH_Mm_P2S2_R7_0927)

description: Mouse RELA Normal RNAPIIS2p


title: P2S5_PDGFB_tumor_7_(20231003_SH_Mm_P2S5_P8_0930)

description: Mouse PDGFB RNAPIIS5p


title: P2S5_RELA_normal_1.1_(20231003_SH_Mm_P2S2_R5_0927)

description: Mouse RELA Normal RNAPIIS2p


title: P2S5_RELA_normal_7.5_(20240118_SH_Mm_P2S5_R8_0114)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_PDGFB_tumor_5_(20231003_SH_Mm_P2S5_P6_0930)

description: Mouse PDGFB RNAPIIS5p


title: P2S5_PDGFB_tumor_6_(20231003_SH_Mm_P2S5_P7_0930)

description: Mouse PDGFB RNAPIIS5p


title: P2S5_colon_normal_3_(20240108_SH_Hs_P2S5_CoN2_1225)

description: Human Colon Normal RNAPIIS5p


title: P2S5_PDGFB_tumor_2_(20231003_SH_Mm_P2S5_P3_0930)

description: Mouse PDGFB RNAPIIS5p


title: P2S5_RELA_normal_7.1_(20240118_SH_Mm_P2S5_R4_0114)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_RELA_normal_7.3_(20240118_SH_Mm_P2S5_R6_0114)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_PDGFB_5_(20231010_SH_Mm_P2S5_P33_1007)

description: Mouse PDGFB Tumor RNAPIIS5p


title: P2S5_PDGFB_6_(20231010_SH_Mm_P2S5_P34_1007)

description: Mouse PDGFB Tumor RNAPIIS5p


title: P2S5_PDGFB_tumor_3_(20231003_SH_Mm_P2S5_P4_0930)

description: Mouse PDGFB RNAPIIS5p


title: P2S5_PDGFB_normal_1_(20231003_SH_Mm_P2S5_P2_0930)

description: Mouse PDGFB RNAPIIS5p


title: P2S5_PDGFB_4_(20231010_SH_Mm_P2S5_P31_1007)

description: Mouse PDGFB Tumor RNAPIIS5p


title: P2S5_PDGFB_normal_2_(20231003_SH_Mm_P2S5_P5_0930)

description: Mouse PDGFB RNAPIIS5p


title: P2S5_PDGFB_3_(20231010_SH_Mm_P2S5_P24_1007)

description: Mouse PDGFB Tumor RNAPIIS5p


title: P2S5_PDGFB_2_(20231010_SH_Mm_P2S5_P23_1007)

description: Mouse PDGFB Tumor RNAPIIS5p


title: P2S5_RELA_normal_2.1_(20231017_SH_Mm_P2S5_R16_1004)

description: Mouse RELA Normal RNAPIIS5p


title: P2S5_PDGFB-2_tumor_2.1_(20240201_SH_Mm_P2S5_P22_0128)

description: Mouse PDGFB-2 Tumor RNAPIIS5p


title: P2S5_PDGFB-2_normal_2.3_(20240201_SH_Mm_P2S5_P25_0128)

description: Mouse PDGFB-2 Normal RNAPIIS5p


title: P2S5_PDGFB-2_normal_2.2_(20240201_SH_Mm_P2S5_P23_0128)

description: Mouse PDGFB-2 Normal RNAPIIS5p


title: P2S5_PDGFB-2_tumor_2.2_(20240201_SH_Mm_P2S5_P24_0128)

description: Mouse PDGFB-2 Tumor RNAPIIS5p


title: P2S5_PDGFB-1_tumor_1.2_(20240201_SH_Mm_P2S5_P15_0128)

description: Mouse PDGFB-1 Tumor RNAPIIS5p


title: P2S5_PDGFB_1_(20231010_SH_Mm_P2S5_P21_1007)

description: Mouse PDGFB Tumor RNAPIIS5p


title: P2S5_PDGFB-1_normal_1.3_(20240201_SH_Mm_P2S5_P13_0128)

description: Mouse PDGFB-1 Normal RNAPIIS5p


title: P2S5_PDGFB-1_normal_1.2_(20240201_SH_Mm_P2S5_P12_0128)

description: Mouse PDGFB-1 Normal RNAPIIS5p


title: P2S5_PDGFB-1_tumor_1.1_(20240201_SH_Mm_P2S5_P14_0128)

description: Mouse PDGFB-1 Tumor RNAPIIS5p


title: P2S5_PDGFB-1_normal_1.1_(20240201_SH_Mm_P2S5_P11_0128)

description: Mouse PDGFB-1 Normal RNAPIIS5p


title: P2S5_RELA_normal_1.2_(20231003_SH_Mm_P2S2_R6_0927)

description: Mouse RELA Normal RNAPIIS2p


title: P2S5_Normal_8_(20231010_SH_Mm_P2S5_N34_1007)

description: Mouse Normal Brain RNAPIIS5p


title: P2S5_Normal_7_(20231010_SH_Mm_P2S5_N33_1007)

description: Mouse Normal Brain RNAPIIS5p


title: P2S5_Normal_6_(20231010_SH_Mm_P2S5_N32_1007)

description: Mouse Normal Brain RNAPIIS5p


title: P2S5_Normal_5_(20231010_SH_Mm_P2S5_N31_1007)

description: Mouse Normal Brain RNAPIIS5p


title: P2S5_Normal_2_(20231010_SH_Mm_P2S5_N22_1007)

description: Mouse Normal Brain RNAPIIS5p


title: P2S5_Normal_3_(20231010_SH_Mm_P2S5_N23_1007)

description: Mouse Normal Brain RNAPIIS5p


title: P2S2_RELA_tumor_4_(20231003_SH_Mm_P2S2_R4_0927)

description: Mouse RELA Tumor RNAPIIS2p


title: P2S5_Normal_1_(20231010_SH_Mm_P2S5_N21_1007)

description: Mouse Normal Brain RNAPIIS5p


title: P2S2_RELA_tumor_2_(20231003_SH_Mm_P2S2_R2_0927)

description: Mouse RELA Tumor RNAPIIS2p


title: hda_1_P3_Kac_ChIP_rep2

city: Athens

first: Zachary

middle: A

last: Lewis

state: GA

address: 120 E. Green St.

department: Microbiology

institute: University of Georiga

description: Library name: 140-42

data_processing:
TrimGalore! V0.6
BWA v0.7.17 mem (option -M)
SAMtools v1.16.1
deepTools v3.5.2 ‘bamCoverage’
Assembly: BioProject PRJNA13841 Genbank accession: GCA_000182925.2
Supplementary files format and content: bigwig files; read counts in 10 base pair bins

organism: Neurospora crassa

source_name: mycelicum

growth_protocol: Overnight liquid culture in Vogel's MInimal Medium + 1.5% sucrose

extract_protocol:
sonication
end repair, adaptor ligation, PRC2 amplification

treatment_protocol: formaldahyde fixation (1%)

value: mycelicum


title: hda_1_P3_Kac_ChIP_rep1

description: Library name: 140-41


title: hda_1_P2_Kac_ChIP_rep2

description: Library name: 140-30


title: P2S2_RELA_tumor_1_(20231003_SH_Mm_P2S2_R1_0927)

description: Mouse RELA Tumor RNAPIIS2p


title: P2S5_PDGFB-2_normal_2.1_(20240201_SH_Mm_P2S5_P21_0128)

description: Mouse PDGFB-2 Normal RNAPIIS5p


title: hda_1_P1_Kac_ChIP_rep2

description: Library name: 140-18


title: K27ac_RELA_tumor_8_(20230906_SH_Mm_K27ac_R1_0902)

description: Mouse RELA Tumor H3K27ac

value: H3K27ac Abcam cat# ab4729


title: P2S2_RELA_tumor_3_(20231003_SH_Mm_P2S2_R3_0927)

description: Mouse RELA Tumor RNAPIIS2p


title: hda_1_P1_Kac_ChIP_rep1

description: Library name: 140-17


title: K27ac_RELA_tumor_7_(20230822_SH_Mm_K27ac_R6_0819)

description: Mouse RELA Tumor H3K27ac


title: hda_1_P3_H3K36me3_ChIP_rep1

description: Library name: 140-39


title: K27ac_RELA_tumor_5_(20230906_SH_Mm_K27ac_R4_0831)

description: Mouse RELA Tumor H3K27ac


title: K27ac_RELA_tumor_4_(20230906_SH_Mm_K27ac_R3_0831)

description: Mouse RELA Tumor H3K27ac


title: WT_old_Kac_ChIP_rep2

description: Library name: 140-65


title: hda_1_P2_Kac_ChIP_rep1

description: Library name: 140-29


title: hda_1_P2_H3K36me3_ChIP_rep2

description: Library name: 140-28


title: K27ac_RELA_tumor_2_(20230906_SH_Mm_K27ac_R1_0831)

description: Mouse RELA Tumor H3K27ac


title: hda_1_P2_H3K36me3_ChIP_rep1

description: Library name: 140-27


title: K27ac_RELA_tumor_3_(20230906_SH_Mm_K27ac_R2_0831)

description: Mouse RELA Tumor H3K27ac


title: P2S5_Normal_4_(20231010_SH_Mm_P2S5_N24_1007)

description: Mouse Normal Brain RNAPIIS5p


title: hda_1_P1_H3K36me3_ChIP_rep2

description: Library name: 140-16


title: K27ac_RELA_tumor_12_(20230906_SH_Mm_K27ac_R5_0902)

description: Mouse RELA Tumor H3K27ac


title: hda_1_P1_H3K36me3_ChIP_rep1

description: Library name: 140-15


title: K27ac_RELA_tumor_11_(20230906_SH_Mm_K27ac_R4_0902)

description: Mouse RELA Tumor H3K27ac


title: K27ac_RELA_tumor_10_(20230906_SH_Mm_K27ac_R3_0902)

description: Mouse RELA Tumor H3K27ac


title: hda_1_P3_H3K9me3_ChIP_rep2

description: Library name: 140-38


title: K27ac_RELA_tumor_9_(20230906_SH_Mm_K27ac_R2_0902)

description: Mouse RELA Tumor H3K27ac


title: hda_1_P3_H3K9me3_ChIP_rep1

description: Library name: 140-37


title: K27ac_RELA_tumor_1_(20230822_SH_Mm_K27ac_R2_0819)

description: Mouse RELA Tumor H3K27ac


title: hda_1_P2_H3K9me3_ChIP_rep2

description: Library name: 140-26


title: Curl_YAP1_9_(20231205_SH_Mm_P2S5_Y101_1126)

description: Mouse YAP1 Curl RNAPIIS5p


title: K27ac_RELA_tumor_6_(20230906_SH_Mm_K27ac_R5_0831)

description: Mouse RELA Tumor H3K27ac


title: hda_1_P1_H3K9me3_ChIP_rep2

description: Library name: 140-14


title: Curl_YAP1_8_(20231215_SH_Mm_P2S5_Y-3_1213)

description: Mouse YAP1 Curl RNAPIIS5p


title: hda_1_P1_H3K9me3_ChIP_rep1

description: Library name: 140-13


title: Curl_YAP1_6_(20240108_SH_Mm_P2S5_Ylo_1228)

description: Mouse YAP1 Curl RNAPIIS5p


title: hda_1_P3_H3K36me3_ChIP_rep2

description: Library name: 140-40


title: hda_1_P3_H3K27me3_ChIP_rep2

description: Library name: 140-36


title: Curl_YAP1_5_(20240108_SH_Mm_P2S5_Y_1228)

description: Mouse YAP1 Curl RNAPIIS5p


title: Curl_YAP1_4_(20231215_SH_Mm_P2S5_Y-1_1213)

description: Mouse YAP1 Curl RNAPIIS5p


title: hda_1_P2_H3K27me3_ChIP_rep2

description: Library name: 140-24


title: hda_1_P3_H3K27me3_ChIP_rep1

description: Library name: 140-35


title: Curl_YAP1_3_(20231213_SH_Mm_P2S5_Yn1_1207)

description: Mouse YAP1 Curl RNAPIIS5p


title: hda_1_P2_H3K27me3_ChIP_rep1

description: Library name: 140-23


title: hda_1_P1_H3K27me3_ChIP_rep2

description: Library name: 140-11


title: hda_1_old_H3K27me3_ChIP_rep2

description: Library name: 140-86


title: Curl_YAP1_12_(20231128_SH_Mm_P2S5_Yblo_1116)

description: Mouse YAP1 Curl RNAPIIS5p


title: Curl_YAP1_11_(20231213_SH_Mm_P2S5_Yx1_1207)

description: Mouse YAP1 Curl RNAPIIS5p


title: hda_1_old_H3K27me3_ChIP_rep1

description: Library name: 140-87


title: Curl_YAP1_10_(20231205_SH_Mm_P2S5_Y102_1126)

description: Mouse YAP1 Curl RNAPIIS5p


title: WT_old_input_ChIP_rep2

description: Library name: 140-80


title: Curl_RELA_7_(20231201_SH_Mm_P2S5_Rlo_1120)

description: Mouse RELA Curl RNAPIIS5p


title: WT_old_input_ChIP_rep1

description: Library name: 140-79


title: Curl_RELA_8_(20231213_SH_Mm_P2S5_R2_1203)

description: Mouse RELA Curl RNAPIIS5p


title: hda-1_Kac_ChIP_rep2

description: Library name: 141-130


title: hda_1_P2_H3K9me3_ChIP_rep1

description: Library name: 140-25


title: Curl_YAP1_1_(20231117_SH_Mm_P2S5_Y_1112)

description: Mouse YAP1 Curl RNAPIIS5p


title: Curl_RELA_5_(20231117_SH_Mm_P2S5_R_1112)

description: Mouse RELA Curl RNAPIIS5p


title: hda-1_K36me3_ChIP_rep2

description: Library name: 143-35


title: Curl_YAP1_7_(20231201_SH_Mm_P2S5_Y_1118)

description: Mouse YAP1 Curl RNAPIIS5p


title: hda-1_K27me3_ChIP_rep2

description: Library name: 143-33


title: hda-1_K36me3_ChIP_rep1

description: Library name: 143-34


title: hda-1_K27me3_ChIP_rep1

description: Library name: 143-32


title: Curl_RELA_4_(20231115_SH_Mm_P2S5_R1_1108)

description: Mouse RELA Curl RNAPIIS5p


title: Curl_RELA_2_(20231115_SH_Mm_P2S5_R3_1108)

description: Mouse RELA Curl RNAPIIS5p


title: hda-1_K9me3_ChIP_rep1

description: Library name: 143-30


title: Curl_RELA_3_(20231115_SH_Mm_P2S5_R2_1108)

description: Mouse RELA Curl RNAPIIS5p


title: Curl_YAP1_2_(20231128_SH_Mm_P2S5_Yb_1116)

description: Mouse YAP1 Curl RNAPIIS5p


title: Curl_PDGFB_9_(20231201_SH_Mm_P2S5_Plo_1120)

description: Mouse PDGFB Curl RNAPIIS5p


title: Curl_RELA_1_(20231115_SH_Mm_P2S5_R4_1108)

description: Mouse RELA Curl RNAPIIS5p


title: WT_Kac_ChIP_rep2

description: Library name: 143-110


title: WT_K27me3_ChIP_rep4

description: Library name: 141-119


title: WT_K27me3_ChIP_rep3

description: Library name: 140-61


title: WT_K9me3_ChIP_rep4

description: Library name: 141-115


title: Curl_PDGFB_7_(20240108_SH_Mm_P2S5_P_1228)

description: Mouse PDGFB Curl RNAPIIS5p


title: Curl_RELA_6_(20231128_SH_Mm_P2S5_Rb_1116)

description: Mouse RELA Curl RNAPIIS5p


title: Curl_PDGFB_6_(20231205_SH_Mm_P2S5_P153_1126)

description: Mouse PDGFB Curl RNAPIIS5p


title: Curl_PDGFB_5_(20231205_SH_Mm_P2S5_P102_1126)

description: Mouse PDGFB Curl RNAPIIS5p


title: WT_old_H3K27me3_ChIP_rep1

description: Library name: 140-62


title: MUT_hda-1-3xflag_K9me3_ChIP_rep1

description: Library name: 141-125


title: Curl_PDGFB_4_(20231115_SH_Mm_P2S5_P1_1108)

description: Mouse PDGFB Curl RNAPIIS5p


title: Curl_PDGFB_3_(20231115_SH_Mm_P2S5_P2_1108)

description: Mouse PDGFB Curl RNAPIIS5p


title: Curl_PDGFB_2_(20231115_SH_Mm_P2S5_P3_1108)

description: Mouse PDGFB Curl RNAPIIS5p


title: MUT_hda-1-3xflag_K9me3_ChIP_rep2

description: Library name: 143-42


title: Curl_PDGFB_1_(20231115_SH_Mm_P2S5_P4_1108)

description: Mouse PDGFB Curl RNAPIIS5p


title: WT_hda-1-3xflag_K27me3_ChIP_rep2

description: Library name: 143-41


title: MUT_hda-1-3xflag_K27me3_ChIP_rep2

description: Library name: 143-45


title: Curl_Normal_6_(20231117_SH_Mm_P2S5_N4_1111)

description: Mouse Normal Brain Curl RNAPIIS5p


title: WT_hda-1-3xflag_K9me3_ChIP_rep1

description: Library name: 143-38


title: WT_hda-1-3xflag_K27me3_ChIP_rep1

description: Library name: 143-40


title: WT_hda-1-3xflag__K9me3_ChIP_rep2

description: Library name: 143-39


title: Curl_Normal_7_(20231117_SH_Mm_P2S5_N414_1111)

description: Mouse Normal Brain Curl RNAPIIS5p


title: MUT_hda-1-3xflag_K27me3_ChIP_rep1

description: Library name: 141-129


title: Curl_Normal_4_(20231117_SH_Mm_P2S5_N3_1111)

description: Mouse Normal Brain Curl RNAPIIS5p


title: WT_K27me3_ChIP_rep2

description: Library name: 143-106


title: Curl_PDGFB_8_(20231117_SH_Mm_P2S5_P_1112)

description: Mouse PDGFB Curl RNAPIIS5p


title: WT_K27me3_ChIP_rep1

description: Library name: 141-1


title: Curl_Normal_2_(20231117_SH_Mm_P2S5_N2_1111)

description: Mouse Normal Brain Curl RNAPIIS5p


title: hda-1_K27me3_CUTnRUN_rep3

description: Library name: 140-87

data_processing:
TrimGalore! V0.6
BWA v0.7.17 mem (option -M)
SAMtools v1.16.1
deepTools v3.5.2 ‘bamCoverage’
Assembly: BioProject PRJNA13841 Genbank accession: GCA_000182925.2
Supplementary files format and content: bigwig files; read counts in 10 base pair bins
Library strategy: CUT&RUN

source_name: mycelia

extract_protocol:
chopping mycelial mat with razor blade
end repair, adaptor ligation, PRC2 amplification

treatment_protocol: no treatment

value: mycelia

tag: treatment

value: Vogel's Minimal Medium


title: Curl_Normal_3_(20231117_SH_Mm_P2S5_N214_1111)

description: Mouse Normal Brain Curl RNAPIIS5p

value: Normal


title: WT_K9me3_ChIP_rep2

description: Library name: 141-121


title: Curl_Normal_1_(20231117_SH_Mm_P2S5_N1_1111)

description: Mouse Normal Brain Curl RNAPIIS5p

value: RNAP2Ser5P Cell Signaling Technology cat# 13523


title: hda-1_K27me3_CUTnRUN_rep2

description: Library name: 140-86


title: hda-1_K9me3_CUTnRUN_rep2

description: Library name: 141-137


title: ahpC KD+-aTc #3 [VS6]

city: Omaha

first: Vandana

last: Singh

state: Nebraska

address: 985900 Nebraska Medical Center

department: Pathology, Microbiology, and Immunology

institute: University of Nebraska Medical Center

description: The level of ahpC is decreased

library_source: transcriptomic

data_processing:
The original fastq format reads were trimmed by fqtirm tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30).
The trimmed fastq files were processed by FastQC (Andrews S. (2010).
FastQC: a quality control tool for high throughput sequence data; available online at http://www.bioinformatics.babraham.ac.uk/projects/fastqc for quality control.
Assembly: Chlamydia trachomatis 434/Bu bacterial reference genome and annotation files were downloaded from Ensembl (http://bacteria.ensembl.org/Chlamydia_trachomatis_434_bu/Info/Index).
Supplementary files format and content: Excel file showing fold changes and statistical significance between uninduced and induced conditions

molecule: total RNA

organism: Chlamydia trachomatis

source_name: Infected human HeLa cell line

growth_protocol: HeLa cells were infected with C. trachomatis L2. Samples were collected at 14 hpi. The infected cells were grown in 1X DMEM containing 10% FBS and 10 ug gentamycin at 37 celcius degree in 5% CO2

extract_protocol:
Total RNA was collected from C. trachomatis infected cell cultures using Trizol. Total RNA was DNased then further purified to remove rRNA using MicrobEnrich, MicrobExpress.
the Illumina Stranded Total RNA Prep protocol

treatment_protocol: 1 nM inducer (Anhydrotetracycline) was treated or not at 10 hpi.

value: Infected human HeLa cell line

value: Induced with 1 nM aTc for 4 h (in DMEM)


title: ahpC KD+-aTc #2 [VS5]

description: The level of ahpC is decreased


title: chap_K27me2_me3_CUTnRUN_rep2

description: Library name: 137-59


title: ahpC KD+-aTc #1 [VS4]

description: The level of ahpC is decreased


title: chap_K27me2_me3_CUTnRUN_rep1

description: Library name: 132-12


title: chap_K9me3_CUTnRUN_rep2

description: Library name: 137-78


title: ahpC KD-aTc #2 [VS2]

description: Normal Developmental Cycle

value: Uninduced condition (in DMEM)


title: chap_K9me3_CUTnRUN_rep1

description: Library name: 137-79


title: ahpC KD-aTc #1 [VS1]

description: Normal Developmental Cycle


title: cdp-2_K27me2_me3_CUTnRUN_rep2

description: Library name: 129-56


title: ZC3H8 chimeric eCLIP Input in K562

city: Houston

first: Eric

last: Van Nostrand

state: TX

address: 1 Baylor Plaza Rm T334

department: Therapeutic Innovation Center

institute: Baylor College of Medicine

description: Library name: ZC3H8 chimeric eCLIP Input in K562

data_processing:
Remove 10nt UMI from 5' end of read: umi_tools extract --random-seed 1 --bc-pattern NNNNNNNNNN --stdin /storage/vannostrand/path/to/clip1.fastq.gz
First adapter trimming: cutadapt -j 8 --match-read-wildcards --times 3 -e 0.1 --quality-cutoff 6 -m 34 -a file:/storage/vannostrand/software/eclip/data/se.2.round.adapters.fasta -O 1 - --report minimal
Second adapter trimming (removes additional adapter-concatamers): cutadapt -j 8 -u -10  -o ${SampleID}.trim.gz
Repeat mapping (takes adapter-trimmed fastq files, and maps to a repeat database to filter repeat elements prior to genome mapping and peak calling, in order to reduce peak artifacts): STAR --runMode alignReads --runThreadN 8 --alignEndsType EndToEnd --genomeDir /storage/vannostrand/genomes/repbase/species_specific/homo_sapiens_repbase_v2 --genomeLoad LoadAndRemove --outBAMcompression 10 --outFileNamePrefix ${SampleID}.repeat.map/ --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterMismatchNmax 10 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped None --outStd Log --readFilesCommand zcat --readFilesIn ${SampleID}.trim.fastq.gz
Unique genomic mapping (takes repeat-removed reads and maps to the genome to remove nonchimeric reads): STAR --runMode alignReads --runThreadN 8 --alignEndsType EndToEnd --genomeDir /storage/vannostrand/genomes/hg19/star_2.4.0j_encode --genomeLoad LoadAndRemove --outBAMcompression 10 --outFileNamePrefix ${SampleID}.genome.map/ --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterMismatchNmax 10 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped None --outStd Log --readFilesIn ${SampleID}.trim.unmap.fastq
snoRNA mapping (takes genome-removed reads and maps to the snoRNA sequence to find putative snoRNA chimeric reads). bowtie2-build --quiet --offrate 2 /directory/snoRNA.txt.fa snoRNA.bowtie2.index 2> /dev/null. bowtie2 -D 20 -R 3 -N 0 -L 16 --local --norc -i S,1,0.50 --score-min L,16,0 --ma 1 --np o --mp 2,2 --rdg 5,1 --rfg 5,1 -p 8 --no-unal -x snoRNA.bowtie2.index -f -U ${SampleID}.mask.fasta -a -S ${SampleID}.mask.map.to.snoRNA.sam 2> ${SampleID}.mask.map.to.snoRNA.log
find putative target(takes the reads mapped to snoRNAs from previous step, if the remaining non-snoRNA fragment is longer than 18, save remaining non-snoRNA fragment to fastq files as putative target regions). We run this step with python script "split_source_map_sam" and "find_putiative_target"."split_source_map_sam" is used to split output sam file from previous step to 25 sub files, which could save the analysis duration and space occupation. find_putative_target ${SampleID}.mask.map.to.snoRNA.*.bam ZS89-IP-NOLC1.mask.map.to.snoRNA.*.target.fasta snoRNA False. All output fasta files from 25 sub sam files will then be merged together into one fasta file.
second snoRNA mapping (takes the fasta file from previous step and maps to snoRNA reference again to remove the reads led by snoRNA:snoRNA ligation). bowtie2 -D 20 -R 3 -N 0 -L 16 --local --norc -i S,1,0.50 --score-min L,12,0 --ma 1 --np o --mp 2,2 --rdg 5,1 --rfg 5,1 -p 8 --no-unal -x snoRNA.bowtie2.index -f -U ${SampleID}.mask.fasta -a -S ${SampleID}.mask.map.to.snoRNA.target.back.map.sam 2> ${SampleID}.mask.map.to.snoRNA.target.back.map.log
rRNA target mapping (takes the sam file from previous step and maps the putative target fragment to rRNA to identify rRNA interactions). bowtie-build --quiet --offrate 2 /directory/rRNA.fa rRNA.bowtie.index 2> /dev/null. bowtie -a --best --strata -e 35 -q -l 8 -n 1 -p 8 -x rRNA.bowtie.index --no-unal --norc -f ${SampleID}.mask.map.to.snoRNA.true.target.fasta --sam ${SampleID}.snoRNA.rRNA.sam --un ${SampleID}.snoRNA.rRNA.unmap.fasta 2>${SampleID}.snoRNA.rRNA.log
snRNA target mapping(takes the sam file from previous step and maps the putative target fragment to snRNA). bowtie-build --quiet --offrate 2 /directory/snRNA.fa snRNA.bowtie.index 2> /dev/null. bowtie -a --best --strata -e 35 -q -l 8 -n 1 -p 8 -x snRNA.bowtie.index --no-unal --norc -f ${SampleID}.mask.map.to.snoRNA.true.target.fasta --sam ${SampleID}.snoRNA.snRNA.sam --un ${SampleID}.snoRNA.snRNA.unmap.fasta 2>${SampleID}.snoRNA.snRNA.log
tRNA target mapping(takes the sam file from previous step and maps the putative target fragment to tRNA). bowtie-build --quiet --offrate 2 /directory/tRNA.fa tRNA.bowtie.index 2> /dev/null. bowtie -a --best --strata -e 35 -q -l 8 -n 1 -p 8 -x tRNA.bowtie.index --no-unal --norc -f ${SampleID}.mask.map.to.snoRNA.true.target.fasta --sam ${SampleID}.snoRNA.tRNA.sam --un ${SampleID}.snoRNA.tRNA.unmap.fasta 2>${SampleID}.snoRNA.tRNA.log
merge all unmaped fastq (takes the putative target reads that cannot mapped above reference sequence, saved as unmap.fasta in previous step, and merge them into one fasta file)
hg19 mapping (takes above merged unmap reads and maps to human genome, hg19, to capture snoRNA targets on other location). STAR --alignEndsType EndToEnd --genomeDir /storage/vannostrand/genomes/hg19/star_2.4.0j_encode --genomeLoad LoadAndRemove --outBAMcompression 10 --outFileNamePrefix ${SampleID}.genome.map/ --outFilterMatchNminOverLread 0.66 --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterScoreMinOverLread 0.66 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype SAM --outSAMunmapped None --outStd Log --readFilesIn ${SampleID}.snoRNA.RNA.unmap.fasta --runMode alignReads --runThreadN 8
identify snoRNA chimeric reads (identifies the real chimeric reads if the target RNA fragments from above step meet the criteria and removes PCR duplicates.) The criteria is that the length of mapped target RNA fragment is longer than 16nt and the gap between snoRNA and target RNA is less than 4nt.  We run this step with python script "identify_chimeric_reads". command: identify_chimeric_read ${SampleID}.snoRNA.rRNA.bam snoRNA.rRNA.scaRNA.snRNA.tRNA.chimeras.count.tsv ${SampleID}.snoRNA.rRNA.chimeras.bam
parse indivudal snoRNA chimeras into single bam file (takes the chimeric bam file that mapped to each targets and split the bam files into per-snoRNA chimeric reads), we run this step with python script "parse_individual_chimeras", parse_individual_chimeras ${SampleID}.snoRNA.${target_RNA}.chimeras.bam --uid ${SampleID} --tag ${target_RNA} --cpus 8 --minimum_chimeras 1 --count_output individual.chimeras.count.tsv
call peaks on bam files mapped to human genome, hg19: clipper --species hg19 --processors 8 --bam ${SampleID}.chimeras.bam -o ${SampleID}.chimeras.bam.peaks.bed
Assembly: UCSC version hg19
Supplementary files format and content: bam files, bigwig files and tab-separated text files include read counts and RPM value for RNAs.
Library strategy: chimeric eCLIP

growth_protocol: 293T (Clontech), K562 (ATCC) and HepG2 (ATCC) cell lines were cultured in proper medium supplemented with 10% FBS (Cytivia) and antibiotics and maintained in a humidified 5% CO2 incubator at 37°C.

extract_protocol:
For each 10cm plate (~15 million cells), cells were washed once with cold phosphate buffered saline, and then UV crosslinked (254 nm, 400 mJ/cm2) on ice. Cells were then spun down, supernatant removed, and washed with cold phosphate buffered saline. Cell pellets were flash frozen on dry ice and stored at -80°C.
Chimeric eCLIP was based off the previously described chimeric eCLIP protocol (Manakov et al. https://doi.org/10.1101/2022.02.13.480296). Lysis was performed in eCLIP lysis buffer, followed by sonication and digestion with RNase I (Ambion). Immunoprecipitation of snoRNA-associated RBPs-RNA complexes was achieved with a primary antibody using magnetic beads pre-coupled to the secondary antibody (typically 200 ul M-280 Sheep Anti-Rabbit IgG Dynabeads, Thermo Fisher Scientific). Where indicated, 2% of each immunoprecipitated (IP) sample was saved as input control. RNA fragments was dephosphorylated with FastAP (Thermo Fisher) and T4 PNK (NEB), followed by 5’ end phosphorylation of cleaved target RNAs with T4 polynucleotide kinase (PNK, 3' -phosphatase minus, NEB)). Chimeric ligation was then performed with T4 RNA ligase (NEB) without adapters. After additional dephosphorylation steps (FastAP, T4 PNK), phosphorylated RNA adapter was ligated to the 3’ end (T4 RNA Ligase, NEB). Samples were then denatured with 1X NuPage buffer (Life Technologies) and DTT, run on 4%–12% Bis-Tris protein gels and transferred to nitrocellulose membranes(GE Amersham). The region from the observed protein size to 75kD above (corresponding to ~250 nt RNA) was then isolated from membrane by razor blade, and RNA was isolated by Proteinase K (NEB) treatment followed by column purification (Zymo). RNA was then reverse transcribed with SuperScript IV Reverse Transcriptase (Invitrogen) using manganese chloride-based buffer to enhance read-through of modified nucleotides [[ref]]. Excess primers were removed with ExoSAP-IT (Thermo Fisher), and RNA was degraded by alkaline hydrolysis, followed by RNA purification (MyOne Silane beads, Thermo Fisher). Next, a 5’ Illumina DNA adapter (/5Phos/NNNNNNNNNNAGATCGGAAGAGCGTCGTGT/3SpC3)  was ligated to the 3’ end of cDNA fragment with T4 RNA ligase HC enzyme on beads overnight. After beads cleanup, an aliquot of each sample was proceeded for qPCR to identify the proper PCR cycles. The remainder of the samples were amplified with barcoded Illumina primers (Q5, NEB) and size selected via AMPure XP beads and 2% agarose gel (195-350bp). Samples were then quantified by Agilent TapeStation and sequenced either on the Illumina NextSeq (150 bp SE) or NovaSeq X Plus (150 bp PE) platforms.


title: cdp-2_K9me3_CUTnRUN_rep2

description: Library name: 137-81


title: cdp-2_K27me2_me3_CUTnRUN_rep1

description: Library name: 133-76


title: Curl_Normal_5_(20231117_SH_Mm_P2S5_N314_1111)

description: Mouse Normal Brain Curl RNAPIIS5p


title: ZC3H8 IP chimeric eCLIP in K562

description: Library name: ZC3H8 IP chimeric eCLIP in K562


title: UTP18 IP chimeric eCLIP in K562

description: Library name: UTP18 IP chimeric eCLIP in K562


title: UTP18 chimeric eCLIP Input in K562

description: Library name: UTP18 chimeric eCLIP Input in K562


title: hpo_K27me2_me3_CUTnRUN_rep2

description: Library name: 137-54


title: hpo_K27me2_me3_CUTnRUN_rep1

description: Library name: 132-9


title: NOLC1 chimeric eCLIP Input in HepG2, biological replicate 2

description: Library name: NOLC1_INPUT_Rep2


title: hpo_K9me3_CUTnRUN_rep2

description: Library name: 137-56


title: NOLC1 IP chimeric eCLIP in HepG2, biological replicate 2

description: Library name: NOLC1_IP_Rep2


title: hpo_K9me3_CUTnRUN_rep1

description: Library name: 6147_136-38


title: NOP10 eCLIP INPUT in K562 cells, biological replicate 2

data_processing:
Steps were performed using an eCLIP processing pipeline, with scripts available at https://github.com/VanNostrandLab/eclip , based off of the published analysis pipeline described in Blue, SM, et al. Nature Protocols (2022), PMID 35322209.
Remove 10nt UMI from 5' end of read: umi_tools extract --random-seed 1 --bc-pattern NNNNNNNNNN --stdin /storage/vannostrand/path/to/clip1.fastq.gz
First adapter trimming. Command: cutadapt -j 8 --match-read-wildcards --times 3 -e 0.1 --quality-cutoff 6 -m 18 -a file:/storage/vannostrand/software/eclip/data/se.2.round.adapters.fasta -O 1 - --report minimal
Second adapter trimming (removes 10nt from 3' end to account for possible UMIs on 3' end of read). Command:  cutadapt -j 8 -u -10 -o clip1.trim.fastq.gz - --report minimal
Repeat mapping (takes adapter-trimmed fastq files, and maps to a repeat database to filter repeat elements prior to genome mapping and peak calling, in order to reduce peak artifacts). Command: STAR --runMode alignReads --runThreadN 8 --alignEndsType EndToEnd --genomeDir /storage/vannostrand/genomes/repbase/species_specific/homo_sapiens_repbase_v2 --genomeLoad LoadAndKeep --outBAMcompression 10 --outFileNamePrefix clip1.repeat.map/ --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped None --outStd Log --readFilesCommand zcat --readFilesIn clip1.trim.fastq.gz
Unique genomic mapping (takes repeat-removed raeds and maps to the reference genome). Command: STAR --runMode alignReads --runThreadN 8 --alignEndsType EndToEnd --genomeDir /storage/vannostrand/genomes/hg19/star_2.4.0j_encode --genomeLoad LoadAndKeep --outBAMcompression 10 --outFileNamePrefix clip1.genome.map/ --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped None --outStd Log --readFilesIn clip1.repeat.unmap.fastq
Sorting (sorts genome mapped output file). Command: samtools sort -@ 8 -m 2G -o clip1.genome.map.bam clip1.genome.map/Aligned.out.bam
Indexing: indexes sorted bam file. Command: samtools index clip1.genome.map.bam
PCR duplicate removal (uses UMI that was appended to read name to remove PCR duplicate reads that map to the same position and have the same UMI). Command: umi_tools dedup --random-seed 1 --stdin clip1.genome.map.bam --method unique --stdout clip1.bam > /dev/null
Index bam file. Command: samtools index input1.bam
Create bigwig from bam file. Command: b2bw --bam clip1.bam --cpus 1
Peak calling (runs CLIPper peak calling algorithm). Command: clipper --species hg19 --processors 8 --bam clip1.bam --outfile clip1.peak.bed
Peak processing (input normalization and identification of reproducible peaks). Command: process_peak --outdir /storage/vannostrand/software/eclip/tests/hg19/--read_type SE --species hg19 --report test.peak.summary.html --ip_bams clip1.bam clip2.bam --input_bams input1.bam input2.bam --peak_beds clip1.peak.bed clip2.peak.bed --ids clip1 clip2
Assembly: UCSC version hg19
Supplementary files format and content: tab-separated text files include read counts and RPM value for RNAs

extract_protocol:
For each 10cm plate (~15 million cells), cells were washed once with cold phosphate buffered saline, and then UV crosslinked (254 nm, 400 mJ/cm2) on ice. Cells were then spun down, supernatant removed, and washed with cold phosphate buffered saline. Cell pellets were flash frozen on dry ice and stored at -80°C.
eCLIP was performed as described in Blue, SM, et al. Nature Protocols (2022), PMID 35322209. IP fragments were ligated to 3' RNA adapters and RNA was isolated and reverse-transcribed following SDS-PAGE and Western blot. cDNA products were ligated to 5' adapters and PCR-amplified.
eCLIP


title: NOP10 eCLIP INPUT in K562 cells, biological replicate 1


title: hda-1_K27me2_me3_CUTnRUN_rep2

description: Library name: 137-50


title: NOP10 eCLIP IP in K562 cells, biological replicate 1


title: NOP10 eCLIP IP in K562 cells, biological replicate 2


title: ahpC KD-aTc #3 [VS3]

description: Normal Developmental Cycle


title: WT_K27me2_me3_CUTnRUN_rep2

description: Library name: 133-75


title: NHP2 eCLIP INPUT in K562 cells, biological replicate 1


title: WT_K27me2_me3_CUTnRUN_rep1

description: Library name: 132-8


title: hda-1_K27me3_CUTnRUN_rep1

description: Library name: 119-42


title: NHP2 eCLIP IP in K562 cells, biological replicate 1


title: hda-1_K9me3_CUTnRUN_rep1

description: Library name: 119-50


title: cdp-2_K9me3_CUTnRUN_rep1

description: Library name: 133-64


title: NHP2 eCLIP IP in K562 cells, biological replicate 2


title: WT_K27me3_CUTnRUN_rep3

description: Library name: 122-12


title: GAR1 eCLIP INPUT in K562 cells, biological replicate 2


title: WT_K9me3_CUTnRUN_rep3

description: Library name: 122-11


title: WT_K27me3_CUTnRUN_rep1

description: Library name: 119-41


title: WT_K9me3_CUTnRUN_rep1

description: Library name: 119-49


title: 𝚫rrpA/B_IRT_3

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

description: Library name: rrpAB_IRT_R3

data_processing:
The sequencing results were analyzed with Unitas (https://doi.org/10.1186/s12864-017-4031-9) using default parameters.
A. fumigatus nuclear tRNAs were referenced from GtRNAdb, mitochondrial tRNAs were scanned from the mitochondrial genome using the 27 tRNAs predicted by tRNAscan-SE. All analyses were performed using “R” version 4.3.1 (2023-06-16) and Rstudio (2022-02-02), an integrated development environment (IDE) for R.
Assembly: Aspergillus fumigatus A1163 ASM15014v1
Supplementary files format and content: A single csv file (IRT_sRNA_processed.csv) contains the abundance of each target from each sample replicate.

organism: Aspergillus fumigatus

source_name: mycelium

growth_protocol: A. fumigatus was grown on Aspergillus minimal medium (AMM) agar plates (70 mM NaNO3, 11.2 mM KH2PO4, 7 mM KCl, 2 mM MgSO4, 1% (w/v) glucose and 1 μl/ml trace element solution (pH 6.5)). The trace element solution was composed of 1 g FeSO4 • 7 H2O, 8.8 g ZnSO4 • 7 H2O, 0.4 g CuSO4 • 5 H2O, 0.15 g MnSO4 • H2O, 0.1 g NaB4O7 • 10 H2O, 0.05 g (NH4)6Mo7O24 • 4 H2O, and ultra-filtrated water to 1000 ml. Spores were harvested after 5 days with 10 ml of sterile distilled water using a T-shaped inoculation spreader and spore suspensions were filtered through a 30-µm cell strainer (MACS, Miltenyi Biotec GmbH, Germany) to exclude mycelium. After counting, 50-mL liquid AMM cultures were inoculated with 1x10^8 freshly harvested spores and incubated at 37°C and 200 rpm. After 16 h, 10 μg/mL of doxycycline was added to the inverted-repeat transgene strains (excluding wild type), followed by 8 h of additional growth (total of 24 h).

extract_protocol:
Mycelium was collected with Miracloth (EMD Millipore Corp., USA) and rinsed with sterile MilliQ water. After being pressed tightly in between paper towels to remove moisture, the dried mycelium was transferred to a 2-mL screw-cap tube filled 1/3 full with 0.5 mm soda lime glass beads (BoSpec). 1 mL of TRIzol (Thermo Fischer Scientific, Dreieich, Germany) was added to efficiently lyse the cells using the FastPrep-24™ Homogenizer by subjecting the cells to three rounds of 30 s, 4.0 m/s homogenization (1 min break between repetitions) and 5 min of incubation at room temperature. 200 μL of chloroform was added to each sample, vigorously mixed and incubated for 3 min at room temperature before centrifuging the samples at 12,000 x g for 15 min at 4°C. The upper aqueous phase containing the RNA was carefully transferred to a clean RNase-free tube and an equal volume of pure ice-cold ethanol was added and mixing thoroughly. Purification of RNA was carried out by using the RNA Clean and Concentrator™ kit (Zymo Research GmbH, Freiburg, Germany) following the manufacturer’s instructions. To eliminate DNase contamination, total RNA was treated with DNase I, RNase-free (Thermo Fisher Scientific, Darmstadt, Germany). For every 1 μg of RNA, 1 U of the enzyme was added along with 2 μL of 10x Reaction Buffer with MgCl2 and adjusted with DEPC-treated water to make up to 20 μL final volume. Following a 1-hour incubation at 37°C, the reaction was terminated by adding 2 μL of 50 mM EDTA and further incubated 65°C for 10 min. DNase treated RNA was purified using the RNA Clean and Concentrator™ kit (Zymo Research, USA) after the manufacturer’s recommendations.
Libraries were constructed by Novogene. According to the manufacturer, 3' and 5' adaptors were ligated to 3' and 5' ends of small RNA, repsectively. Then the first strand cDNA was synthesized after hybridization with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18-40 bp were ready for sequencing with SE50.
50-bp single read sequencing
sRNA-seq

value: mycelium

value: CEA17 delta_akuB::KU80

tag: growth condition

value: Aspergillus minimal media liquid culture + doxcycline

tag: genotype

value: delta_rrpA/B +IRT

tag: time


title: 𝚫rrpA/B_IRT_2

description: Library name: rrpAB_IRT_R2


title: DKC1 eCLIP INPUT in K562 cells, biological replicate 1


title: hda-1_K27me2_me3_CUTnRUN_rep1

description: Library name: 6147_136-18


title: GAR1 eCLIP IP in K562 cells, biological replicate 1


title: DKC1 eCLIP IP in K562 cells, biological replicate 2


title: 𝚫ppdA/B_IRT_2

description: Library name: ppdAB_IRT_R2

value: delta_ppdA/B +IRT


title: DKC1 eCLIP INPUT in HEK293T cells, biological replicate 2


title: 𝚫ppdA/B_IRT_1

description: Library name: ppdAB_IRT_R1


title: 𝚫dclA/B_IRT_3

description: Library name: dclAB_IRT_R3

value: delta_dclA/B +IRT


title: DKC1 eCLIP IP in HEK293T cells, biological replicate 2


title: DKC1 eCLIP INPUT in HEK293T cells, biological replicate 1


title: NHP2 eCLIP INPUT in K562 cells, biological replicate 2


title: 𝚫ppdA/B_IRT_3

description: Library name: ppdAB_IRT_R3


title: 𝚫dclA/B_IRT_2

description: Library name: dclAB_IRT_R2


title: 𝚫dclA/B_IRT_1

description: Library name: dclAB_IRT_R1


title: GAR1 eCLIP IP in K562 cells, biological replicate 2


title: Wild-type_IRT_2

description: Library name: CEA17_IRT_R2

value: wild type +IRT


title: Wild-type_IRT_3

description: Library name: CEA17_IRT_R3


title: SNU13 eCLIP INPUT in K562 cells, biological replicate 2


title: SNU13 eCLIP IP in K562 cells, biological replicate 2


title: SNU13 eCLIP IP in K562 cells, biological replicate 1


title: SNU13 eCLIP INPUT in K562 cells, biological replicate 1


title: GAR1 eCLIP INPUT in K562 cells, biological replicate 1


title: Wild-type_IRT_1

description: Library name: CEA17_IRT_R1


title: DKC1 eCLIP INPUT in K562 cells, biological replicate 2


title: DKC1 eCLIP IP in HEK293T cells, biological replicate 1


title: Wild-type_2

description: Library name: CEA17_R2

value: Aspergillus minimal media liquid culture

value: wild type


title: NOP58 eCLIP INPUT in K562 cells, biological replicate 2


title: 𝚫rrpA/B_IRT_1

description: Library name: rrpAB_IRT_R1


title: Wild-type_3

description: Library name: CEA17_R3


title: Wild-type_1

description: Library name: CEA17_R1


title: NOP58 eCLIP INPUT in K562 cells, biological replicate 1


title: NOP58 eCLIP IP in K562 cells, biological replicate 2


title: DKC1 eCLIP IP in K562 cells, biological replicate 1


title: NOP58 eCLIP IP in K562 cells, biological replicate 1


title: H9 cells,Control 3

city: Guiyang

first: Liangxia

last: Jiang

address: No. 6 Ankang Avenue, Gui'an New District

country: China

institute: Guizhou Medical University

data_processing:
Raw data of fastq format were firstly processed by fastp software (version 0.23.0), low-quality reads, reads containing poly-N and reads with insert size less than 18bp were removed and adaptor sequences from the reads were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
Deduplicated Reads were mapped to the reference genome of human from https://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/dna/ using STRA software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Assembly: GRCh38 release101
Supplementary files format and content: reads counts for each Sample

molecule: polyA RNA

growth_protocol: H9 embryonic stem cells were maintained on 1:30 diluted hESC-qualified Matrigel with DMEM/F-12  coated plates and cultured in mTeSR1 medium(STEMCELL Technologies) in a humidified incubator under 5% CO2 at 37℃.

extract_protocol:
The total RNA of each of above listed samples was extracted using TRIzol reagent(Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
A amount of 2 μg total RNA per sample was used for stranded RNA sequencing library preparation using polyA selection method and KC-DigitalTM Stranded mRNA Library Prep Kit(Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer's instruction.

treatment_protocol: For trophoblast differentiation, the day after passaging onto Matrigel-coated dishes at 1.2 × 104 cells/cm2, the culture medium was changed to DMEM/F12 medium (Gibco) with KnockOut SR (Gibco) that had been conditioned by MEFs and supplemented with 10 ng/ml FGF2. On the next day, the medium was changed to 10 ng/ml BMP4 (Peprotech), 1 μM A83-01 (SELLECK), and the 0.1 μM PD173074 (SELLECK) containing (BAP) DMEM/F12/KOSR medium not conditioned with MEF feeder cells. Control cultures were maintained in conditioned medium containing 10 ng/ml FGF2.

value: embryonic stem cells

value: WT

value: trophoblasts differentiation


title: H9 cells,Control 4


title: NOP56 eCLIP IP in K562 cells, biological replicate 2


title: NOP56 eCLIP INPUT in K562 cells, biological replicate 2


title: H9 cells,Control 2


title: H9 cells,Control 1


title: H9 cells,CRISPR/Cas9 NLRP7 2

value: NLRP7 knockout


title: NOP56 eCLIP INPUT in K562 cells, biological replicate 1


title: NOP56 eCLIP IP in K562 cells, biological replicate 1


title: H9 cells,CRISPR/Cas9 NLRP7 1


title: Fibrillarin eCLIP IP in HepG2 cells, biological replicate 2


title: Fibrillarin eCLIP INPUT in HepG2 cells, biological replicate 2


title: Fibrillarin eCLIP INPUT in HepG2 cells, biological replicate 1


title: PDAC6, shNTC 3D (paired with shMOV10)_rep3

city: Charlestown

first: Eunae

last: You

address: 149, 13th street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description: Library name: PDAC6-shNTC-Rep3

data_processing:
reads trimmed and quality checked using skewer
aligned to hg38 and repeat elements using STAR
reads assigned to genes and repeats (Gencode and repeat masker) using featureCounts
unassigned reads remapped to Repbase consensus sequence
Assembly: GRCH38; REP
Supplementary files format and content: rawcounts in .tsv format

source_name: Pancreas

growth_protocol: Patient-derived PDAC cell lines (PDAC3, PDAC6) were cultured in DMEM (Gibco, cat# 11995065) supplemented with 10% (v/v) FBS and antibiotics (100 U/ml penicillin, 100 µg/ml streptomycin; Gibco, cat# 15140122) in a 37℃ incubator supplied with 5% CO2.

extract_protocol:
Total RNA extraction was performed using the miRNeasy Mini Kit (QIAGEN, cat# 217004). 7 ng of RNA was used for library construction.
Libraries were prepared for sequencing using the SMARTer Stranded Total RNA-seq Kit v2 (cat# 634413) – Pico Input Mammalian (Takara Bio USA). RNA samples were first converted into cDNA, then adaptors for Illumina sequencing were added through PCR. The PCR products are purified using AMPure Beads (Beckman Coulter, cat# A63881), then ribosomal cDNA was depleted. After depletion, the samples were further amplified using PCR, then purified again using AMPure Beads. Each sample was then qPCR quantified using a KAPA Library Quantification Kit (Roche, cat# 07960140001) and Phix Control Kit V3 (Illumina, cat# FC-110-3001). Samples were then pooled together and quantified again using the KAPA Library Quantification Kit. The Pooled library was then sequenced using the NextSeq 1000 Sequencing Kit.

treatment_protocol: PDAC cells were grown in 2D (adherent) or 3D (tumorsphere) for 7 days for RNA-sequencing.

value: Pancreas

value: Pancreatic ductal adenocarcinoma

value: shNTC (paired with shMOV10)

value: 3D tumorsphere


title: PDAC6, shNTC 3D (paired with shMOV10)_rep2

description: Library name: PDAC6-shNTC-Rep2


title: PDAC6, shMOV10 3D_rep3

description: Library name: PDAC6-shMOV10-Rep3


title: PDAC6, shNTC 3D (paired with shMOV10)_rep1

description: Library name: PDAC6-shNTC-Rep1


title: Fibrillarin eCLIP INPUT in K562 cells, biological replicate 2


title: PDAC6, shNTC 3D_rep3

description: Library name: PDAC6NTC3D3

value: shNTC


title: PDAC6, shMOV10 3D_rep1

description: Library name: PDAC6-shMOV10-Rep1


title: Fibrillarin eCLIP IP in K562 cells, biological replicate 2


title: Fibrillarin eCLIP IP in K562 cells, biological replicate 1


title: PDAC6, shMOV10 3D_rep2

description: Library name: PDAC6-shMOV10-Rep2


title: Fibrillarin eCLIP INPUT in K562 cells, biological replicate 1


title: PDAC6, shNTC 3D_rep2

description: Library name: PDAC6NTC3D2


title: PDAC6, shNTC 3D_rep1

description: Library name: PDAC6NTC3D1


title: PDAC6, shNTC 2D_rep3

description: Library name: PDAC6NTC2D3

value: 2D adherent


title: PDAC6, shNTC 2D_rep2

description: Library name: PDAC6NTC2D2


title: Fibrillarin eCLIP INPUT in HEK293T cells, biological replicate 1


title: Fibrillarin eCLIP INPUT in HEK293T cells, biological replicate 2


title: PDAC6, shNTC 2D_rep1

description: Library name: PDAC6NTC2D1


title: Fibrillarin eCLIP IP in HEK293T cells, biological replicate 1


title: UNT2

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Reads were mapped and aligned using the STAR alignment tool v2.5.3a
Reads were quantified and normalized using HOMER to generate raw counts.
Assembly: hg19
Supplementary files format and content: tab-delimited file includes raw counts for each sample

growth_protocol: IMR90 cells were maintained in EMEM supplemented with 10% Fetal Bovine Serum in humidified atmphosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
Libraries were generated using the Illumina TruSeq Stranded mRNA library prep kit according to the manufacturer's protocol

treatment_protocol: 20 uM 2'3'-dideoxycytidine or vehicle/untreated (water) for 0, 24, 48, 72, or 96 hours

value: fibroblast

value: vehicle (water)

value: 4 Days


title: PDAC6, shORF1-2 3D_rep3

description: Library name: PDAC6L1KD2-3D3


title: PDAC6, shORF1-2 3D_rep2

description: Library name: PDAC6L1KD2-3D2


title: PDAC6, shORF1-2 3D_rep1

description: Library name: PDAC6L1KD2-3D1


title: Fibrillarin eCLIP IP in HepG2 cells, biological replicate 1


title: PDAC3, shNTC 3D_rep2

description: Library name: PDAC3NTC3D2


title: Replicate 3-Day4


title: Fibrillarin chimeric eCLIP Input in HepG2, biological replicate 2

data_processing:
Remove 10nt UMI from 5' end of read: umi_tools extract --random-seed 1 --bc-pattern NNNNNNNNNN --stdin /storage/vannostrand/path/to/clip1.fastq.gz
First adapter trimming: cutadapt -j 8 --match-read-wildcards --times 3 -e 0.1 --quality-cutoff 6 -m 34 -a file:/storage/vannostrand/software/eclip/data/se.2.round.adapters.fasta -O 1 - --report minimal
Second adapter trimming (removes additional adapter-concatamers): cutadapt -j 8 -u -10  -o ${SampleID}.trim.gz
Repeat mapping (takes adapter-trimmed fastq files, and maps to a repeat database to filter repeat elements prior to genome mapping and peak calling, in order to reduce peak artifacts): STAR --runMode alignReads --runThreadN 8 --alignEndsType EndToEnd --genomeDir /storage/vannostrand/genomes/repbase/species_specific/homo_sapiens_repbase_v2 --genomeLoad LoadAndRemove --outBAMcompression 10 --outFileNamePrefix ${SampleID}.repeat.map/ --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterMismatchNmax 10 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped None --outStd Log --readFilesCommand zcat --readFilesIn ${SampleID}.trim.fastq.gz
Unique genomic mapping (takes repeat-removed reads and maps to the genome to remove nonchimeric reads): STAR --runMode alignReads --runThreadN 8 --alignEndsType EndToEnd --genomeDir /storage/vannostrand/genomes/hg19/star_2.4.0j_encode --genomeLoad LoadAndRemove --outBAMcompression 10 --outFileNamePrefix ${SampleID}.genome.map/ --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterMismatchNmax 10 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped None --outStd Log --readFilesIn ${SampleID}.trim.unmap.fastq
snoRNA mapping (takes genome-removed reads and maps to the snoRNA sequence to find putative snoRNA chimeric reads). bowtie2-build --quiet --offrate 2 /directory/snoRNA.txt.fa snoRNA.bowtie2.index 2> /dev/null. bowtie2 -D 20 -R 3 -N 0 -L 16 --local --norc -i S,1,0.50 --score-min L,16,0 --ma 1 --np o --mp 2,2 --rdg 5,1 --rfg 5,1 -p 8 --no-unal -x snoRNA.bowtie2.index -f -U ${SampleID}.mask.fasta -a -S ${SampleID}.mask.map.to.snoRNA.sam 2> ${SampleID}.mask.map.to.snoRNA.log
find putative target(takes the reads mapped to snoRNAs from previous step, if the remaining non-snoRNA fragment is longer than 18, save remaining non-snoRNA fragment to fastq files as putative target regions). We run this step with python script "split_source_map_sam" and "find_putiative_target"."split_source_map_sam" is used to split output sam file from previous step to 25 sub files, which could save the analysis duration and space occupation. find_putative_target ${SampleID}.mask.map.to.snoRNA.*.bam ZS89-IP-NOLC1.mask.map.to.snoRNA.*.target.fasta snoRNA False. All output fasta files from 25 sub sam files will then be merged together into one fasta file.
second snoRNA mapping (takes the fasta file from previous step and maps to snoRNA reference again to remove the reads led by snoRNA:snoRNA ligation). bowtie2 -D 20 -R 3 -N 0 -L 16 --local --norc -i S,1,0.50 --score-min L,12,0 --ma 1 --np o --mp 2,2 --rdg 5,1 --rfg 5,1 -p 8 --no-unal -x snoRNA.bowtie2.index -f -U ${SampleID}.mask.fasta -a -S ${SampleID}.mask.map.to.snoRNA.target.back.map.sam 2> ${SampleID}.mask.map.to.snoRNA.target.back.map.log
rRNA target mapping (takes the sam file from previous step and maps the putative target fragment to rRNA to identify rRNA interactions). bowtie-build --quiet --offrate 2 /directory/rRNA.fa rRNA.bowtie.index 2> /dev/null. bowtie -a --best --strata -e 35 -q -l 8 -n 1 -p 8 -x rRNA.bowtie.index --no-unal --norc -f ${SampleID}.mask.map.to.snoRNA.true.target.fasta --sam ${SampleID}.snoRNA.rRNA.sam --un ${SampleID}.snoRNA.rRNA.unmap.fasta 2>${SampleID}.snoRNA.rRNA.log
snRNA target mapping(takes the sam file from previous step and maps the putative target fragment to snRNA). bowtie-build --quiet --offrate 2 /directory/snRNA.fa snRNA.bowtie.index 2> /dev/null. bowtie -a --best --strata -e 35 -q -l 8 -n 1 -p 8 -x snRNA.bowtie.index --no-unal --norc -f ${SampleID}.mask.map.to.snoRNA.true.target.fasta --sam ${SampleID}.snoRNA.snRNA.sam --un ${SampleID}.snoRNA.snRNA.unmap.fasta 2>${SampleID}.snoRNA.snRNA.log
tRNA target mapping(takes the sam file from previous step and maps the putative target fragment to tRNA). bowtie-build --quiet --offrate 2 /directory/tRNA.fa tRNA.bowtie.index 2> /dev/null. bowtie -a --best --strata -e 35 -q -l 8 -n 1 -p 8 -x tRNA.bowtie.index --no-unal --norc -f ${SampleID}.mask.map.to.snoRNA.true.target.fasta --sam ${SampleID}.snoRNA.tRNA.sam --un ${SampleID}.snoRNA.tRNA.unmap.fasta 2>${SampleID}.snoRNA.tRNA.log
merge all unmaped fastq (takes the putative target reads that cannot mapped above reference sequence, saved as unmap.fasta in previous step, and merge them into one fasta file)
hg19 mapping (takes above merged unmap reads and maps to human genome, hg19, to capture snoRNA targets on other location). STAR --alignEndsType EndToEnd --genomeDir /storage/vannostrand/genomes/hg19/star_2.4.0j_encode --genomeLoad LoadAndRemove --outBAMcompression 10 --outFileNamePrefix ${SampleID}.genome.map/ --outFilterMatchNminOverLread 0.66 --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterScoreMinOverLread 0.66 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype SAM --outSAMunmapped None --outStd Log --readFilesIn ${SampleID}.snoRNA.RNA.unmap.fasta --runMode alignReads --runThreadN 8
identify snoRNA chimeric reads (identifies the real chimeric reads if the target RNA fragments from above step meet the criteria and removes PCR duplicates.) The criteria is that the length of mapped target RNA fragment is longer than 16nt and the gap between snoRNA and target RNA is less than 4nt.  We run this step with python script "identify_chimeric_reads". command: identify_chimeric_read ${SampleID}.snoRNA.rRNA.bam snoRNA.rRNA.scaRNA.snRNA.tRNA.chimeras.count.tsv ${SampleID}.snoRNA.rRNA.chimeras.bam
parse indivudal snoRNA chimeras into single bam file (takes the chimeric bam file that mapped to each targets and split the bam files into per-snoRNA chimeric reads), we run this step with python script "parse_individual_chimeras", parse_individual_chimeras ${SampleID}.snoRNA.${target_RNA}.chimeras.bam --uid ${SampleID} --tag ${target_RNA} --cpus 8 --minimum_chimeras 1 --count_output individual.chimeras.count.tsv
call peaks on bam files mapped to human genome, hg19: clipper --species hg19 --processors 8 --bam ${SampleID}.chimeras.bam -o ${SampleID}.chimeras.bam.peaks.bed
Assembly: UCSC version hg19
Supplementary files format and content: bigwig files and tab-separated text files include read counts and RPM value for RNAs.
Library strategy: chimeric eCLIP


title: PDAC3, shNTC 3D_rep3

description: Library name: PDAC3NTC3D3


title: Fibrillarin IP chimeric eCLIP in HepG2, biological replicate 1


title: PDAC3, shNTC 2D_rep3

description: Library name: PDAC3NTC2D3


title: Fibrillarin chimeric eCLIP Input in HepG2, biological replicate 1


title: PDAC3, shNTC 2D_rep1

description: Library name: PDAC3NTC2D1


title: Replicate 1-Day4


title: PDAC3, shNTC 3D_rep1

description: Library name: PDAC3NTC3D1


title: WDR43 IP chimeric eCLIP in K562


title: PDAC3, shORF1-2 3D_rep2

description: Library name: PDAC3L1KD2-3D2


title: Replicate 2-Day4


title: PDAC3, shNTC 2D_rep2

description: Library name: PDAC3NTC2D2


title: Fibrillarin IP chimeric eCLIP in HepG2, biological replicate 2


title: Replicate 2-Day3

value: 3 Days


title: Fibrillarin eCLIP IP in HEK293T cells, biological replicate 2


title: PDAC8, 3D ORF1p RIP_rep2

description: Library name: PDAC8-ORF1p-2

data_processing:
reads trimmed and quality checked using skewer
aligned to hg38 and repeat elements using STAR
reads assigned to genes and repeats (Gencode and repeat masker) using featureCounts
unassigned reads remapped to Repbase consensus sequence
Assembly: GRCH38; REP
Supplementary files format and content: rawcounts in .tsv format
Supplementary files format and content: counts_annot.tsv

growth_protocol: Patient-derived PDAC cell lines (PDAC3, PDAC6, PDAC8) were cultured in DMEM (Gibco, cat# 11995065) supplemented with 10% (v/v) FBS and antibiotics (100 U/ml penicillin, 100 µg/ml streptomycin; Gibco, cat# 15140122) in a 37℃ incubator supplied with 5% CO2.

extract_protocol:
Purified RNA was isolated using the miRNeasy Mini Kit (QIAGEN, cat# 217004). A total of 7 ng of RNA was used for library construction.
Libraries were prepared for sequencing using the SMARTer Stranded Total RNA-seq Kit v2 (cat# 634413) – Pico Input Mammalian (Takara Bio USA). RNA samples were first converted into cDNA, then adaptors for Illumina sequencing were added through PCR. The PCR products are purified using AMPure Beads (Beckman Coulter, cat# A63881), then ribosomal cDNA was depleted. After depletion, the samples were further amplified using PCR, then purified again using AMPure Beads. Each sample was then qPCR quantified using a KAPA Library Quantification Kit (Roche, cat# 07960140001) and Phix Control Kit V3 (Illumina, cat# FC-110-3001). Samples were then pooled together and quantified again using the KAPA Library Quantification Kit. The Pooled library was then sequenced using the NextSeq 1000 Sequencing Kit.

treatment_protocol: PDAC3, PDAC6 and PDAC8 cells were plated into the T75 cm2 ultra-low attachment (ULA) flasks containing DMEM medium at 2 M cells per flask. After 7 days, the cells were collected for RIP-seq.

value: ORF1p RIP


title: WDR43 chimeric eCLIP Input in K562


title: SMNDC1 IP chimeric eCLIP in K562


title: PDAC8, 3D ORF1p RIP_rep1

description: Library name: PDAC8-ORF1p-1


title: SMNDC1 chimeric eCLIP Input in K562


title: Replicate 3-Day3


title: UNT1


title: PDAC8, 3D Input_rep3

description: Library name: PDAC8-Input-3

value: Input


title: Replicate 3-Day2

value: 2 Days


title: PDAC8, 3D Input_rep2

description: Library name: PDAC8-Input-2


title: Replicate 2-Day2


title: NOLC1 IP chimeric eCLIP in HepG2


title: PDAC8, 3D Input_rep1

description: Library name: PDAC8-Input-1


title: NOLC1 chimeric eCLIP Input in HepG2


title: PDAC6, 3D ORF1p RIP_rep2

description: Library name: PDAC6-ORF1p-2


title: PDAC3, shORF1-2 3D_rep3

description: Library name: PDAC3L1KD2-3D3


title: PDAC6, 3D ORF1p RIP_rep3

description: Library name: PDAC6-ORF1p-3


title: PDAC8, 3D ORF1p RIP_rep3

description: Library name: PDAC8-ORF1p-3


title: PDAC3, shORF1-2 3D_rep1

description: Library name: PDAC3L1KD2-3D1


title: Replicate 1-Day2


title: LARP7 IP chimeric eCLIP in HepG2


title: PDAC6, 3D Input_rep3

description: Library name: PDAC6-Input-3


title: Replicate 1-Day3


title: LARP7 chimeric eCLIP Input in HepG2


title: PDAC6, 3D Input_rep1

description: Library name: PDAC6-Input-1


title: PDAC6, 3D Input_rep2

description: Library name: PDAC6-Input-2


title: PDAC3, 3D ORF1p RIP_rep2

description: Library name: PDAC3-ORF1p-2


title: PDAC3, 3D ORF1p RIP_rep3

description: Library name: PDAC3-ORF1p-3


title: Replicate 2-Day1

value: 1 Day


title: GAR1 chimeric eCLIP Input in HEK293T


title: PDAC3, 3D Input_rep3

description: Library name: PDAC3-Input-3

value: WT


title: hda_1_old_H3K36me3_ChIP_rep2

description: Library name: 107-5

value: mycelicum


title: GAR1 IP chimeric eCLIP in HEK293T


title: PDAC3, 3D Input_rep2

description: Library name: PDAC3-Input-2


title: hda_1_old_H3K36me3_ChIP_rep1

description: Library name: 130-82


title: DCK1 IP chimeric eCLIP in HEK293T


title: ESF

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

description: Library name: ESF

data_processing:
RNA-seq data of mouse ganglia were processed by Cutadapt (v2.7; --quality-cutoff=15,10 --minimum-length=36) to remove adapters and FastQC (v0.11.4) to estimate the sequencing quality. Trimmed reads were then aligned to the mouse genome mm10 with GENCODE annotation vM28 using STAR (v2.5.4) with default parameters58. Transcript quantification was performed using featureCounts from the subread package (v1.6.3). Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
Assembly: mouse mm10
Supplementary files format and content: gene expression counting

source_name: ganglia

extract_protocol:
Total RNA integrity was determined using Agilent Bioanalyzer.
Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

value: ganglia

value: sensory ganglion

value: Sub

value: ESF


title: DKC1 chimeric eCLIP Input in HEK293T


title: PDAC6, 3D ORF1p RIP_rep1

description: Library name: PDAC6-ORF1p-1

value: Pancreas

value: Pancreatic ductal adenocarcinoma


title: EVFN2

description: Library name: EVFN2

value: Vis

value: EVFN


title: Replicate 3-Day1

value: fibroblast


title: hda_1_old_H3K9me3_ChIP_rep2

description: Library name: 129-21


title: ESM2

description: Library name: ESM2

value: ESM


title: hda_1_P1_H3K27me3_ChIP_rep1

description: Library name: 6147_136-68


title: Replicate 1-Day1


title: NOP58 IP chimeric eCLIP in HEK293T


title: MKM2

description: Library name: MKM2

value: KO

value: MKM


title: EVM2

description: Library name: EVM2

value: EVM


title: PDAC3, 3D ORF1p RIP_rep1

description: Library name: PDAC3-ORF1p-1

value: ORF1p RIP


title: NOP58 chimeric eCLIP Input in HEK293T


title: MWM2

description: Library name: MWM2

value: MWM


title: hda-1_Kac_ChIP_rep1

description: Library name: 136-31


title: hda_1_old_input_ChIP_rep2

description: Library name: 138-19


title: PDAC3, 3D Input_rep1

description: Library name: PDAC3-Input-1

value: WT

value: Input


title: MKF2

description: Library name: MKF2

value: ganglia

value: MKF


title: NOP56 IP chimeric eCLIP in HEK293T


title: MWF2

description: Library name: MWF2

value: sensory ganglion

value: MWF


title: hda_1_old_input_ChIP_rep1

description: Library name: 138-18

value: mycelicum


title: EVM1

description: Library name: EVM1


title: MWM1

description: Library name: MWM1


title: MKF1

description: Library name: MKF1


title: Fibrillarin IP chimeric eCLIP in HEK293T


title: ESM1

description: Library name: ESM1

value: Sub


title: Fibrillarin chimeric eCLIP Input in HEK293T


title: EVFY2

description: Library name: EVFY2

value: Vis

value: EVFY


title: hda-1_K9me3_ChIP_rep2

description: Library name: 130-81


title: EVFY1

description: Library name: EVFY1


title: WT_Kac_ChIP_rep1

description: Library name: 136-30


title: MKM1

description: Library name: MKM1


title: WTP3

city: Harbin

first: Hao

middle: Cheng

state: Heilongjiang

address: 26 Hexing Road

institute: Northeast Forestry University

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
The reference genomes and the annotation file were downloaded from the Populus genome (version3.0,https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa ). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Genome_build: Populus trichocarpa v3.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa)
Supplementary_files_format_and_content: Processed file with phytozome Populus trichocarpa gene model name and the read counts. The gene information provided in our processed data file correspond to Popgenie Transcript name.

organism: Populus ussuriensis

source_name: root tip (0.5 cm)

growth_protocol: Approximately 3 cm stem segments were excised from 4-week-old in vitro plants and cultured on half-strength Murashige and Skoog (1/2 MS) medium (Duchefa) containing 20 g/L sucrose. Media used in experiments were adjusted to pH 5.8 before adding 3 g l-1 Gelrite (Duchefa). Cultures were performed in 150 ml Erlenmeyer flasks with 50 ml medium and incubated under a 16 h light/8 h dark photoperiod at 25°C under illumination with cool white fluorescent lights at 45 µmol m−2 s−1.

extract_protocol:
Root tip (0.5 cm) were harvested, flash frozen on dry ice, and RNA was isolated using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One week-old in-vitro plants were transfered to 1/2 MS agar medium supplemented with or without 6% PEG6000 for 7 days.

value: root tip (0.5 cm)

value: Wild type


title: EVFN1

description: Library name: EVFN1

value: EVFN


title: NOP56 chimeric eCLIP Input in HEK293T


title: WTP2


title: Cux2ERT,M,Saline,1month,rep5,b3

city: Berkeley

first: Andrea

middle: M

last: Gomez

state: CA

address: 163 Weill Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: Library name: AG-4541

data_processing:
Data quality assessment and sequence read primer trimming were performed by FastQC v0.11.9 and Cutadapt 3.5, respectively. We considered trim_galore version 0.6.7 with --phred33 parameter. The data was then aligned to a mouse reference genome build (Mus musculus; GRCm39: RefSeq assembly accession = GCF_000001635.27) using RSEM v1.3.1. Bowtie2 version 2.4.4 aligner index was created using rsem-prepare-reference --bowtie2 command and a gene-level read count matrix was generated using rsem-calculate-expression --bowtie2 command. Gene-level counts of each sample were combined using rsem-generate-data-matrix command.
For alternative splicing analysis, we first applied the same procedures for assessing data quality and sequence read primer trimming. The reads were then aligned to a mouse reference genome build (Mus musculus; GRCm39) using STAR 2.7.10a.
Assembly: Mus musculus; GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file include raw counts for all samples combined

source_name: mouse prefrontal cortex

extract_protocol:
RNA purification from RiboTag mice were modified from previously published protocols (see methods for details). RNA purification was performed using a RNeasy Mini kit following the manufacturer’s instructions.
Samples with RNA integrity number (RIN) values >7 were used for library prep. 50 ng of RNA was used for library preparation with TruSeq stranded RNA library prep kit with poly-A enrichment. The libraries were sequenced 150bp paired-end on a NovaSeq 6000 platform for DOI samples, and X Plus for psilocybin samples, at 200 million reads per sample.

treatment_protocol: DOI (2mg/kg), psilocybin (2mg/kg) or saline were injected intraperitoneally (IP).

value: mouse prefrontal cortex

tag: cre line

tag: Sex

value: male

tag: replicate

value: Saline

tag: batch


title: MWF1

description: Library name: MWF1


title: WT_K9me3_ChIP_rep3

description: Library name: 130-2


title: Cux2ERT,M,DOI,1month,rep5,b3

description: Library name: AG-4539

value: DOI


title: WT_K9me3_ChIP_rep1

description: Library name: 135-16


title: Cux2ERT,M,DOI,1month,rep4,b3

description: Library name: AG-4470


title: WTP1


title: Cux2ERT,F,DOI,1month,rep3,b3

description: Library name: AG-4468

value: female


title: PV,M,DOI,1month,rep5,b3

description: Library name: AG-4631

value: PV


title: WT2

value: Control


title: WT3


title: Cux2ERT,F,Saline,1month,rep4,b3

description: Library name: AG-4469


title: Cux2ERT,M,DOI,48hrs,rep5,b2

description: Library name: AG-3445


title: WT1


title: spermatozoa, infertility, 831L

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

description:
no duplicate
831L

data_processing:
Raw sequence data (.bcl files) generated by the Illumina HiSeq Control Software (HCS) was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.
Sequence reads were trimmed to remove adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Three subjects in the infertility group were sequenced in two samples, and these technical duplicates are combined. This yields a final count matrix of dimension 57500 x 67 where each row represents a gene with its unique ENSEMBL ID, and each column represents a subject.
Before conducting DA analysis, we first filtered genes with low counts among all samples (sum over all sequencing samples below 700; roughly 10 counts per sample). For the 27,809 genes that passed the filtering, we applied median normalization to account for differences in sequencing depth among samples. The normalized counts are log 2 transformed after adding one pseudo count.
Assembly: GRCh38
Supplementary files format and content: .fastq.gz files contain raw counts for each sample
Supplementary files format and content: log2_norm_count_collapsed.csv is a matrix of log2-transformed counts for all samples

source_name: ejaculate

extract_protocol:
Sperm were isolated from the ejaculate by a washing and somatic cell lysis procedure, followed by isolation with the miRvana kit, as described in Bianchi et al. (2018. doi: 10.1111/andr.12471).
RNA libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA). mRNAs were selected using oligo-dT beads, fragmented for 15 minutes at 94 °C, followed by first strand and second strand cDNA synthesis, followed by adaptor ligation, indexing, and PCR enrichment.

value: ejaculate

value: spermatozoa

tag: population

value: infertility


title: spermatozoa, infertility, 835L

description:
no duplicate
835L


title: spermatozoa, infertility, 816L

description:
no duplicate
816L


title: Cux2ERT,M,Saline,1week,rep5,b2

description: Library name: AG-3444


title: spermatozoa, infertility, 814L

description:
no duplicate
814L


title: Cux2ERT,M,Saline,1month,rep3,b2

description: Library name: AG-3442


title: OEP3

value: PuC3H40-OE line


title: WT_K36me3_ChIP_rep1

description: Library name: 130-12

value: mycelicum


title: Cux2ERT,F,DOI,48hrs,rep4,b2

description: Library name: AG-3441


title: OEP2

value: PuC3H39-OE line


title: Cux2ERT,F,Saline,48hrs,rep5,b2

description: Library name: AG-3440


title: spermatozoa, infertility, 809L

description:
no duplicate
809L


title: OEP1

value: PuC3H38-OE line


title: Cux2ERT,F,DOI,1week,rep5,b2

description: Library name: AG-3439


title: PV,F,DOI,1week,rep5,b2

description: Library name: AG-3582


title: spermatozoa, infertility, 807L

description:
no duplicate
807L


title: PV,F,Saline,48hrs,rep4,b2

description: Library name: AG-2989


title: OE3

value: root tip (0.5 cm)

value: PuC3H37-OE line


title: spermatozoa, infertility, 803L

description:
no duplicate
803L


title: PV,M,DOI,48hrs,rep4,b2

description: Library name: AG-2986


title: PV,F,DOI,48hrs,rep5,b2

description: Library name: AG-2988


title: PV,M,Saline,1week,rep5,b2

description: Library name: AG-2877


title: OE2

value: PuC3H36-OE line


title: spermatozoa, infertility, 802L

description:
no duplicate
802L


title: Cux2ERT,M,Saline,1week,rep4,b2

description: Library name: AG-3443

value: mouse prefrontal cortex


title: PV,M,Saline,48hrs,rep3,b2

description: Library name: AG-2769

value: male


title: PV,M,Saline,48hrs,rep2,b2

description: Library name: AG-2768

value: Saline


title: OE1

value: PuC3H35-OE line


title: NMFs from healthy C57BL6 mice repetition 3

city: Rehovot

first: Aviad

last: Ben-Shmuel

state: Other

address: Nella and Leon Benoziyo Building for Biological Sciences, Herzl

department: Biomolecular Sciences

country: Israel

institute: Wiezmann Institute

description: Library name: c57b3

data_processing:
Illumina bcl2fastq software used for base calling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
aligment: STAR v2.4.2a parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No
We used the 3’ end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count (DOI: 10.1093/bioinformatics/btu638) in union mode.
Further analysis was done for genes having minimum 10 reads in at least one sample
Assembly: mm10
Supplementary files format and content: tab delimited text files include mRNA molecule count values for each sample

source_name: Mammary fat pad

growth_protocol: 8 week-old mice housed at the Weizmann Institute animal facility under specific pathogen-free conditions.

extract_protocol:
NMFs were collected from healthy 8-12 week old BALB/c or C57BL/6 females. Fat pad tissue was minced and dissociated using the gentleMACS dissociator with an enzymatic digestion solution consisting of 1 mg/ml collagenase II, 1 mg/ml collagenase IV, and 70 U ml−1 DNase in DMEM. The samples were filtered through a 70-μm cell strainer into ice-cold MACS buffer (PBS with 0.5% BSA and 0.4% EDTA pH=8) and cells were pelleted by centrifugation at 350g for 5 min at 4 °C followed by Red Blood lysis treatment and seeding onto a cell-culture treated plate pre-coated with rat-tail collagen type I.
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science

value: Mammary fat pad

tag: strain

value: Primary fibroblast


title: Cux2ERT,M,Saline,48hrs,rep4,b2

description: Library name: AG-2763


title: PV,F,Saline,48hrs,rep1,b2

description: Library name: AG-2765

value: PV

value: female


title: spermatozoa, infertility, 798L

description:
no duplicate
798L

value: ejaculate

value: spermatozoa


title: Cux2ERT,M,Saline,48hrs,rep3,b2

description: Library name: AG-2761


title: NMFs from healthy C57BL6 mice repetition 2

description: Library name: c57b2


title: Cux2ERT,M,DOI,48hrs,rep3,b2

description: Library name: AG-2760

value: DOI


title: spermatozoa, infertility, 797L

description:
no duplicate
797L

value: infertility


title: NMFs from healthy C57BL6 mice repetition 1

description: Library name: c57b1


title: PV,M,DOI,48hrs,rep3,b2

description: Library name: AG-2756


title: PV,F,DOI,48hrs,rep2,b2

description: Library name: AG-2753


title: spermatozoa, infertility, 794L

description:
no duplicate
794L


title: PV,F,Saline,48hrs,rep5,b2

description: Library name: AG-2991


title: Rbp4,M,DOI,48hrs,rep5,b2

description: Library name: AG-2693


title: spermatozoa, infertility, 792L

description:
no duplicate
792L


title: Rbp4,M,Saline,48hrs,rep5,b2

description: Library name: AG-2699


title: NMFs from healthy BALB/C mice repetition 2

description: Library name: balb2

value: BALB/C


title: spermatozoa, infertility, 786L

description:
no duplicate
786L


title: NMFs from healthy BALB/C mice repetition 3

description: Library name: balb3